PROJECT NUMBER
•
2023-170
PROJECT STATUS:
CURRENT
ORGANISATION:
Fisheries Research and Development Corporation (FRDC)
TAGS
418 results
PROJECT NUMBER
•
2023-196
PROJECT STATUS:
CURRENT
ORGANISATION:
Honey and Fox Pty Ltd
TAGS
PROJECT NUMBER
•
2016-407
PROJECT STATUS:
CURRENT
Capability and Capacity: Nuffield Australia Scholarships
The Australian seafood industry has a long and proud history of employment of very sound environmental and economic management principles which have made it the envy of much of the world.
An altogether robust Australian seafood industry is hyper critical to the social and economic fabric of...
ORGANISATION:
Nuffield Australia
PROJECT NUMBER
•
2021-125
PROJECT STATUS:
CURRENT
ORGANISATION:
Australian Prawn Farmers Association (APFA)
TAGS
SPECIES
PROJECT NUMBER
•
2023-074
PROJECT STATUS:
CURRENT
ORGANISATION:
Australian Society For Fish Biology Inc
Diagnostic detection of aquatic pathogens using real-time next generation sequencing
Project number:
2018-147
Project Status:
Current
Budget expenditure:
$216,000.00
Principal Investigator:
David Cummins
Organisation:
CSIRO Australian Animal Health Laboratory
Project start/end date:
30 Jun 2019
-
28 Oct 2021
Contact:
FRDC
Current diagnostic programs generally rely on highly -specific assays for pathogen detection. While these techniques are invaluable, they are one dimensional and do not provide detailed information critical to a disease investigation. These gaps include the inability to detect unknown pathogens and potential variants of know pathogens and provide no additional genomic or transcriptomic data. Moreover, samples must be shipped to trained personnel in a laboratory, further delaying the time to diagnosis. The MinION, on the other hand, can theoretically detect any pathogen and can potentially be deployed to the field. Moreover, the MinION can rapidly generate full-length genomes, allowing for epidemiological tracking of viral or bacterial strains in near real-time. Such rapid data, which cannot be obtained as quickly using existing methods, are vital if the intention is to intervene in an outbreak and reduce impacts on the productivity and profitability of aquaculture facilities. For example, a rapid, early diagnosis may allow mitigating actions to be taken on-farm, such as the diversion of intake water, movement restrictions of stock and the isolation of infected ponds.
These qualities make the MinION an attractive complimentary platform to fill several gaps in the data obtained during disease outbreak investigations, or routine diagnostics, and potentially for use in the field. However, results from the misuse or lack of understanding of the technology could also have adverse regulatory implications for aquaculture industries. For example, without appropriate guidelines, an inexperienced diagnostician may misinterpret a distant DNA match in a pathogen database as a significant result, this may create unwanted attention to industry and potential stock destruction or changes to disease status that are unjustified. Thus, it is critical that the MinION is evaluated at the Australian Animal Health Laboratory, and guidelines and procedures are developed for accurate diagnostic evaluations. The activities detailed in this application will establish the feasibility of using the MinION for diagnostic applications, and ensure that the data is reliably generated and interpreted appropriately.
1. Evaluate if MinION data meets or exceeds the data obtained using established laboratory-based NGS platforms. Objectives (1) and (2) align with Methods section (1).The first objective of this project is to demonstrate if the MinION can obtain quality genome assemblies of known pathogens, such as WSSV, AHPND, OsHV-1 and HaHV that have been created using existing NGS technology. Moreover, determine if the MinION is capable of producing a diagnostic result more rapidly and with greater confidence than traditional techniques. STOP/GO POINT: If MinION data does not produce reliable genome assemblies, no improvement in genome quality, or is significantly more laborious to set-up/run or analyse than existing NGS technologies, do not proceed with objective 2.
2. Evaluate the performance of the MinION using existing diagnostic extraction techniques and produce robust methods and protocols for sample preparation, sequencing and data analysis. This objective will optimise MinION protocols for sample pre-processing, optimal sequencing conditions, and data post-processing. We will then evaluate the MinION data produced from a range of aquatic organisms against data produced using traditional techniques from the same samples. STOP/GO POINT: If after these optimisations, the MinION cannot detect pathogens as reliably as traditional techniques, do not proceed with objective 3.
3. Compare the applicability of MinION to standard molecular assays for identification of pathogens in diagnostic samples. Objective (3) is aligned with Methods section (2).In this objective, diagnostic samples will be tested using existing diagnostics tools (qPCR, cPCR) and MinION sequencing. Analysis between the methods will be detailed, including time to result, pathogen identity and genomic information. This objective will not only provide an insight into real-time sequencing for diagnostics, but in addition the feasibility of MinION technology for field application in the future.
Toolbox for the estimation of fish population abundance
Project number:
2021-007
Project Status:
Current
Budget expenditure:
$175,000.00
Principal Investigator:
Alistair Hobday
Organisation:
CSIRO Oceans and Atmosphere Hobart
Project start/end date:
31 Jul 2023
-
29 Aug 2024
Contact:
FRDC
Abundance estimates are used both directly and indirectly in stock assessment processes to support fishery management. Australia’s fisheries research agencies all estimate fish population abundance in some way. These include genetic and conventional tagging, acoustics (active and passive), trawl and egg surveys, as well as using proxies of abundance such as catch. Each of these methods have benefits, biases and caveats linked to the method and to the fish species being assessed. For example, differences between life history and habitat can make an abundance estimation method that has worked for one species unsuitable for another. As the application of each method of estimating abundance is potentially species/scenario specific, potential use by researchers and managers can be fraught.
In developing or proposing an abundance estimate for use in fisheries assessment, researchers must have a clear understanding of the assessment framework in order to make sure that an abundance estimate can be used. Claims such as “this time series can then be used in stock assessment” must be verified by funding agencies (particularly beyond FRDC) and defensible. Proliferation of abundance estimation methods without links to the assessment process will not yield an expected benefit beyond knowledge accumulation.
A project is needed to capture the range of methods of estimating abundance for management purposes, and specify the conditions of use, limitations and readiness level for operational use. A decision tree and methods ‘toolbox’ that describes the techniques, their relative strengths and weaknesses will help researchers and managers identify the best suited abundance estimate approach, and guide research effort to overcome known weaknesses.
The development of a ‘toolbox’ of techniques would be used to inform:
1. techniques available to estimate abundance
2. suitability of them to different conditions such as life history, and data availability
3. requirements of the technique such as methods used, prerequisite expertise, data and cost; and
4. circumstances under which the technique can be used.
This project would also identify potential new approaches and technologies that might complement or replace current ones.
1. To document the various methods available to fisheries managers for estimating abundance.
2. To document a cost / benefit / needs and requirements basis for the various methods available to fisheries managers for estimating abundance.
3. Develop a ‘toolbox’ to disseminate details of fit-for-purpose methods of estimating abundance to fisheries managers and management agencies, that will informi. the techniques that are available to estimate abundanceii.the suitability of the technique to different scenarios such as life history parameters of species, data availability (or absence), assumed low population sizeiii.the requirements of the technique such as methods used, pre-requisite expertise, data and costiv.under what circumstances can the technique be used and the underlying assumptions.
4. To identify potential new (and non-lethal) approaches and emerging technologies that may offer an opportunity for capturing fishery dependent data that can be used to estimate abundance
PROJECT NUMBER
•
2024-030
PROJECT STATUS:
CURRENT
ORGANISATION:
Deakin University Geelong Waurn Ponds Campus
TAGS
SPECIES
PROJECT NUMBER
•
2019-173
PROJECT STATUS:
CURRENT
Security of resource access - what is legislative best practice for the commercial seafood industry?
ORGANISATION:
Seafood Industry Australia (SIA)
PROJECT NUMBER
•
2023-102
PROJECT STATUS:
CURRENT
Capability & Capacity: 2024 Electric & Hybrid Marine Expo North America and Conference
I believe the value that bursary recipients received from attending the Electric and Hybrid Expo was valuable in a number of ways. The networking opportunity for the younger members was valuable as they all shared experiences and were a little removed from what was happening on a global stage for...
ORGANISATION:
Fisheries Research and Development Corporation (FRDC)
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