77,994 results

Pacific oyster feeds and feeding in South Australian waters: towards ecosystem based management

Project number: 2014-027
Project Status:
Current
Budget expenditure: $391,000.00
Principal Investigator: Xiaoxu Li
Organisation: SARDI Food Safety and Innovation
Project start/end date: 16 Jul 2014 - 29 Jun 2017
Contact:
FRDC
TAGS
Sustainability
Supply Chain
Resource Access And Allocation
Rac Sa
Mortality
SPECIES
Pacific Oyster
Blue Mussel
Cockles

Need

To help establish an improved basis for ecologically sustainable aquaculture development and ecosystem based resource management, there is a strong research need to a) determine what Pacific oysters, blue mussels and cockles consume in the unique, typically large, shallow, high salinity and apparently low productivity waters of South Australian (SA) bays, and b) understand the temporal and spatial fluctuation in food availability, and c) the relationship between food availability and Pacific oyster farm productivity. This need is driven by:
1) bivalves could not be included in the modeling of carrying capacity of Spencer Gulf mainly due to the lack of knowledge on the trophic function and feeding physiology of oysters;
2) the oyster industry has been experiencing average Pacific oyster mortalities between stocking and harvesting on an ongoing basis of 35% (up to 50%) in some areas, and believe this loss is associated with a complex interaction between food availability, oyster condition and a variety of biological, chemical and physical stressors; and
3) an interest of the State Government, industry and potential new aquaculture entrants to maximize the use of existing lease allocations and diversify the bivalve species farmed as a risk management strategy for a potential OsHV-1 µvar outbreak in SA. Additional Pacific oyster or new species stock will potentially increase competition for the limited available food.

Objectives

1. Determine what Pacific oysters (Crassostrea gigas), blue mussels (Mytilus galloprovincialis) and mud cockles (Katelysia sp) are feeding on in selected SA bays, and identify the overlap in food resource utilization among all 3 species.
2. Determine the temporal and spatial variability in the food availability of Pacific oysters, mussels and cockles in selected SA bays.
3. Determine key factors affecting oyster performance (growth, condition and survival) in selected SA bays.
4. Determine the factors regulating the relationship between oyster growth/condition and sustainable production in selected locations in SA.
5. Transfer the results of this project to interested stakeholders, in particular the SA oyster industry and SA Government aquaculture policy makers.

Improving the precision of estimates of egg production and spawning biomass obtained using the Daily Egg Production Method

Project number: 2014-026
Project Status:
Completed
Budget expenditure: $200,000.00
Principal Investigator: Timothy M. Ward
Organisation: SARDI Food Safety and Innovation
Project start/end date: 11 May 2014 - 9 Jan 2016
Contact:
FRDC
TAGS
Workforce
Survey
Reproduction
Rac Wa
Rac Vic
SPECIES
Blue Mackerel
Redbaits
Sardines

Need

A project to refine methods for estimating egg production in application of the DEPM is needed because:

1) spawning biomass estimates obtained using the DEPM are the key biological performance indicators in the SASF and SPF;

2) the DEPM is recognized as being imprecise and the main source of this imprecision is associated with estimation of mean daily egg production;

3) a range of field and statistical methods are used to estimate total daily egg production but there is no consensus about which approach is most appropriate for the range of circumstances that are encountered, with different methods currently used in the Americas, Europe and Australia.

Uncertainty in the method used to estimate the spawning biomass of Jack Mackerel off the east coast of Australia was raised as an issue of particular concern in the recent public debate associated with the introduction of a large factory trawler into the SPF.

That debate undermined public confidence in the stock assessment and management of the SPF and has the potential to undermine other fisheries species of small pelagic fishes.

Objectives

1. Compare the performance of current and developmental statistical methods for estimating egg production using long-term datasets for several species
2. Conduct simulations to formally evaluate the performance of different approaches to sampling and statistical analysis on estimates of egg production
3. Establish improved methods for estimating daily egg production in applications of the DEPM

Final report

ISBN: 978-1-876007-07-2
Authors: T.M. Ward J. Carroll G.L. Grammer C. James R. McGarvey J. Smart A. Ivey
Final Report • 2018-02-22 • 6.96 MB
2014-026-DLD.pdf

Summary

This project was undertaken to refine the application of the Daily Egg Production Method to Australia’s largest fishery, the South Australian Sardine Fishery and the Commonwealth Small Pelagic Fishery. Key findings and outcomes from this study include: 1) a new generalised egg staging method that has several advantages over previous egg staging systems; 2) refinements to methods used to identify samples where a zero count should be allocated to one or more egg cohorts; 3) identification of factors that cause the high levels of uncertainty associated with estimates of mean daily egg production (P0) and egg mortality (z); 4) confirmation that the log-linear model is the most precise method currently available for estimating P0 and z for Australian Sardine off South Australia; 5) a simulation model that can be used to evaluate the effects of key processes on the precision of estimates of P0 and z; and 6) recommendations to trial a new oblique plankton sampler that may improve the precision of future estimates of P0. These findings and outcomes will improve the ongoing application of the Daily Egg Production Method to small pelagic species as well as other species to which the method is being applied. 
Final Report • 2018-02-22 • 6.96 MB
2014-026-DLD.pdf

Summary

This project was undertaken to refine the application of the Daily Egg Production Method to Australia’s largest fishery, the South Australian Sardine Fishery and the Commonwealth Small Pelagic Fishery. Key findings and outcomes from this study include: 1) a new generalised egg staging method that has several advantages over previous egg staging systems; 2) refinements to methods used to identify samples where a zero count should be allocated to one or more egg cohorts; 3) identification of factors that cause the high levels of uncertainty associated with estimates of mean daily egg production (P0) and egg mortality (z); 4) confirmation that the log-linear model is the most precise method currently available for estimating P0 and z for Australian Sardine off South Australia; 5) a simulation model that can be used to evaluate the effects of key processes on the precision of estimates of P0 and z; and 6) recommendations to trial a new oblique plankton sampler that may improve the precision of future estimates of P0. These findings and outcomes will improve the ongoing application of the Daily Egg Production Method to small pelagic species as well as other species to which the method is being applied. 
Final Report • 2018-02-22 • 6.96 MB
2014-026-DLD.pdf

Summary

This project was undertaken to refine the application of the Daily Egg Production Method to Australia’s largest fishery, the South Australian Sardine Fishery and the Commonwealth Small Pelagic Fishery. Key findings and outcomes from this study include: 1) a new generalised egg staging method that has several advantages over previous egg staging systems; 2) refinements to methods used to identify samples where a zero count should be allocated to one or more egg cohorts; 3) identification of factors that cause the high levels of uncertainty associated with estimates of mean daily egg production (P0) and egg mortality (z); 4) confirmation that the log-linear model is the most precise method currently available for estimating P0 and z for Australian Sardine off South Australia; 5) a simulation model that can be used to evaluate the effects of key processes on the precision of estimates of P0 and z; and 6) recommendations to trial a new oblique plankton sampler that may improve the precision of future estimates of P0. These findings and outcomes will improve the ongoing application of the Daily Egg Production Method to small pelagic species as well as other species to which the method is being applied. 
Final Report • 2018-02-22 • 6.96 MB
2014-026-DLD.pdf

Summary

This project was undertaken to refine the application of the Daily Egg Production Method to Australia’s largest fishery, the South Australian Sardine Fishery and the Commonwealth Small Pelagic Fishery. Key findings and outcomes from this study include: 1) a new generalised egg staging method that has several advantages over previous egg staging systems; 2) refinements to methods used to identify samples where a zero count should be allocated to one or more egg cohorts; 3) identification of factors that cause the high levels of uncertainty associated with estimates of mean daily egg production (P0) and egg mortality (z); 4) confirmation that the log-linear model is the most precise method currently available for estimating P0 and z for Australian Sardine off South Australia; 5) a simulation model that can be used to evaluate the effects of key processes on the precision of estimates of P0 and z; and 6) recommendations to trial a new oblique plankton sampler that may improve the precision of future estimates of P0. These findings and outcomes will improve the ongoing application of the Daily Egg Production Method to small pelagic species as well as other species to which the method is being applied. 
Final Report • 2018-02-22 • 6.96 MB
2014-026-DLD.pdf

Summary

This project was undertaken to refine the application of the Daily Egg Production Method to Australia’s largest fishery, the South Australian Sardine Fishery and the Commonwealth Small Pelagic Fishery. Key findings and outcomes from this study include: 1) a new generalised egg staging method that has several advantages over previous egg staging systems; 2) refinements to methods used to identify samples where a zero count should be allocated to one or more egg cohorts; 3) identification of factors that cause the high levels of uncertainty associated with estimates of mean daily egg production (P0) and egg mortality (z); 4) confirmation that the log-linear model is the most precise method currently available for estimating P0 and z for Australian Sardine off South Australia; 5) a simulation model that can be used to evaluate the effects of key processes on the precision of estimates of P0 and z; and 6) recommendations to trial a new oblique plankton sampler that may improve the precision of future estimates of P0. These findings and outcomes will improve the ongoing application of the Daily Egg Production Method to small pelagic species as well as other species to which the method is being applied. 

Developing cost-effective industry based techniques for monitoring puerulus settlement in all conditions: Phase 2

Project number: 2014-025
Project Status:
Completed
Budget expenditure: $281,407.52
Principal Investigator: Stewart Frusher
Organisation: University of Tasmania (UTAS)
Project start/end date: 14 Jan 2015 - 13 Mar 2017
Contact:
FRDC
TAGS
Life History
Inshore
Fishing Technology
Fishing Gear
Climate Adaptation
SPECIES
Southern Rock Lobster

Need

Rock lobster fisheries throughout southern Australia show substantial fluctuations in recruitment which if not carefully monitored and managed may lead to lost opportunity and substantial loss in revenue. In Australia, larval (puerulus) collectors have been established in shallow water regions to provide early warning of future changes in abundance. These collectors are serviced either by divers (SA, Tas & Vic) or from dinghies (WA) which make them expensive to service and thus limited in their regional distribution to a few sites. For southern rock lobster there has been concern over how well the observed larval settlement represents the entire fishery as sampling sites are few and limited to the East Coast whereas the majority of catch is from deeper reefs on the South and West Coasts where no collectors are deployed. To improve our understanding of the relationship between recruitment, future catches and short and long term recruitment trends, there is a need to improve spatial (region and depth) coverage.

This proposal follows on from Phase 1 which:
(1) Successfully developed a deep water collector that is easily serviceable by fishers and that captures puerulus.
(2) Developed an in-situ camera system that enables real time remote viewing of puerulus settlement

The need is to determine the sampling strategy that will provide meaningful results to industry and managers on recruitment patterns and trends to the fishery in regions important to the fishery and currently not represented in existing monitoring programs.

To meet this need, this phase aims to determine the depths, times and number/collectors of puerulus that settle in deeper water to determine the number of sites and the number of collectors per site that will provide meaningful settlement data to support management decisions.

Objectives

1. To determine an appropriate and cost effective sampling strategy (number of collectors, depth and time) to enable statistically meaningful analysis of spatial and depth trends in puerulus settlement.
2. To compare shallow and deep water survey methods (e.g. diver based, fisher servicing) to establish the most cost effective methods for on-going monitoring of puerulus settlement.

Final report

ISBN: 978-1-925646-34-4
Authors: Stewart Frusher Graeme Ewing Justin Rizari and Ruari Colqhoun
Final Report • 2018-10-29 • 4.10 MB
2014-025-DLD.pdf

Summary

Outcomes achieved to date
The outputs from this second phase of the project have led to the following outcomes:
1. A refined puerulus collector design that:
• Collects puerulus as effectively as traditional diver-serviced inshore collector systems
• Collects puerulus effectively from deep water (>50m)
• Can be easily and safely deployed, retrieved and serviced by vessels from the Tasmanian commercial lobster fleet during routine fishing operations
2. Deployments at various locations around the Tasmanian coast over 4 settlement seasons have shown that:
• Puerulus settlement is considerably lower in deeper offshore waters than in shallow inshore waters although sufficient to demonstrate major changes in recruitment.
• Puerulus settlement in deeper waters was higher in the 2016/2017 settlement season on the south coast of Tasmania than it was on the east coast
• Puerulus settlement rates in deep waters varied between recent seasons similarly to settlement in inshore waters
3. A cost-benefit analysis comparing traditional diver-based and deep-water fisher serviced puerulus collection strategies has shown that:
• Fisher-serviced is more cost-effective than diver-based methods for similar arrays of collectors
• The current fisher-serviced design is not suitable for deployment in inshore shallow exposed waters due to sedimentation from mobile sediments
• The fisher-serviced collection system developed in this project is a cost-effective way to monitor puerulus settlement in deep water
• Despite yielding lower catch rates than inshore settlement monitoring, the number of offshore collectors used in this project displayed similar temporal patterns of settlement with similar statistical power.
• Offshore collectors retain puerulus settlers similarly to inshore collectors
• Fisher-serviced puerulus monitoring would be even more cost effective if industry agreed to provide support without the requirement for financial compensation

A review of the Tasmanian puerulus program undertaken in 2008 involving government, industry and an external review identified that the current puerulus collectors were all on the East Coast (with the exception of King Island); despite the southern and western regions supporting the largest catches in the fishery. The review identified as a priority to "investigate options for collection on the west coast using boat-based collection and using the commercial fleet to reduce cost of collection".

In phase 1 of this project a design for a deep water collector was developed through consultation with industry and prototypes of this design were constructed and tested in aquaria with captured pueruli, on the seafloor adjacent to an existing inshore shallow collector site on the east coast of Tasmania, and in deep water on the south and southwest coasts of Tasmania. The prototype collectors were successfully deployed, retrieved and serviced by vessels in the commercial lobster fleet and vessel masters reported that the design facilitated safe and efficient handling on deck. The prototypes collected significantly more puerulus than adjacent routine collectors in deployments at the shallow site and collected puerulus for the first time on the deeper and more exposed southwest coast of Tasmania.

This phase 2 of the project saw deployment of a refined collector design onto reefs around Tasmania over 2 puerulus settlement seasons and provided evidence that; (1) puerulus settle in larger numbers in shallow inshore waters; (2) puerulus settlement in deeper water varies in space, time and depth around the Tasmanian coast (eg. Puerulus settlement was higher on the south coast than on the east coast in the 2016/2017 settlement season and puerulus settlement in waters deeper than 100m appears to be very low). 

When deployed alongside traditional diver based collectors, the fisher-serviced puerulus collector captures and retains more puerulus than traditional diver-based methods and is more cost-effective per collector. However, refinements to the design would be required for its use in inshore puerulus monitoring due to siltation issues from mobile sediments in exposed inshore locations. 

Despite experiencing lower catch rates than inshore settlement monitoring, the number and consistence of settlement on offshore deeper water collectors enabled similar temporal patterns of settlement to be determined. The deep water collectors also retained puerulus for similar periods to the traditional collectors.  Consequently, deep water puerulus collection is a feasible alternative to costly inshore diver-serviced monitoring programs and would be expected to indicate similar trends in recruitment. Industry involvement in servicing offshore collectors during routine fishing operations greatly increases the cost-effectiveness of this approach; particularly if this support was provided without the requirement for financial compensation.

Final Report • 2018-10-29 • 4.10 MB
2014-025-DLD.pdf

Summary

Outcomes achieved to date
The outputs from this second phase of the project have led to the following outcomes:
1. A refined puerulus collector design that:
• Collects puerulus as effectively as traditional diver-serviced inshore collector systems
• Collects puerulus effectively from deep water (>50m)
• Can be easily and safely deployed, retrieved and serviced by vessels from the Tasmanian commercial lobster fleet during routine fishing operations
2. Deployments at various locations around the Tasmanian coast over 4 settlement seasons have shown that:
• Puerulus settlement is considerably lower in deeper offshore waters than in shallow inshore waters although sufficient to demonstrate major changes in recruitment.
• Puerulus settlement in deeper waters was higher in the 2016/2017 settlement season on the south coast of Tasmania than it was on the east coast
• Puerulus settlement rates in deep waters varied between recent seasons similarly to settlement in inshore waters
3. A cost-benefit analysis comparing traditional diver-based and deep-water fisher serviced puerulus collection strategies has shown that:
• Fisher-serviced is more cost-effective than diver-based methods for similar arrays of collectors
• The current fisher-serviced design is not suitable for deployment in inshore shallow exposed waters due to sedimentation from mobile sediments
• The fisher-serviced collection system developed in this project is a cost-effective way to monitor puerulus settlement in deep water
• Despite yielding lower catch rates than inshore settlement monitoring, the number of offshore collectors used in this project displayed similar temporal patterns of settlement with similar statistical power.
• Offshore collectors retain puerulus settlers similarly to inshore collectors
• Fisher-serviced puerulus monitoring would be even more cost effective if industry agreed to provide support without the requirement for financial compensation

A review of the Tasmanian puerulus program undertaken in 2008 involving government, industry and an external review identified that the current puerulus collectors were all on the East Coast (with the exception of King Island); despite the southern and western regions supporting the largest catches in the fishery. The review identified as a priority to "investigate options for collection on the west coast using boat-based collection and using the commercial fleet to reduce cost of collection".

In phase 1 of this project a design for a deep water collector was developed through consultation with industry and prototypes of this design were constructed and tested in aquaria with captured pueruli, on the seafloor adjacent to an existing inshore shallow collector site on the east coast of Tasmania, and in deep water on the south and southwest coasts of Tasmania. The prototype collectors were successfully deployed, retrieved and serviced by vessels in the commercial lobster fleet and vessel masters reported that the design facilitated safe and efficient handling on deck. The prototypes collected significantly more puerulus than adjacent routine collectors in deployments at the shallow site and collected puerulus for the first time on the deeper and more exposed southwest coast of Tasmania.

This phase 2 of the project saw deployment of a refined collector design onto reefs around Tasmania over 2 puerulus settlement seasons and provided evidence that; (1) puerulus settle in larger numbers in shallow inshore waters; (2) puerulus settlement in deeper water varies in space, time and depth around the Tasmanian coast (eg. Puerulus settlement was higher on the south coast than on the east coast in the 2016/2017 settlement season and puerulus settlement in waters deeper than 100m appears to be very low). 

When deployed alongside traditional diver based collectors, the fisher-serviced puerulus collector captures and retains more puerulus than traditional diver-based methods and is more cost-effective per collector. However, refinements to the design would be required for its use in inshore puerulus monitoring due to siltation issues from mobile sediments in exposed inshore locations. 

Despite experiencing lower catch rates than inshore settlement monitoring, the number and consistence of settlement on offshore deeper water collectors enabled similar temporal patterns of settlement to be determined. The deep water collectors also retained puerulus for similar periods to the traditional collectors.  Consequently, deep water puerulus collection is a feasible alternative to costly inshore diver-serviced monitoring programs and would be expected to indicate similar trends in recruitment. Industry involvement in servicing offshore collectors during routine fishing operations greatly increases the cost-effectiveness of this approach; particularly if this support was provided without the requirement for financial compensation.

Final Report • 2018-10-29 • 4.10 MB
2014-025-DLD.pdf

Summary

Outcomes achieved to date
The outputs from this second phase of the project have led to the following outcomes:
1. A refined puerulus collector design that:
• Collects puerulus as effectively as traditional diver-serviced inshore collector systems
• Collects puerulus effectively from deep water (>50m)
• Can be easily and safely deployed, retrieved and serviced by vessels from the Tasmanian commercial lobster fleet during routine fishing operations
2. Deployments at various locations around the Tasmanian coast over 4 settlement seasons have shown that:
• Puerulus settlement is considerably lower in deeper offshore waters than in shallow inshore waters although sufficient to demonstrate major changes in recruitment.
• Puerulus settlement in deeper waters was higher in the 2016/2017 settlement season on the south coast of Tasmania than it was on the east coast
• Puerulus settlement rates in deep waters varied between recent seasons similarly to settlement in inshore waters
3. A cost-benefit analysis comparing traditional diver-based and deep-water fisher serviced puerulus collection strategies has shown that:
• Fisher-serviced is more cost-effective than diver-based methods for similar arrays of collectors
• The current fisher-serviced design is not suitable for deployment in inshore shallow exposed waters due to sedimentation from mobile sediments
• The fisher-serviced collection system developed in this project is a cost-effective way to monitor puerulus settlement in deep water
• Despite yielding lower catch rates than inshore settlement monitoring, the number of offshore collectors used in this project displayed similar temporal patterns of settlement with similar statistical power.
• Offshore collectors retain puerulus settlers similarly to inshore collectors
• Fisher-serviced puerulus monitoring would be even more cost effective if industry agreed to provide support without the requirement for financial compensation

A review of the Tasmanian puerulus program undertaken in 2008 involving government, industry and an external review identified that the current puerulus collectors were all on the East Coast (with the exception of King Island); despite the southern and western regions supporting the largest catches in the fishery. The review identified as a priority to "investigate options for collection on the west coast using boat-based collection and using the commercial fleet to reduce cost of collection".

In phase 1 of this project a design for a deep water collector was developed through consultation with industry and prototypes of this design were constructed and tested in aquaria with captured pueruli, on the seafloor adjacent to an existing inshore shallow collector site on the east coast of Tasmania, and in deep water on the south and southwest coasts of Tasmania. The prototype collectors were successfully deployed, retrieved and serviced by vessels in the commercial lobster fleet and vessel masters reported that the design facilitated safe and efficient handling on deck. The prototypes collected significantly more puerulus than adjacent routine collectors in deployments at the shallow site and collected puerulus for the first time on the deeper and more exposed southwest coast of Tasmania.

This phase 2 of the project saw deployment of a refined collector design onto reefs around Tasmania over 2 puerulus settlement seasons and provided evidence that; (1) puerulus settle in larger numbers in shallow inshore waters; (2) puerulus settlement in deeper water varies in space, time and depth around the Tasmanian coast (eg. Puerulus settlement was higher on the south coast than on the east coast in the 2016/2017 settlement season and puerulus settlement in waters deeper than 100m appears to be very low). 

When deployed alongside traditional diver based collectors, the fisher-serviced puerulus collector captures and retains more puerulus than traditional diver-based methods and is more cost-effective per collector. However, refinements to the design would be required for its use in inshore puerulus monitoring due to siltation issues from mobile sediments in exposed inshore locations. 

Despite experiencing lower catch rates than inshore settlement monitoring, the number and consistence of settlement on offshore deeper water collectors enabled similar temporal patterns of settlement to be determined. The deep water collectors also retained puerulus for similar periods to the traditional collectors.  Consequently, deep water puerulus collection is a feasible alternative to costly inshore diver-serviced monitoring programs and would be expected to indicate similar trends in recruitment. Industry involvement in servicing offshore collectors during routine fishing operations greatly increases the cost-effectiveness of this approach; particularly if this support was provided without the requirement for financial compensation.

Final Report • 2018-10-29 • 4.10 MB
2014-025-DLD.pdf

Summary

Outcomes achieved to date
The outputs from this second phase of the project have led to the following outcomes:
1. A refined puerulus collector design that:
• Collects puerulus as effectively as traditional diver-serviced inshore collector systems
• Collects puerulus effectively from deep water (>50m)
• Can be easily and safely deployed, retrieved and serviced by vessels from the Tasmanian commercial lobster fleet during routine fishing operations
2. Deployments at various locations around the Tasmanian coast over 4 settlement seasons have shown that:
• Puerulus settlement is considerably lower in deeper offshore waters than in shallow inshore waters although sufficient to demonstrate major changes in recruitment.
• Puerulus settlement in deeper waters was higher in the 2016/2017 settlement season on the south coast of Tasmania than it was on the east coast
• Puerulus settlement rates in deep waters varied between recent seasons similarly to settlement in inshore waters
3. A cost-benefit analysis comparing traditional diver-based and deep-water fisher serviced puerulus collection strategies has shown that:
• Fisher-serviced is more cost-effective than diver-based methods for similar arrays of collectors
• The current fisher-serviced design is not suitable for deployment in inshore shallow exposed waters due to sedimentation from mobile sediments
• The fisher-serviced collection system developed in this project is a cost-effective way to monitor puerulus settlement in deep water
• Despite yielding lower catch rates than inshore settlement monitoring, the number of offshore collectors used in this project displayed similar temporal patterns of settlement with similar statistical power.
• Offshore collectors retain puerulus settlers similarly to inshore collectors
• Fisher-serviced puerulus monitoring would be even more cost effective if industry agreed to provide support without the requirement for financial compensation

A review of the Tasmanian puerulus program undertaken in 2008 involving government, industry and an external review identified that the current puerulus collectors were all on the East Coast (with the exception of King Island); despite the southern and western regions supporting the largest catches in the fishery. The review identified as a priority to "investigate options for collection on the west coast using boat-based collection and using the commercial fleet to reduce cost of collection".

In phase 1 of this project a design for a deep water collector was developed through consultation with industry and prototypes of this design were constructed and tested in aquaria with captured pueruli, on the seafloor adjacent to an existing inshore shallow collector site on the east coast of Tasmania, and in deep water on the south and southwest coasts of Tasmania. The prototype collectors were successfully deployed, retrieved and serviced by vessels in the commercial lobster fleet and vessel masters reported that the design facilitated safe and efficient handling on deck. The prototypes collected significantly more puerulus than adjacent routine collectors in deployments at the shallow site and collected puerulus for the first time on the deeper and more exposed southwest coast of Tasmania.

This phase 2 of the project saw deployment of a refined collector design onto reefs around Tasmania over 2 puerulus settlement seasons and provided evidence that; (1) puerulus settle in larger numbers in shallow inshore waters; (2) puerulus settlement in deeper water varies in space, time and depth around the Tasmanian coast (eg. Puerulus settlement was higher on the south coast than on the east coast in the 2016/2017 settlement season and puerulus settlement in waters deeper than 100m appears to be very low). 

When deployed alongside traditional diver based collectors, the fisher-serviced puerulus collector captures and retains more puerulus than traditional diver-based methods and is more cost-effective per collector. However, refinements to the design would be required for its use in inshore puerulus monitoring due to siltation issues from mobile sediments in exposed inshore locations. 

Despite experiencing lower catch rates than inshore settlement monitoring, the number and consistence of settlement on offshore deeper water collectors enabled similar temporal patterns of settlement to be determined. The deep water collectors also retained puerulus for similar periods to the traditional collectors.  Consequently, deep water puerulus collection is a feasible alternative to costly inshore diver-serviced monitoring programs and would be expected to indicate similar trends in recruitment. Industry involvement in servicing offshore collectors during routine fishing operations greatly increases the cost-effectiveness of this approach; particularly if this support was provided without the requirement for financial compensation.

Final Report • 2018-10-29 • 4.10 MB
2014-025-DLD.pdf

Summary

Outcomes achieved to date
The outputs from this second phase of the project have led to the following outcomes:
1. A refined puerulus collector design that:
• Collects puerulus as effectively as traditional diver-serviced inshore collector systems
• Collects puerulus effectively from deep water (>50m)
• Can be easily and safely deployed, retrieved and serviced by vessels from the Tasmanian commercial lobster fleet during routine fishing operations
2. Deployments at various locations around the Tasmanian coast over 4 settlement seasons have shown that:
• Puerulus settlement is considerably lower in deeper offshore waters than in shallow inshore waters although sufficient to demonstrate major changes in recruitment.
• Puerulus settlement in deeper waters was higher in the 2016/2017 settlement season on the south coast of Tasmania than it was on the east coast
• Puerulus settlement rates in deep waters varied between recent seasons similarly to settlement in inshore waters
3. A cost-benefit analysis comparing traditional diver-based and deep-water fisher serviced puerulus collection strategies has shown that:
• Fisher-serviced is more cost-effective than diver-based methods for similar arrays of collectors
• The current fisher-serviced design is not suitable for deployment in inshore shallow exposed waters due to sedimentation from mobile sediments
• The fisher-serviced collection system developed in this project is a cost-effective way to monitor puerulus settlement in deep water
• Despite yielding lower catch rates than inshore settlement monitoring, the number of offshore collectors used in this project displayed similar temporal patterns of settlement with similar statistical power.
• Offshore collectors retain puerulus settlers similarly to inshore collectors
• Fisher-serviced puerulus monitoring would be even more cost effective if industry agreed to provide support without the requirement for financial compensation

A review of the Tasmanian puerulus program undertaken in 2008 involving government, industry and an external review identified that the current puerulus collectors were all on the East Coast (with the exception of King Island); despite the southern and western regions supporting the largest catches in the fishery. The review identified as a priority to "investigate options for collection on the west coast using boat-based collection and using the commercial fleet to reduce cost of collection".

In phase 1 of this project a design for a deep water collector was developed through consultation with industry and prototypes of this design were constructed and tested in aquaria with captured pueruli, on the seafloor adjacent to an existing inshore shallow collector site on the east coast of Tasmania, and in deep water on the south and southwest coasts of Tasmania. The prototype collectors were successfully deployed, retrieved and serviced by vessels in the commercial lobster fleet and vessel masters reported that the design facilitated safe and efficient handling on deck. The prototypes collected significantly more puerulus than adjacent routine collectors in deployments at the shallow site and collected puerulus for the first time on the deeper and more exposed southwest coast of Tasmania.

This phase 2 of the project saw deployment of a refined collector design onto reefs around Tasmania over 2 puerulus settlement seasons and provided evidence that; (1) puerulus settle in larger numbers in shallow inshore waters; (2) puerulus settlement in deeper water varies in space, time and depth around the Tasmanian coast (eg. Puerulus settlement was higher on the south coast than on the east coast in the 2016/2017 settlement season and puerulus settlement in waters deeper than 100m appears to be very low). 

When deployed alongside traditional diver based collectors, the fisher-serviced puerulus collector captures and retains more puerulus than traditional diver-based methods and is more cost-effective per collector. However, refinements to the design would be required for its use in inshore puerulus monitoring due to siltation issues from mobile sediments in exposed inshore locations. 

Despite experiencing lower catch rates than inshore settlement monitoring, the number and consistence of settlement on offshore deeper water collectors enabled similar temporal patterns of settlement to be determined. The deep water collectors also retained puerulus for similar periods to the traditional collectors.  Consequently, deep water puerulus collection is a feasible alternative to costly inshore diver-serviced monitoring programs and would be expected to indicate similar trends in recruitment. Industry involvement in servicing offshore collectors during routine fishing operations greatly increases the cost-effectiveness of this approach; particularly if this support was provided without the requirement for financial compensation.

Estimating the abundance of School Shark in Australia using close kin genetic methods

Project number: 2014-024
Project Status:
Completed
Budget expenditure: $495,486.00
Principal Investigator: Robin Thomson
Organisation: CSIRO Oceans and Atmosphere Hobart
Project start/end date: 11 Jan 2015 - 30 Dec 2017
Contact:
FRDC
TAGS
Stock Assessment
Reproduction
Rac Cmwth
Mortality
Fishing Gear
SPECIES
School Shark

Need

The school shark stock is subject to a recovery plan so commercial targeting cannot resume until adequate recovery is demonstrated. The consequent avoidance of school shark means CPUE is no longer a valid index of relative abundance. The existing stock assessment is effectively being used to project the population forward in time (from 1997), given known catches, and is thus predicting the rate and level of recovery of the stock. No information is currently available to compare the predicted recovery rate with the actual rate. Anecdotal reports from the fishing industry suggest that recovery is more rapid than predicted, suggesting lost revenue from current low bycatch TACs.

Avoidance of school shark is reducing the economic efficiency of the gummy shark industry. Economic losses are most keenly felt in South Australia where sea-lion and dolphin protection has closed large areas of traditional fishing grounds. The 20% school:gummy ratio imposes additional, effective, closures of areas of high school shark abundance. The need to protect school shark has also lead to a conservative response from SharkRAG when stock assessments have suggested increases in the gummy shark TAC (SharkRAG 2013).

School shark are highly mobile and the current stock assessment model relies heavily on a model of movement that hasn’t been tested against data. The true movements and underlying stock structure of school sharks are key uncertainties for understanding and effectively managing this stock, complicating the interpretation of any CPUE based abundance index. This project is likely to better understanding of stock structure and movement, and may facilitate use of the existing Pittwater pup index, which stretches back to the 1940s.

This research proposal is in response to the updated ComFRAB call for research on 23 May 2013, which asked for proposals relating to "Develop better measures for School Shark abundance".

Objectives

1. Calculate an absolute estimate of spawning stock abundance with sufficient precision to inform a new stock assessment and to update the Rebuilding Strategy.
2. Update the school shark stock assessment, giving specific recommendations for future management and rebuilding.
3. Establish (and cost) the methods for an ongoing time series of cost effective, fishery independent, school shark abundance estimates.
4. Improve understanding of stock structure and broad scale movements of school sharks.
5. Advance close kin methodology.

Final report

ISBN: 978-1-925994-11-7
Authors: Thomson R.B. Bravington M.V. Feutry P. Gunasekera R. and Grewe P.
Final Report • 2020-08-01 • 4.30 MB
2014-024-DLD.pdf

Summary

Close kin mark recapture (CKMR) provides an estimate of absolute abundance that is independent of fishing behaviour. We present a first CKMR estimate of abundance for School Shark and discuss the management implications of our findings. 

We found 65 half sibling pairs (HSPs), 3 parent-offspring pairs (POPs) and 34 full sibling pairs (FSPs); sufficient for close kin modelling. Our model estimates a School Shark stock in the region of 50,000 mature individuals during 2000. Although the coefficient of variation (CV) for our abundance estimate ranges from 0.23 to 0.28 over 2000 to 2011 (most precise in 2002-2003, at 0.23) the standard error on the trend in mature abundance is large relative to the trend itself so that although the median trend is slightly upwards, a downward trend cannot be ruled out. 

Future projections assuming varying levels of future close kin sampling for up to four years showed that standard errors on trend and abundance should greatly reduce. SharkRAG have recognised that CKMR provides a viable alternative to conventional stock assessment for School Shark and have recommended that CKMR continue to be used as a monitoring tool for School Shark and we scoped such continuing work.We developed two, very simple, models that provided similar abundance estimates to those of our more sophisticated close kin model, giving us confidence that the close kin model correctly interpreted the close kin data. Our estimate of abundance is three to four times lower than that of the most recent stock assessment model, when that was projected forwards assuming similar levels of catch to those that have occurred (Thomson, 2012). Our model was not able to sustain the catches that occurred during the 1990s, even under optimal survival conditions for juvenile School Shark. This suggests that the School Shark population consists of more than one reproductively isolated stock, and that the population that we measured is likely to be a remnant of what was present in the 1990s.

It is possible that environmental degradation of School Shark nursery areas (DEWR, 2008) is the explanation for our finding. As there has been little recovery of those areas, School Shark might not have the capability to recover to their previous stock size. In this case, management reference points that rely on the assumption that stocks will recover to their pristine abundance in the absence of fishing, are not useful for School Shark. Conventional stock assessment models give more precise estimates of relative, than of absolute, abundance but CKMR gives reliable estimates of absolute abundance. This provides managers the opportunity to manage School Shark according to a more relevant quantity than abundance relative to a no longer attainable pristine state last seen in the 1920s.

Our work has advanced close kin methodology through the refinement of software developed for quality control of genetic sequencing data, and for kin finding. Our work represents the first application of CKMR to a commercially exploited shark population.
Final Report • 2020-08-01 • 4.30 MB
2014-024-DLD.pdf

Summary

Close kin mark recapture (CKMR) provides an estimate of absolute abundance that is independent of fishing behaviour. We present a first CKMR estimate of abundance for School Shark and discuss the management implications of our findings. 

We found 65 half sibling pairs (HSPs), 3 parent-offspring pairs (POPs) and 34 full sibling pairs (FSPs); sufficient for close kin modelling. Our model estimates a School Shark stock in the region of 50,000 mature individuals during 2000. Although the coefficient of variation (CV) for our abundance estimate ranges from 0.23 to 0.28 over 2000 to 2011 (most precise in 2002-2003, at 0.23) the standard error on the trend in mature abundance is large relative to the trend itself so that although the median trend is slightly upwards, a downward trend cannot be ruled out. 

Future projections assuming varying levels of future close kin sampling for up to four years showed that standard errors on trend and abundance should greatly reduce. SharkRAG have recognised that CKMR provides a viable alternative to conventional stock assessment for School Shark and have recommended that CKMR continue to be used as a monitoring tool for School Shark and we scoped such continuing work.We developed two, very simple, models that provided similar abundance estimates to those of our more sophisticated close kin model, giving us confidence that the close kin model correctly interpreted the close kin data. Our estimate of abundance is three to four times lower than that of the most recent stock assessment model, when that was projected forwards assuming similar levels of catch to those that have occurred (Thomson, 2012). Our model was not able to sustain the catches that occurred during the 1990s, even under optimal survival conditions for juvenile School Shark. This suggests that the School Shark population consists of more than one reproductively isolated stock, and that the population that we measured is likely to be a remnant of what was present in the 1990s.

It is possible that environmental degradation of School Shark nursery areas (DEWR, 2008) is the explanation for our finding. As there has been little recovery of those areas, School Shark might not have the capability to recover to their previous stock size. In this case, management reference points that rely on the assumption that stocks will recover to their pristine abundance in the absence of fishing, are not useful for School Shark. Conventional stock assessment models give more precise estimates of relative, than of absolute, abundance but CKMR gives reliable estimates of absolute abundance. This provides managers the opportunity to manage School Shark according to a more relevant quantity than abundance relative to a no longer attainable pristine state last seen in the 1920s.

Our work has advanced close kin methodology through the refinement of software developed for quality control of genetic sequencing data, and for kin finding. Our work represents the first application of CKMR to a commercially exploited shark population.
Final Report • 2020-08-01 • 4.30 MB
2014-024-DLD.pdf

Summary

Close kin mark recapture (CKMR) provides an estimate of absolute abundance that is independent of fishing behaviour. We present a first CKMR estimate of abundance for School Shark and discuss the management implications of our findings. 

We found 65 half sibling pairs (HSPs), 3 parent-offspring pairs (POPs) and 34 full sibling pairs (FSPs); sufficient for close kin modelling. Our model estimates a School Shark stock in the region of 50,000 mature individuals during 2000. Although the coefficient of variation (CV) for our abundance estimate ranges from 0.23 to 0.28 over 2000 to 2011 (most precise in 2002-2003, at 0.23) the standard error on the trend in mature abundance is large relative to the trend itself so that although the median trend is slightly upwards, a downward trend cannot be ruled out. 

Future projections assuming varying levels of future close kin sampling for up to four years showed that standard errors on trend and abundance should greatly reduce. SharkRAG have recognised that CKMR provides a viable alternative to conventional stock assessment for School Shark and have recommended that CKMR continue to be used as a monitoring tool for School Shark and we scoped such continuing work.We developed two, very simple, models that provided similar abundance estimates to those of our more sophisticated close kin model, giving us confidence that the close kin model correctly interpreted the close kin data. Our estimate of abundance is three to four times lower than that of the most recent stock assessment model, when that was projected forwards assuming similar levels of catch to those that have occurred (Thomson, 2012). Our model was not able to sustain the catches that occurred during the 1990s, even under optimal survival conditions for juvenile School Shark. This suggests that the School Shark population consists of more than one reproductively isolated stock, and that the population that we measured is likely to be a remnant of what was present in the 1990s.

It is possible that environmental degradation of School Shark nursery areas (DEWR, 2008) is the explanation for our finding. As there has been little recovery of those areas, School Shark might not have the capability to recover to their previous stock size. In this case, management reference points that rely on the assumption that stocks will recover to their pristine abundance in the absence of fishing, are not useful for School Shark. Conventional stock assessment models give more precise estimates of relative, than of absolute, abundance but CKMR gives reliable estimates of absolute abundance. This provides managers the opportunity to manage School Shark according to a more relevant quantity than abundance relative to a no longer attainable pristine state last seen in the 1920s.

Our work has advanced close kin methodology through the refinement of software developed for quality control of genetic sequencing data, and for kin finding. Our work represents the first application of CKMR to a commercially exploited shark population.
Final Report • 2020-08-01 • 4.30 MB
2014-024-DLD.pdf

Summary

Close kin mark recapture (CKMR) provides an estimate of absolute abundance that is independent of fishing behaviour. We present a first CKMR estimate of abundance for School Shark and discuss the management implications of our findings. 

We found 65 half sibling pairs (HSPs), 3 parent-offspring pairs (POPs) and 34 full sibling pairs (FSPs); sufficient for close kin modelling. Our model estimates a School Shark stock in the region of 50,000 mature individuals during 2000. Although the coefficient of variation (CV) for our abundance estimate ranges from 0.23 to 0.28 over 2000 to 2011 (most precise in 2002-2003, at 0.23) the standard error on the trend in mature abundance is large relative to the trend itself so that although the median trend is slightly upwards, a downward trend cannot be ruled out. 

Future projections assuming varying levels of future close kin sampling for up to four years showed that standard errors on trend and abundance should greatly reduce. SharkRAG have recognised that CKMR provides a viable alternative to conventional stock assessment for School Shark and have recommended that CKMR continue to be used as a monitoring tool for School Shark and we scoped such continuing work.We developed two, very simple, models that provided similar abundance estimates to those of our more sophisticated close kin model, giving us confidence that the close kin model correctly interpreted the close kin data. Our estimate of abundance is three to four times lower than that of the most recent stock assessment model, when that was projected forwards assuming similar levels of catch to those that have occurred (Thomson, 2012). Our model was not able to sustain the catches that occurred during the 1990s, even under optimal survival conditions for juvenile School Shark. This suggests that the School Shark population consists of more than one reproductively isolated stock, and that the population that we measured is likely to be a remnant of what was present in the 1990s.

It is possible that environmental degradation of School Shark nursery areas (DEWR, 2008) is the explanation for our finding. As there has been little recovery of those areas, School Shark might not have the capability to recover to their previous stock size. In this case, management reference points that rely on the assumption that stocks will recover to their pristine abundance in the absence of fishing, are not useful for School Shark. Conventional stock assessment models give more precise estimates of relative, than of absolute, abundance but CKMR gives reliable estimates of absolute abundance. This provides managers the opportunity to manage School Shark according to a more relevant quantity than abundance relative to a no longer attainable pristine state last seen in the 1920s.

Our work has advanced close kin methodology through the refinement of software developed for quality control of genetic sequencing data, and for kin finding. Our work represents the first application of CKMR to a commercially exploited shark population.
Final Report • 2020-08-01 • 4.30 MB
2014-024-DLD.pdf

Summary

Close kin mark recapture (CKMR) provides an estimate of absolute abundance that is independent of fishing behaviour. We present a first CKMR estimate of abundance for School Shark and discuss the management implications of our findings. 

We found 65 half sibling pairs (HSPs), 3 parent-offspring pairs (POPs) and 34 full sibling pairs (FSPs); sufficient for close kin modelling. Our model estimates a School Shark stock in the region of 50,000 mature individuals during 2000. Although the coefficient of variation (CV) for our abundance estimate ranges from 0.23 to 0.28 over 2000 to 2011 (most precise in 2002-2003, at 0.23) the standard error on the trend in mature abundance is large relative to the trend itself so that although the median trend is slightly upwards, a downward trend cannot be ruled out. 

Future projections assuming varying levels of future close kin sampling for up to four years showed that standard errors on trend and abundance should greatly reduce. SharkRAG have recognised that CKMR provides a viable alternative to conventional stock assessment for School Shark and have recommended that CKMR continue to be used as a monitoring tool for School Shark and we scoped such continuing work.We developed two, very simple, models that provided similar abundance estimates to those of our more sophisticated close kin model, giving us confidence that the close kin model correctly interpreted the close kin data. Our estimate of abundance is three to four times lower than that of the most recent stock assessment model, when that was projected forwards assuming similar levels of catch to those that have occurred (Thomson, 2012). Our model was not able to sustain the catches that occurred during the 1990s, even under optimal survival conditions for juvenile School Shark. This suggests that the School Shark population consists of more than one reproductively isolated stock, and that the population that we measured is likely to be a remnant of what was present in the 1990s.

It is possible that environmental degradation of School Shark nursery areas (DEWR, 2008) is the explanation for our finding. As there has been little recovery of those areas, School Shark might not have the capability to recover to their previous stock size. In this case, management reference points that rely on the assumption that stocks will recover to their pristine abundance in the absence of fishing, are not useful for School Shark. Conventional stock assessment models give more precise estimates of relative, than of absolute, abundance but CKMR gives reliable estimates of absolute abundance. This provides managers the opportunity to manage School Shark according to a more relevant quantity than abundance relative to a no longer attainable pristine state last seen in the 1920s.

Our work has advanced close kin methodology through the refinement of software developed for quality control of genetic sequencing data, and for kin finding. Our work represents the first application of CKMR to a commercially exploited shark population.

An industry based mark recapture program to provide stock assessment inputs for the Western Rock Lobster Fishery following introduction of quota management

Project number: 2014-023
Project Status:
Completed
Budget expenditure: $330,222.10
Principal Investigator: Jason How
Organisation: Department of Primary Industries and Regional Development (DPIRD) WA
Project start/end date: 18 May 2014 - 29 Jun 2017
Contact:
FRDC
TAGS
Tagging
Stock Assessment
Stakeholder
Rac Wa
Modelling
SPECIES
Western Rock Lobster

Need

The recent change to quota management for the Western Rock Lobster fishery has resulted in significant changes in fishing behaviour which has affected the ability to use the long standing empirical catch rate indices that have been a major component of the assessment of lobster stocks (e.g. catch rates of legal, undersize and breeding lobsters). A recent FRDC funded study (2009/019) examined the possibility of using alternative data sources unbiased by effort to monitor biomass levels and exploitation rates using change-in-ratio techniques. The project concluded that:
1. The current data sources available to the fishery had too many unknowns including size and sex specific timing of growth and movement to enable the assessment of exploitation rates using these techniques.
2. A robust tag-recapture study using multiple release periods across different fishing seasons could generate independent assessments of legal biomass and exploitation rates providing an additional baseline level to improve the interpretation of post quota catch rate indices.
A comprehensive tag-recapture study would also provide increased resolution of the movement dynamics of lobsters, especially the rate of migration between management zones. Such information is considered vital by industry in their discussions of the potential benefits of voluntarily reducing quotas to generate increased localised catch rates.

Objectives

1. Determine spatially specific exploitation rates and legal biomass levels
2. Increase precision of estimates for movement rates between management zones
3. Improve understanding of the variability of growth throughout the range of the fishery

Final report

ISBN: 978-1-921258-76-3 (Print); 978-1-921258-77-0 (Online)
Author: Simon de Lestang
Final Report • 2020-08-01 • 5.40 MB
2014-023-DLD.pdf

Summary

The West Coast Lobster Managed Fishery (WCRLMF) moved from input to output controls in 2010. This change directly affected the relativity of a number of fisherybased data sources, making assessment of the fishery more problematic. A novel examination of the stock dynamics was required to help ensure the stock assessment and associated management outcomes for this valuable resource were maintained. This study derived estimates of current biomass levels and harvest rates throughout the WCRLMF based on the release (over 40,000) of tagged Western Rock Lobsters (Panulirus cygnus) and the recapture of tagged lobsters, using a multi-stage modelling process. Components of this study, such as tag loss and reporting rates, were initially independently examined, before a generalised “Brownie” tag-recapture (BTR) model was implemented that provided an assessment on a fishery-wide basis. Finally a novel purpose-built individual-based model (IBM) was developed that was capable of producing estimates of biomass and harvest rates on finer spatial and temporal scale, as well as providing estimates of migration and growth. 
Final Report • 2020-08-01 • 5.40 MB
2014-023-DLD.pdf

Summary

The West Coast Lobster Managed Fishery (WCRLMF) moved from input to output controls in 2010. This change directly affected the relativity of a number of fisherybased data sources, making assessment of the fishery more problematic. A novel examination of the stock dynamics was required to help ensure the stock assessment and associated management outcomes for this valuable resource were maintained. This study derived estimates of current biomass levels and harvest rates throughout the WCRLMF based on the release (over 40,000) of tagged Western Rock Lobsters (Panulirus cygnus) and the recapture of tagged lobsters, using a multi-stage modelling process. Components of this study, such as tag loss and reporting rates, were initially independently examined, before a generalised “Brownie” tag-recapture (BTR) model was implemented that provided an assessment on a fishery-wide basis. Finally a novel purpose-built individual-based model (IBM) was developed that was capable of producing estimates of biomass and harvest rates on finer spatial and temporal scale, as well as providing estimates of migration and growth. 
Final Report • 2020-08-01 • 5.40 MB
2014-023-DLD.pdf

Summary

The West Coast Lobster Managed Fishery (WCRLMF) moved from input to output controls in 2010. This change directly affected the relativity of a number of fisherybased data sources, making assessment of the fishery more problematic. A novel examination of the stock dynamics was required to help ensure the stock assessment and associated management outcomes for this valuable resource were maintained. This study derived estimates of current biomass levels and harvest rates throughout the WCRLMF based on the release (over 40,000) of tagged Western Rock Lobsters (Panulirus cygnus) and the recapture of tagged lobsters, using a multi-stage modelling process. Components of this study, such as tag loss and reporting rates, were initially independently examined, before a generalised “Brownie” tag-recapture (BTR) model was implemented that provided an assessment on a fishery-wide basis. Finally a novel purpose-built individual-based model (IBM) was developed that was capable of producing estimates of biomass and harvest rates on finer spatial and temporal scale, as well as providing estimates of migration and growth. 
Final Report • 2020-08-01 • 5.40 MB
2014-023-DLD.pdf

Summary

The West Coast Lobster Managed Fishery (WCRLMF) moved from input to output controls in 2010. This change directly affected the relativity of a number of fisherybased data sources, making assessment of the fishery more problematic. A novel examination of the stock dynamics was required to help ensure the stock assessment and associated management outcomes for this valuable resource were maintained. This study derived estimates of current biomass levels and harvest rates throughout the WCRLMF based on the release (over 40,000) of tagged Western Rock Lobsters (Panulirus cygnus) and the recapture of tagged lobsters, using a multi-stage modelling process. Components of this study, such as tag loss and reporting rates, were initially independently examined, before a generalised “Brownie” tag-recapture (BTR) model was implemented that provided an assessment on a fishery-wide basis. Finally a novel purpose-built individual-based model (IBM) was developed that was capable of producing estimates of biomass and harvest rates on finer spatial and temporal scale, as well as providing estimates of migration and growth. 
Final Report • 2020-08-01 • 5.40 MB
2014-023-DLD.pdf

Summary

The West Coast Lobster Managed Fishery (WCRLMF) moved from input to output controls in 2010. This change directly affected the relativity of a number of fisherybased data sources, making assessment of the fishery more problematic. A novel examination of the stock dynamics was required to help ensure the stock assessment and associated management outcomes for this valuable resource were maintained. This study derived estimates of current biomass levels and harvest rates throughout the WCRLMF based on the release (over 40,000) of tagged Western Rock Lobsters (Panulirus cygnus) and the recapture of tagged lobsters, using a multi-stage modelling process. Components of this study, such as tag loss and reporting rates, were initially independently examined, before a generalised “Brownie” tag-recapture (BTR) model was implemented that provided an assessment on a fishery-wide basis. Finally a novel purpose-built individual-based model (IBM) was developed that was capable of producing estimates of biomass and harvest rates on finer spatial and temporal scale, as well as providing estimates of migration and growth. 

Developing a rapid molecular identification technique to improve egg production based fish biomass assessments

Project number: 2014-022
Project Status:
Completed
Budget expenditure: $175,121.21
Principal Investigator: Richard J. Saunders
Organisation: James Cook University (JCU)
Project start/end date: 8 May 2014 - 14 Aug 2017
Contact:
FRDC
TAGS
Survey
Stock Assessment
Rac Nt
Genomics
Biotechnology
SPECIES
Grey Mackerel
Spanish Mackerel
Black Jewfish
Sardines

Need

Our ability to assess the status of many important fish species is restricted by the inability to accurately estimate their biomass. In addition, the high costs of such surveys mean that they are not conducted for many species within Australia's Fisheries. Ichthyoplankton surveys to determine egg production and biomass (such as through the daily egg production method (DEPM)) offer an effective means to get this information. However, current techniques cannot be applied broadly because many fish have morphologically identical eggs and molecular sequencing is prohibitively expensive and time consuming. These issues were highlighted in the DEPM assessments for blue mackerel and red bait (FRDC 2002/061 & 2004/39) where there was poor success in morphological identification of fish eggs collected in plankton tows. These projects identified the need to develop an accurate, rapid and inexpensive technique for fish eggs identification. This project will assess the suitability of developing this technique with the ultimate aim of conducting icthyoplankton surveys to inform a DEPM for mackerel species (Qld, NT and WA), pilchard and herring species in the developing tropical small pelagics fishery(NT) and black jewfish (NT, WA, Qld). While the development is focused on tropical species the technique will have application in many southern fisheries.
This project was developed under the steerage of the Northern Research Partnership (NRP) and addresses northern Australia priorities around developing better biomass estimation methods for Spanish/grey mackerel and for the new multi-species small pelagic and Coastal Line Fisheries in the NT.

Objectives

1. To develop a novel high-throughput, low cost DNA-based egg identification method for important fish species in northern Australia.
2. To assess the application of the technology developed for use in the daily egg production method (DEPM) for biomass estimation.

Final report

ISBN: 978-0-6485037-0-5
Authors: Richard J. Saunders Shannon Kjeldsen Roger Huerlimann Thor Saunders Shane Penny Andrew Tobin and Dean Jerry
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.
Final Report • 2019-12-01 • 2.27 MB
2014-022-DLD.pdf

Summary

This project aimed to develop a rapid and affordable molecular method to identify fish eggs from plankton samples. The method selected was a multiplex bead array method where species-specific probes are developed and bound to beads which fluoresce when passed through a flow cytometer if bound to the target species DNA. This allows for identification of multiple species at one time as different probe-bead combinations can be used to identify different fish species. Furthermore, as molecular methods usually require preservation in ethanol which causes problems of egg staging, a critical component in modelling egg mortality and thus initial egg abundance, we also considered the impact of preservation method on egg staging and on DNA amplification.
 
The method was able to identify eggs of several target species from wild collected plankton samples (confirmed by sequencing) with success rates varying between species from 50 to 100% identification success. We identified a series of issues that potentially limit the application of this method in the context of DEPM and egg identification. The principal issues were reliability of the chemistry and identified false negative results resultant from preservation of DNA. DNA amplification and egg staging were both impacted by preservation method with the best preservation method for egg staging being 5% formalin, however, this was the worst performer for DNA amplification. An ethanol based preservation method is essential for DNA based identification and this also allows for some egg staging, although egg staging prior to the presence of an embryo is very challenging, even for an experienced technician.

Developing innovative approaches to improve CPUE standardisation for Australia's multi-species pelagic longline fisheries

Project number: 2014-021
Project Status:
Completed
Budget expenditure: $298,741.86
Principal Investigator: Robert A. Campbell
Organisation: CSIRO Oceans and Atmosphere Hobart
Project start/end date: 15 Jun 2014 - 29 Aug 2016
Contact:
FRDC
TAGS
Sustainability
Stock Assessment
Rac Cmwth
Modelling
Harvest Strategy
SPECIES
Swordfish
Marlins

Need

Indices of abundance based on standardised CPUE are critical inputs to both the stock assessments of tunas and billfish and associated harvest strategies. However, a major constraint for assessing multi-species fisheries is a lack of reliable abundance indices that are a pre-requisite for the accompanying stock assessments. Improvements in our ability to standardise multi-species CPUE will therefore improve the accuracy of assessment outcomes as well as implementation of harvest strategies such as those used in multi-species fisheries such as the Eastern Tuna and Billfish Fishery (ETBF) which are rely heavily on standardised CPUE. Within the ETBF standardised CPUE indices for some target species display large inter-annual variation which is not thought to truly reflect variation in the stock availability. The multi-species nature of the ETBF also means that it can be difficult to standardise CPUE for individual species as changes in the targeting of different species can change CPUE in a manner not related to stock abundance. Imperfect CPUE standardisation impacts on the output of the harvest strategy, in particular the Recommended Biological Commercial Catches (RBCC). New techniques to improve the CPUE standardisation would consequently improve the quality of resultant RBCCs and subsequent TACCs. There will also be follow-on improvements in assessing the status of other pelagic resources (e.g. byproduct and bycatch speices, both domestically and internationally), most of which rely on the standardisation of CPUE. The recent CPUE Standardisation Workshop held by TTRAG in March 2013 supported this need which was also subsequently endorsed by TTMAC which included the project “Identification, application and appraisal of novel statistical techniques for use in the CPUE standardisation“ as a high priority in the annual research statement for 2013/14.

Objectives

1. Identify the factors likely to influence pelagic longline CPUE and review the data requirements and data availability so that these factors can be used for standardising CPUE.
2. Review all methods (both those currently used and all other and novel methods) which may be used for standardising CPUE.
3. Based on our experiences in other relevant research and the outcomes of objectives 1 and 2 identify, develop and compare the most appropriate methods for standardising CPUE for pelagic longline fisheries.
4. Use simulated catch and effort data to test the potential of each method to adequately account for the influence of factors influencing CPUE and accurately reflect the underlying resource abundance.
5. Investigate the sensitivity of the outcomes of the ETBF harvest strategy on the adoption of the candidate methods for standardising CPUE within the ETBF.

Final report

ISBN: 9781486308521
Authors: Robert Campbell Shijie Zhou Simon Hoyle Rich Hillary Malcolm Haddon and Steve Auld
Final Report • 2017-05-01 • 6.32 MB
2014-021-DLD.pdf

Summary

This project was undertaken by a collaboration of senior fishery scientists at CSIRO and from New Zealand, together with a former fisheries manager now with the Commonwealth Department of Agriculture and Water Resources in Canberra, on the development of methods to construct indices of stock abundance trends from commercial catch-per-unit-effort (CPUE) in multispecies pelagic longline fisheries. Such indices are crucial inputs into stock assessments undertaken around the world and play a vital role in achieving the sustainable management of global fisheries. The project work was undertaken during 2015 and 2016, using the multispecies longline fishery for tuna and billfish on the east coast of Australia (the Eastern Tuna and Billfish Fishery) as the example case study. As indices of stock abundance constructed from CPUE data are the central inputs into the harvest strategy used in this fishery to inform the determination of annual Total Allowable Commercial Catch (TACC) limits, there was a need to identify the accuracy of current methods and develop new methods to construct more reliable indices of stock abundance. In this regard, the analyses undertaken during the project and presented here were designed to address specific issues related to this fishery. 

However, it is also hoped that the general results of this project will have broader applicability to other multispecies species, both domestically and internationally.
Final Report • 2017-05-01 • 6.32 MB
2014-021-DLD.pdf

Summary

This project was undertaken by a collaboration of senior fishery scientists at CSIRO and from New Zealand, together with a former fisheries manager now with the Commonwealth Department of Agriculture and Water Resources in Canberra, on the development of methods to construct indices of stock abundance trends from commercial catch-per-unit-effort (CPUE) in multispecies pelagic longline fisheries. Such indices are crucial inputs into stock assessments undertaken around the world and play a vital role in achieving the sustainable management of global fisheries. The project work was undertaken during 2015 and 2016, using the multispecies longline fishery for tuna and billfish on the east coast of Australia (the Eastern Tuna and Billfish Fishery) as the example case study. As indices of stock abundance constructed from CPUE data are the central inputs into the harvest strategy used in this fishery to inform the determination of annual Total Allowable Commercial Catch (TACC) limits, there was a need to identify the accuracy of current methods and develop new methods to construct more reliable indices of stock abundance. In this regard, the analyses undertaken during the project and presented here were designed to address specific issues related to this fishery. 

However, it is also hoped that the general results of this project will have broader applicability to other multispecies species, both domestically and internationally.
Final Report • 2017-05-01 • 6.32 MB
2014-021-DLD.pdf

Summary

This project was undertaken by a collaboration of senior fishery scientists at CSIRO and from New Zealand, together with a former fisheries manager now with the Commonwealth Department of Agriculture and Water Resources in Canberra, on the development of methods to construct indices of stock abundance trends from commercial catch-per-unit-effort (CPUE) in multispecies pelagic longline fisheries. Such indices are crucial inputs into stock assessments undertaken around the world and play a vital role in achieving the sustainable management of global fisheries. The project work was undertaken during 2015 and 2016, using the multispecies longline fishery for tuna and billfish on the east coast of Australia (the Eastern Tuna and Billfish Fishery) as the example case study. As indices of stock abundance constructed from CPUE data are the central inputs into the harvest strategy used in this fishery to inform the determination of annual Total Allowable Commercial Catch (TACC) limits, there was a need to identify the accuracy of current methods and develop new methods to construct more reliable indices of stock abundance. In this regard, the analyses undertaken during the project and presented here were designed to address specific issues related to this fishery. 

However, it is also hoped that the general results of this project will have broader applicability to other multispecies species, both domestically and internationally.
Final Report • 2017-05-01 • 6.32 MB
2014-021-DLD.pdf

Summary

This project was undertaken by a collaboration of senior fishery scientists at CSIRO and from New Zealand, together with a former fisheries manager now with the Commonwealth Department of Agriculture and Water Resources in Canberra, on the development of methods to construct indices of stock abundance trends from commercial catch-per-unit-effort (CPUE) in multispecies pelagic longline fisheries. Such indices are crucial inputs into stock assessments undertaken around the world and play a vital role in achieving the sustainable management of global fisheries. The project work was undertaken during 2015 and 2016, using the multispecies longline fishery for tuna and billfish on the east coast of Australia (the Eastern Tuna and Billfish Fishery) as the example case study. As indices of stock abundance constructed from CPUE data are the central inputs into the harvest strategy used in this fishery to inform the determination of annual Total Allowable Commercial Catch (TACC) limits, there was a need to identify the accuracy of current methods and develop new methods to construct more reliable indices of stock abundance. In this regard, the analyses undertaken during the project and presented here were designed to address specific issues related to this fishery. 

However, it is also hoped that the general results of this project will have broader applicability to other multispecies species, both domestically and internationally.
Final Report • 2017-05-01 • 6.32 MB
2014-021-DLD.pdf

Summary

This project was undertaken by a collaboration of senior fishery scientists at CSIRO and from New Zealand, together with a former fisheries manager now with the Commonwealth Department of Agriculture and Water Resources in Canberra, on the development of methods to construct indices of stock abundance trends from commercial catch-per-unit-effort (CPUE) in multispecies pelagic longline fisheries. Such indices are crucial inputs into stock assessments undertaken around the world and play a vital role in achieving the sustainable management of global fisheries. The project work was undertaken during 2015 and 2016, using the multispecies longline fishery for tuna and billfish on the east coast of Australia (the Eastern Tuna and Billfish Fishery) as the example case study. As indices of stock abundance constructed from CPUE data are the central inputs into the harvest strategy used in this fishery to inform the determination of annual Total Allowable Commercial Catch (TACC) limits, there was a need to identify the accuracy of current methods and develop new methods to construct more reliable indices of stock abundance. In this regard, the analyses undertaken during the project and presented here were designed to address specific issues related to this fishery. 

However, it is also hoped that the general results of this project will have broader applicability to other multispecies species, both domestically and internationally.

Application of tracking technologies to understand space-time explicit patterns of movement, residency and habitat use of pelagic sharks in Spencer Gulf: resolving overlaps with key community activities and marine industries

Project number: 2014-020
Project Status:
Completed
Budget expenditure: $382,063.00
Principal Investigator: Paul J. Rogers
Organisation: SARDI Food Safety and Innovation
Project start/end date: 31 May 2014 - 31 Jul 2016
Contact:
FRDC
TAGS
Tourism
Social Science
Social Science
Recreational Fishing
Rac Sa
SPECIES
Bronze Whaler

Need

Following many expressions of public concern regarding the potential for finfish/tuna aquaculture to attract sharks to coastal areas, at both regional development and individual site applications, PIRSA Fisheries and Aquaculture identified the need for an understanding of the factors that may explain associations between sharks and finfish/tuna aquaculture activities. This view was reinforced at meetings of the AAC (including a presentation from the PI on 22 Feb 2013), who are a legislated body under the Aquaculture Act 2001, advising the State Minister for Agriculture, Food and Fisheries on matters relating to aquaculture development. As a consequence, this project was listed as a priority area for investment by the SAFRAB.

A previous FRDC funded workshop (2002/040) identified a need to understand factors that may explain interactions between pelagic sharks and aquaculture activities. Some of the findings highlighted during this workshop are now considered to be outdated. For example, anecdotal accounts from finfish farmers and commercial fishers suggest that white sharks sightings have increased in the past decade in Spencer Gulf and this may have implications for the frequency of interactions with the fishing and aquaculture industry. The provision of data to further inform the public’s current perception of the aquaculture industry represents a key priority in South Australia’s Fisheries and Aquaculture R&D Strategy. During the development of this project the need for this research was discussed with key industry representatives.
This proposal addresses key objectives of the Draft White Shark Recovery Plan, 2010 (2c, 7a, 9a and 9b).

Objectives

1. Determine if activities associated with finfish aquaculture correlate with spatial and temporal residency and migration patterns of pelagic sharks.
2. Assess and compare patterns of residency of pelagic sharks in ‘natural’ foraging areas, and any overlaps with community activities.
3. Develop a Code of Practice for removal and release of pelagic sharks from finfish aquaculture cages.

Final report

ISBN: 978-1-876007-09-6
Author: Dr Paul Rogers
Final Report • 2018-09-01 • 5.12 MB
2014-020-DLD.pdf

Summary

The report focuses on the movement dynamics of two pelagic sharks, the White Shark (Carcharadon carcharias) and Bronze Whaler (Carcharinhus brachyurus), in South Australia. Specific aims were to: (1) determine if aquaculture activities correlated with patterns on fidelity and migration; and (2) assess and compare the use of natural foraging areas and areas used during human marine activities. Additional objectives included the development of: industry guidelines for removal and release of pelagic sharks from finfish aquaculture pontoons, and surveys to collect baseline information on perceptions of shark associations with aquaculture and other marine activities. 
Key outcomes of the project include provision of advice to marine policy-makers regarding overlaps between sharks, marine industries and areas used during community activities (including marine parks). This project addressed important research and management questions that existed for over a decade. 
Final Report • 2018-09-01 • 5.12 MB
2014-020-DLD.pdf

Summary

The report focuses on the movement dynamics of two pelagic sharks, the White Shark (Carcharadon carcharias) and Bronze Whaler (Carcharinhus brachyurus), in South Australia. Specific aims were to: (1) determine if aquaculture activities correlated with patterns on fidelity and migration; and (2) assess and compare the use of natural foraging areas and areas used during human marine activities. Additional objectives included the development of: industry guidelines for removal and release of pelagic sharks from finfish aquaculture pontoons, and surveys to collect baseline information on perceptions of shark associations with aquaculture and other marine activities. 
Key outcomes of the project include provision of advice to marine policy-makers regarding overlaps between sharks, marine industries and areas used during community activities (including marine parks). This project addressed important research and management questions that existed for over a decade. 
Final Report • 2018-09-01 • 5.12 MB
2014-020-DLD.pdf

Summary

The report focuses on the movement dynamics of two pelagic sharks, the White Shark (Carcharadon carcharias) and Bronze Whaler (Carcharinhus brachyurus), in South Australia. Specific aims were to: (1) determine if aquaculture activities correlated with patterns on fidelity and migration; and (2) assess and compare the use of natural foraging areas and areas used during human marine activities. Additional objectives included the development of: industry guidelines for removal and release of pelagic sharks from finfish aquaculture pontoons, and surveys to collect baseline information on perceptions of shark associations with aquaculture and other marine activities. 
Key outcomes of the project include provision of advice to marine policy-makers regarding overlaps between sharks, marine industries and areas used during community activities (including marine parks). This project addressed important research and management questions that existed for over a decade. 
Final Report • 2018-09-01 • 5.12 MB
2014-020-DLD.pdf

Summary

The report focuses on the movement dynamics of two pelagic sharks, the White Shark (Carcharadon carcharias) and Bronze Whaler (Carcharinhus brachyurus), in South Australia. Specific aims were to: (1) determine if aquaculture activities correlated with patterns on fidelity and migration; and (2) assess and compare the use of natural foraging areas and areas used during human marine activities. Additional objectives included the development of: industry guidelines for removal and release of pelagic sharks from finfish aquaculture pontoons, and surveys to collect baseline information on perceptions of shark associations with aquaculture and other marine activities. 
Key outcomes of the project include provision of advice to marine policy-makers regarding overlaps between sharks, marine industries and areas used during community activities (including marine parks). This project addressed important research and management questions that existed for over a decade. 
Final Report • 2018-09-01 • 5.12 MB
2014-020-DLD.pdf

Summary

The report focuses on the movement dynamics of two pelagic sharks, the White Shark (Carcharadon carcharias) and Bronze Whaler (Carcharinhus brachyurus), in South Australia. Specific aims were to: (1) determine if aquaculture activities correlated with patterns on fidelity and migration; and (2) assess and compare the use of natural foraging areas and areas used during human marine activities. Additional objectives included the development of: industry guidelines for removal and release of pelagic sharks from finfish aquaculture pontoons, and surveys to collect baseline information on perceptions of shark associations with aquaculture and other marine activities. 
Key outcomes of the project include provision of advice to marine policy-makers regarding overlaps between sharks, marine industries and areas used during community activities (including marine parks). This project addressed important research and management questions that existed for over a decade. 

Developing a fishery independent estimate of biomass for snapper

Project number: 2014-019
Project Status:
Completed
Budget expenditure: $316,985.00
Principal Investigator: Mike A. Steer
Organisation: SARDI Food Safety and Innovation
Project start/end date: 13 Jul 2014 - 29 Jun 2016
Contact:
FRDC
TAGS
Sustainability
Survey
Stock Assessment
Reproduction
Rac Sa
SPECIES
Snapper

Need

Increased formalisation of harvest strategies for snapper across Australia’s four main jurisdictions (East Coast, Western Victoria, South Australia and Western Australia) was identified as a national priority (at the National Strategic Planning Workshop for Snapper Research – 1st March 2013). Two key processes were recognised as being fundamental to achieving this: 1. development of a snapper-specific integrated fishery model; and 2. integration of a fishery-independent estimate of abundance. Each jurisdiction is currently at a different level of advancement in their assessment and management capability, with WA leading the way. A snapper model is currently used to underpin the assessment of South Australia’s snapper resource, whereas Western Victoria is in the process of developing their own and the East Coast is yet to develop one. South Australia and Western Victoria are at a level where the development and integration of a DEPM, that would provide a fishery-independent estimate of biomass, would considerably enhance their respective stock assessment programs.

The need for a DEPM is more urgent for South Australia, as recent structural changes in the snapper fishery have compromised the integrity of the time series of fishery-dependent statistics that have been relied on to assess the resource in the past. Fishery-independent estimates of snapper biomass are required to feed into the existing stock assessment model to ensure that future assessments and harvest strategies are developed from unbiased information. This research direction has been unanimously supported by the relevant stakeholders in South Australia’s Snapper Fishery. The Western Victorian fishery is likely to encounter similar issues to South Australia, particularly as their fishery is dominated by the recreational sector where the routine collection of catch and effort data to integrate into the assessment process is often challenging.

Objectives

1. To develop a DEPM for snapper that provides the most accurate estimate of biomass and integrates with the on-going assessment and management of the resource.

Final report

ISBN: 978-1-921563-96-6
Authors: M.A. Steer R. McGarvey A. Oxley A.J. Fowler G. Grammer T.M Ward E. Westlake D. Matthews and J. Matthews
Final Report • 2017-07-01 • 2.08 MB
2014-019-DLD.pdf

Summary

This study was undertaken by the South Australia Research and Development Institute (SARDI). Through overcoming considerable technical challenges, this study was the first to successfully develop a relatively non-destructive molecular probe that can reliably identify Snapper (Chrysophrys auratus) eggs and larvae in mixed ichthyoplankton samples. This highly-specific molecular probe targets Snapper ribosomal (r)RNA and when conjugated with a reactive molecule produces a highly visible blue colour in positive reactions. Snapper eggs are subsequently easily detected using a standard stereo dissecting microscope. This novel use of an established molecular technique has re-invigorated the capability of using the daily egg production method (DEPM) to provide a fishery-independent estimate of spawning biomass for Snapper and has also increased its applicability to other species where egg identification has been problematic. This research has reduced the need to exclusively rely on fishery-dependent catch and effort data to assess Snapper fisheries and has demonstrated that the incorporation of the DEPM into South Australia’s existing assessment program is relatively cost-effective and likely to benefit the management and industry. Adding the DEPM will contribute an extra unbiased source of information that can be synthesised with existing fishery-dependent data streams that will lead to more confident assessments of the stock and ensure the long term sustainability of the State’s Snapper resource.

Final Report • 2017-07-01 • 2.08 MB
2014-019-DLD.pdf

Summary

This study was undertaken by the South Australia Research and Development Institute (SARDI). Through overcoming considerable technical challenges, this study was the first to successfully develop a relatively non-destructive molecular probe that can reliably identify Snapper (Chrysophrys auratus) eggs and larvae in mixed ichthyoplankton samples. This highly-specific molecular probe targets Snapper ribosomal (r)RNA and when conjugated with a reactive molecule produces a highly visible blue colour in positive reactions. Snapper eggs are subsequently easily detected using a standard stereo dissecting microscope. This novel use of an established molecular technique has re-invigorated the capability of using the daily egg production method (DEPM) to provide a fishery-independent estimate of spawning biomass for Snapper and has also increased its applicability to other species where egg identification has been problematic. This research has reduced the need to exclusively rely on fishery-dependent catch and effort data to assess Snapper fisheries and has demonstrated that the incorporation of the DEPM into South Australia’s existing assessment program is relatively cost-effective and likely to benefit the management and industry. Adding the DEPM will contribute an extra unbiased source of information that can be synthesised with existing fishery-dependent data streams that will lead to more confident assessments of the stock and ensure the long term sustainability of the State’s Snapper resource.

Final Report • 2017-07-01 • 2.08 MB
2014-019-DLD.pdf

Summary

This study was undertaken by the South Australia Research and Development Institute (SARDI). Through overcoming considerable technical challenges, this study was the first to successfully develop a relatively non-destructive molecular probe that can reliably identify Snapper (Chrysophrys auratus) eggs and larvae in mixed ichthyoplankton samples. This highly-specific molecular probe targets Snapper ribosomal (r)RNA and when conjugated with a reactive molecule produces a highly visible blue colour in positive reactions. Snapper eggs are subsequently easily detected using a standard stereo dissecting microscope. This novel use of an established molecular technique has re-invigorated the capability of using the daily egg production method (DEPM) to provide a fishery-independent estimate of spawning biomass for Snapper and has also increased its applicability to other species where egg identification has been problematic. This research has reduced the need to exclusively rely on fishery-dependent catch and effort data to assess Snapper fisheries and has demonstrated that the incorporation of the DEPM into South Australia’s existing assessment program is relatively cost-effective and likely to benefit the management and industry. Adding the DEPM will contribute an extra unbiased source of information that can be synthesised with existing fishery-dependent data streams that will lead to more confident assessments of the stock and ensure the long term sustainability of the State’s Snapper resource.

Final Report • 2017-07-01 • 2.08 MB
2014-019-DLD.pdf

Summary

This study was undertaken by the South Australia Research and Development Institute (SARDI). Through overcoming considerable technical challenges, this study was the first to successfully develop a relatively non-destructive molecular probe that can reliably identify Snapper (Chrysophrys auratus) eggs and larvae in mixed ichthyoplankton samples. This highly-specific molecular probe targets Snapper ribosomal (r)RNA and when conjugated with a reactive molecule produces a highly visible blue colour in positive reactions. Snapper eggs are subsequently easily detected using a standard stereo dissecting microscope. This novel use of an established molecular technique has re-invigorated the capability of using the daily egg production method (DEPM) to provide a fishery-independent estimate of spawning biomass for Snapper and has also increased its applicability to other species where egg identification has been problematic. This research has reduced the need to exclusively rely on fishery-dependent catch and effort data to assess Snapper fisheries and has demonstrated that the incorporation of the DEPM into South Australia’s existing assessment program is relatively cost-effective and likely to benefit the management and industry. Adding the DEPM will contribute an extra unbiased source of information that can be synthesised with existing fishery-dependent data streams that will lead to more confident assessments of the stock and ensure the long term sustainability of the State’s Snapper resource.

Final Report • 2017-07-01 • 2.08 MB
2014-019-DLD.pdf

Summary

This study was undertaken by the South Australia Research and Development Institute (SARDI). Through overcoming considerable technical challenges, this study was the first to successfully develop a relatively non-destructive molecular probe that can reliably identify Snapper (Chrysophrys auratus) eggs and larvae in mixed ichthyoplankton samples. This highly-specific molecular probe targets Snapper ribosomal (r)RNA and when conjugated with a reactive molecule produces a highly visible blue colour in positive reactions. Snapper eggs are subsequently easily detected using a standard stereo dissecting microscope. This novel use of an established molecular technique has re-invigorated the capability of using the daily egg production method (DEPM) to provide a fishery-independent estimate of spawning biomass for Snapper and has also increased its applicability to other species where egg identification has been problematic. This research has reduced the need to exclusively rely on fishery-dependent catch and effort data to assess Snapper fisheries and has demonstrated that the incorporation of the DEPM into South Australia’s existing assessment program is relatively cost-effective and likely to benefit the management and industry. Adding the DEPM will contribute an extra unbiased source of information that can be synthesised with existing fishery-dependent data streams that will lead to more confident assessments of the stock and ensure the long term sustainability of the State’s Snapper resource.

Tasmania's coastal reefs: deep reef habitats and significance for finfish production and biodiversity

Project number: 2014-012
Project Status:
Completed
Budget expenditure: $227,904.26
Principal Investigator: Jeremy Lyle
Organisation: University of Tasmania (UTAS)
Project start/end date: 29 May 2014 - 29 Sep 2016
Contact:
FRDC
TAGS
Survey
Recreational Fishing
Rac Tas
Habitat
Fishing Gear
SPECIES
Striped Trumpeter
Banded Morwong
Longsnout Boarfish
Leatherjackets
Trumpeters

Need

Reefs represent important habitats for commercially and recreationally exploited species under Tasmanian jurisdiction. In Tasmania, shallow reefs (25 m) are significant to commercial and recreational fisheries for scalefish and invertebrates. These include live-fish fisheries for banded morwong (gillnet) and wrasse (trap and line), as well as recreational and commercial gillnet fisheries for species such as bastard trumpeter, striped trumpeter and blue warehou. Other species including jackass morwong, various leatherjackets and boarfish, are also relatively commonly caught on shallow inshore reefs. Most of these species also occur at greater depths but as only striped trumpeter are subjected to a targeted (line) deepwater fishery; deep reefs are therefore assumed to be important refuges from fishing pressure. While recent research has improved our understanding of the population biology of some of these species, management of these fisheries is primarily based on characteristics observed from shallow reefs. The lack of quantitative information on the significance of deep reef habitats as refuges and/or their role in population structuring limits our ability to undertake informed risk assessments of the impacts of current fishing practices and evaluate alternative management options.

While the structure, composition and functioning of shallow-reefs (10m) and their associated fish communities has been studied extensively, the ecological importance of deeper reef ecosystems has not been investigated apart from recent baseline studies of offshore Commonwealth MPAs. Linkages and associations between fish communities in shallow and deeper reef areas remain a distinct knowledge gap.

Objectives

1. Characterise reef fish communities on the east and south-east coasts of Tasmania by depth and habitat structure
2. Describe habitat associations for the key reef fish species and their links to life-history characteristics
3. Assess the potential to use habitat characteristics to describe and predict fish community structure
4. Assess the significance of reef habitats for fisheries production and fishery assessments

Final report

ISBN: 978-1-86295-902-6
Author: Jeremy Lyle
Final Report • 2017-05-30 • 8.36 MB
2014-012-DLD.pdf
Final Report • 2017-05-30 • 8.36 MB
2014-012-DLD.pdf
Final Report • 2017-05-30 • 8.36 MB
2014-012-DLD.pdf
Final Report • 2017-05-30 • 8.36 MB
2014-012-DLD.pdf
Final Report • 2017-05-30 • 8.36 MB
2014-012-DLD.pdf
View Filter

Research

Category

Product Type

Species

Organisation