19 results
Environment
PROJECT NUMBER • 2018-091
PROJECT STATUS:
COMPLETED

Assessment of national-scale tracking of commercially important fish species

In this FRDC project, a team from Integrated Marine Observing System Animal Tracking Facility (IMOS ATF), in coordination with state and federal agencies and the Fisheries and Aquaculture Research Providers Network (RPN) met. They systematically reconfigured the IMOS ATF national network to...
ORGANISATION:
Sydney Institute of Marine Science (SIMS)
TAGS
Stock Assessment
Remote Sensing
Recreational Fishing
Migration
Fisheries Management
SPECIES
Spanish Mackerel
Southern Bluefin Tuna
Yellowfin Bream
Black Bream
Snapper
Environment
PROJECT NUMBER • 1999-217
PROJECT STATUS:
COMPLETED

Stable isotope tracing of the contribution of seagrass production to subtropical fisheries species occurring outside seagrass areas

Results from this project affect the relative importance coastal managers will place on different estuarine habitats. Until now primary production from mangrove forests has been ranked highly for its presumed contribution to fisheries species occurring seaward of mangroves. This project...
ORGANISATION:
Griffith University Nathan Campus
TAGS
Sustainability
Offshore
Laboratory Procedures
Inshore
Habitat
SPECIES
Spanish Mackerel
Sea Mullet
Tailor
Sand Whiting
Blue Swimmer Crab
Industry
PROJECT NUMBER • 2015-215
PROJECT STATUS:
COMPLETED

Low cost management regimes for sustainable, small low-value fisheries based on coastal inshore species

This study provides a comprehensive, process-based guidance to developing low-cost management regimes for small-scale, low-value fisheries. The approach outlined is strongly “bottom-up” in that it seeks to identify pragmatic options and provide practical advice that specifically...
ORGANISATION:
CSIRO Oceans and Atmosphere Hobart
TAGS
Stakeholder
Rac Nt
Inshore
Harvest Strategy
Fisheries Management
SPECIES
Spanish Mackerel
Environment
Environment

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.

Using commercial and recreational fisher knowledge to reconstruct historical catch rates for Queensland Snapper (Chrysophrys auratus), Spanish Mackerel (Scomberomorus commerson) and Coral Trout (Plectropomus spp.): long-term data for incorporation into future stock assessments

Project number: 2013-018
Project Status:
Completed
Budget expenditure: $44,800.00
Principal Investigator: Ruth H. Thurstan
Organisation: University of Queensland (UQ)
Project start/end date: 30 Jun 2013 - 22 Dec 2013
Contact:
FRDC
TAGS
Wild Catch
Training
Stock Assessment
Recreational Fishing
Rac Qld
SPECIES
Spanish Mackerel
Snapper

Need

It is acknowledged that there is a lack of information on past fisheries (i.e. catch rates, fishing effort, proportion of recorded landings) throughout Queensland prior to the start of individual logbook records in 1988 (Halliday and Robins 2007). Yet information prior to this period is critical for successful management, as longer-term perspectives provide data that can help reduce uncertainty associated with projected historical catch levels (Campbell et al. 2009). Long-term data also informs past fishery states, thus equipping managers, stock assessment modellers and the fishing industry with knowledge of historical fishery trends. This can then be used to facilitate informed discussion of appropriate management methods into the future.

During a review of the 2008 Queensland snapper stock assessment, Francis (2009) called for consultation of ‘knowledgeable people’ in order to reconstruct past catch histories, thereby improving estimates for future stock assessments. We aim to fill this gap in research for two fish species that are of particular economic, social and cultural importance to Queensland, pink snapper (Pagrus auratus) and Spanish mackerel (Scomberomorus commerson), through the collation and synthesis of commercial and recreational fisher knowledge.

Our project has broad application to the FRDC’s Research Plan, as it provides a long-term view of the use and management of aquatic resources. It applies to the National Fishing and Aquaculture RD&E Strategy, as it will gather knowledge that can inform environmentally sustainable fishing through determining past changes to catch rates, locations fished and relative fishing effort. In addition, perceptions of changes to fisheries and the broader ecosystem as a result of non-fishery drivers, i.e. coastal development, resource management measures and social drivers of change, will be gathered. Our proposed research will focus upon commercial and recreational fishers, thus incorporating the two major sectors involved in wild-catch fisheries.

Objectives

1. • To reconstruct relative changes in abundance and distribution of pink snapper (Pagrus auratus) and Spanish mackerel (Scomberomorus commerson), using commercial and recreational fishers’ testimony and historical data.
2. • ‘To use fishers’ data to expand our temporal scope of knowledge by providing robust historical data, thereby reducing uncertainty in past exploitation rates and making information available for potential use in future management decisions.’
3. • To determine the impact of evolving fishing technologies, fishing effort and changing management regimes upon fish catches and abundance over time.
4. • To compare perceptions of change between commercial and recreational groups, and identify common areas/species of concern held by both groups.

Final report

ISBN: 978-1-74272-123-1
Final Report • 2016-01-31 • 9.19 MB
2013-018-DLD.pdf
Communities
PROJECT NUMBER • 2017-098
PROJECT STATUS:
COMPLETED

Southern Bluefin Tuna: Changing The Trajectory

Life on the Line is the true story of the Southern Bluefin Tuna, its biological traits and its history of exploitation and most recently its recovery. This documentary covers how research, managers and the fishing industry - commercial and recreational have contributed to the recovering status of...
ORGANISATION:
Australian Fisheries Management Authority (AFMA)
TAGS
Wild Catch
Sustainability
Stock Assessment
Recreational Fishing
Rac Cmwth
SPECIES
Chub Mackerel
Atlantic Mackerel
Shark Mackerel
Slender Tuna
Grey Mackerel
Environment
Industry
PROJECT NUMBER • 2019-060
PROJECT STATUS:
COMPLETED

The Detection of Ciguatera Toxins in NSW Spanish Mackerel

Ciguatera Poisoning (CP) is an illness through the consumption of fish containing naturally occurring toxins, and is considered a high risk for Australian seafood safety. Ciguatoxins (CTXs) are produced by benthic microalgae (Gambierdiscus spp). In Australia, CP cases are related to fish caught in...
ORGANISATION:
University of Technology Sydney (UTS)
TAGS
Toxin
Stock Assessment
Recreational Fishing
Rac Nsw
Health And Safety
SPECIES
Spanish Mackerel
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