Creating new stochastic models to understand the evolution of gene families. This project aims to extend stochastic modelling techniques in order to develop mathematically rigorous and biologically relevant models for the evolution of gene families. The project expects to model evolutionary processes such as gene retention, duplication and loss, and the generation of new gene functions. The duplication and subsequent re-purposing of genes is thought to be a key mechanism for generating evolution ....Creating new stochastic models to understand the evolution of gene families. This project aims to extend stochastic modelling techniques in order to develop mathematically rigorous and biologically relevant models for the evolution of gene families. The project expects to model evolutionary processes such as gene retention, duplication and loss, and the generation of new gene functions. The duplication and subsequent re-purposing of genes is thought to be a key mechanism for generating evolutionary novelty. By applying these models to genome data, the project expects to be able to quantify the importance of these different evolutionary mechanisms. The project will strengthen collaborative links between researchers in stochastic modelling and molecular evolutionary biology.Read moreRead less
Mastering pyrimidine editing in RNA. Many plants and animals can alter their genetic information via RNA (ribonucleic acid) editing, a process that is often essential for the growth and development of the organism. This ability provides accurate control over gene expression and has great potential as a biotechnological tool in agriculture and medicine. RNA editing could be used to switch genes on or off in biotechnological production systems with an unprecedented degree of precision, or to corre ....Mastering pyrimidine editing in RNA. Many plants and animals can alter their genetic information via RNA (ribonucleic acid) editing, a process that is often essential for the growth and development of the organism. This ability provides accurate control over gene expression and has great potential as a biotechnological tool in agriculture and medicine. RNA editing could be used to switch genes on or off in biotechnological production systems with an unprecedented degree of precision, or to correct genetic diseases. This project aims to understand two RNA editing pathways in plants, one of which is found nowhere else and likely to involve a novel enzymatic mechanism. We will use the understanding gained to develop novel RNA processing tools usable in any living organism.Read moreRead less
Comparing properties of innate immune proteins of bats and humans. Supra-molecular protein complexes known as signalosomes drive our innate immune response by forming large signaling hubs capable of recruiting downstream effectors. This project aims to compare the properties and structure of human and bat signalosomes and discover the molecular origins of the “supra-immunity” of bats. In this context, the project expects to generate new knowledge concerning the fundamental molecular mechanisms t ....Comparing properties of innate immune proteins of bats and humans. Supra-molecular protein complexes known as signalosomes drive our innate immune response by forming large signaling hubs capable of recruiting downstream effectors. This project aims to compare the properties and structure of human and bat signalosomes and discover the molecular origins of the “supra-immunity” of bats. In this context, the project expects to generate new knowledge concerning the fundamental molecular mechanisms that regulate the signalosomes. The intended outcome is to answer the long-standing question of control of speed and amplitude of innate immune response at the molecular level. Both locally and internationally, this new approach should provide benefits across structural biology, molecular evolution and biotechnology.Read moreRead less
Discovery Early Career Researcher Award - Grant ID: DE240100992
Funder
Australian Research Council
Funding Amount
$448,237.00
Summary
New methods to capture protein dynamics of the TSC-mTOR signalling axis. Protein flexibility, the way proteins move, has a major role in how they function. However, we still do not have the tools to analyse this flexibility. Our cells have evolved many complex and flexible systems to sense and respond to their environment. For example, the TSC-mTOR system is found across life, from baker’s yeast to humans, however it remains poorly understood. This proposal will study TSC as an exemplar to devel ....New methods to capture protein dynamics of the TSC-mTOR signalling axis. Protein flexibility, the way proteins move, has a major role in how they function. However, we still do not have the tools to analyse this flexibility. Our cells have evolved many complex and flexible systems to sense and respond to their environment. For example, the TSC-mTOR system is found across life, from baker’s yeast to humans, however it remains poorly understood. This proposal will study TSC as an exemplar to develop novel machine-learning approaches to capture protein flexibility and shape. This proposal will advance fundamental understanding of the TSC-mTOR pathway and build transformative methodologies to study flexible proteins more broadly.Read moreRead less
In depth characterisation of the gamma delta T cell immune synapse. This project aims to comprehensively characterise the activation principles of gamma delta T cells. These cells have an understudied but central role in vertebrate immunity and development. A missing piece of the puzzle is how gamma delta T cells sense stress and how this signal leads to activation. Expected outcomes include the generation of fundamental knowledge in immunology and structural biology. This proposal uses high-ski ....In depth characterisation of the gamma delta T cell immune synapse. This project aims to comprehensively characterise the activation principles of gamma delta T cells. These cells have an understudied but central role in vertebrate immunity and development. A missing piece of the puzzle is how gamma delta T cells sense stress and how this signal leads to activation. Expected outcomes include the generation of fundamental knowledge in immunology and structural biology. This proposal uses high-skilled techniques, including cryo-electron microscopy and single-molecule imaging and holds ancillary benefits to postgraduate students. Anticipated outcomes include influential publications, building a critical mass of expertise in Australia and fostering international collaborations with Australia at the epicentre.Read moreRead less
Assessment Of The Sensitivity Of Australia’s Aquatic Animal Disease Surveillance System Using Scenario Tree Modelling
Funder
Fisheries Research and Development Corporation
Funding Amount
$224,000.00
Summary
The sensitivity of an overall passive surveillance system is difficult to determine due to variability in factors such as disease characteristics, passive surveillance stakeholders and the likelihood that disease events will be reported and investigated. The WOAH Aquatic Animal Health Code also stipulates the primary evidence for historical freedom is passive surveillant information generated by a country’s early detection system that needs to be sufficiently sensitive.
Scenario tree m ....The sensitivity of an overall passive surveillance system is difficult to determine due to variability in factors such as disease characteristics, passive surveillance stakeholders and the likelihood that disease events will be reported and investigated. The WOAH Aquatic Animal Health Code also stipulates the primary evidence for historical freedom is passive surveillant information generated by a country’s early detection system that needs to be sufficiently sensitive.
Scenario tree modelling (STM) can be used to overcome those challenges. STM uses quantitative statistical methods to estimate the sensitivity of various components of the surveillance system (e.g. presentation of disease signs, disease recognition and reporting). These estimates can then be used to identify critical points in the system to which interventions can be targeted to improve the system. STM can be applied to any aquatic disease/industry of interest and there are some successful examples for terrestrial diseases/industries, both in Australia and overseas.
Two aquatic animal disease agents of trade and biosecurity significance, WSSV and megalocytiviruses, will be evaluated as case studies. These diseases are subject to import biosecurity measures and have significant production impacts, as they severely affect farmed and wild aquatic animal species that are valued by many stakeholders (e.g. aquaculture, capture fisheries, recreational fisheries and conservation groups). A sound STM assessment of each case study will support our early detection system through a quantitative evaluation of the speed of the detection, and improve our emergency disease response strategy by determining areas in our passive surveillance that, once strengthened, will provide a greater return on future investment.
As mentioned above, increasing the sensitivity of Australia’s passive surveillance is a national priority. This project is identified in AQUAPLAN 2022-2017 as Activity 3.3. The outcomes of this project are also used for other AQUAPLAN activities, National surveillance strategy (Activity 3.1) and Sector-specific surveillance plans (Activity 3.2). The data produced from this project will provide recommendations for various interventions to improve the overall performance of the passive surveillance system for the participating industries.
More broadly, the Fisheries Research and Development Corporation R&D Plan 2020-2025 identified building capability and capacity for biosecurity as a priority. In alignment with the R&D plan, successful outcomes of this project will improve understanding of disease transmission pathways which will enhance biosecurity practices. It will improve allocation of biosecurity resources (by identifying the most effective and cost-efficient way of investing resources in surveillance to get the best return), minimise biosecurity threats (by enhancing passive surveillance to accelerate an early detection) and improve market access for associated industry producers (by providing quantitative information on their passive surveillance sensitivity as a market access negotiation tool).
Objectives: 1. Quantitatively evaluate the sensitivity of Australia’s passive surveillance system for white spot disease 2. Quantitatively evaluate the sensitivity of Australia’s passive surveillance system for megalocytiviruses Read moreRead less
Discovery Early Career Researcher Award - Grant ID: DE200101061
Funder
Australian Research Council
Funding Amount
$424,848.00
Summary
Single particle imaging: x-ray imaging of individual dynamic biomolecules. X-ray lasers produce powerful ultra-short pulses of light that can take temporal snap shots of small radiation-sensitive biological complexes. Thanks to superconducting technology, the next generation of x-ray lasers will be able to produce x-ray pulses at greater rates than ever before. But because of the sheer number of possible molecular configurations, these molecular movies will have only a small amount of data per f ....Single particle imaging: x-ray imaging of individual dynamic biomolecules. X-ray lasers produce powerful ultra-short pulses of light that can take temporal snap shots of small radiation-sensitive biological complexes. Thanks to superconducting technology, the next generation of x-ray lasers will be able to produce x-ray pulses at greater rates than ever before. But because of the sheer number of possible molecular configurations, these molecular movies will have only a small amount of data per frame, posing an enormous challenge for current imaging methods. I aim to meet this challenge by developing an innovative multi-conformational image reconstruction algorithm. This will provide a new window into the molecular dynamics of biological systems, the building blocks of life, and enable rational drug design.Read moreRead less
Developing A Cost-efficient Stock Assessment Program For Southern Calamari Fisheries
Funder
Fisheries Research and Development Corporation
Funding Amount
$496,827.00
Summary
Southern Calamari are important to multiple commercial and community fishery sectors in SA. Southern Calamari are now managed using a TACC for the commercial MSF and have specified resource allocations for recreational, Aboriginal/Traditional, Charter Boat, GSV prawn and SG prawn fisheries. However, the current assessment program does not capture the importance of this species and cannot support the level of management required. The primary outcome of this project will be to develop an assessmen ....Southern Calamari are important to multiple commercial and community fishery sectors in SA. Southern Calamari are now managed using a TACC for the commercial MSF and have specified resource allocations for recreational, Aboriginal/Traditional, Charter Boat, GSV prawn and SG prawn fisheries. However, the current assessment program does not capture the importance of this species and cannot support the level of management required. The primary outcome of this project will be to develop an assessment program for Southern Calamari in SA that can be used to assign stock status and provide TACC setting advice to fisheries management.
Like many cephalopod assessments, the current SA Southern Calamari assessment is basic as scientific advances have not occurred at the same rate as advances for finfish or crustacean assessment methods. Therefore, the successful development of an assessment program for Southern Calamari in SA would provide a valuable scientific contribution to several other Australian squid fisheries as they often encounter similar assessment difficulties
Overcoming key knowledge gaps and incorporating information on environmental drivers will be a key focus of this project, in order to develop an assessment that accounts for the full complexity of cephalopod population dynamics. However, there are limited resources to undertake an assessment in SA as the commercial MSF has a low gross value product (GVP) but has high assessment needs across several species. Therefore, a cost-effective assessment program must be developed to allow for its regular application, which is necessary for short lived species such as Southern Calamari.
The proposed project will address two FRDC strategic plan outcomes (Growth for enduring prosperity, and best practices and production systems) by developing a best practice assessment program that can be applied for Southern Calamari in SA and be extended for use in other fishery jurisdictions. An assessment program that provides confident management advice, such as TACC setting, will maximise resource use across all sectors by establishing a robust stock assessment that increases certainty in stock abundance and allows sustainable fishing strategies to be developed.
Objectives: 1. Review global cephalopod assessments to identify potential assessment methods for Southern Calamari and how environmental variables could be incorporated. 2. Evaluate the suitability of available fishery-dependent and fishery-independent data from the SG and GSV prawn fisheries to develop recruitment indices. 3. Develop Southern Calamari growth models for SG and GSV and evaluate the influence of environment on seasonal growth rates. 4. Outline the most suitable and cost-effective assessment program option for Southern Calamari in SG and GSV Read moreRead less
Understanding The Economics And Markets Of The Western Rock Lobster Industry
Funder
Fisheries Research and Development Corporation
Funding Amount
$749,000.00
Summary
The Program is required to enable the economics research required over the next 3-4 years by retaining the WRL Economist and engaging a WRL Data Analyst to :
1. undertake research and demonstrate the effects of COVID-19 and international trade disruptions on the industry’s financial wellbeing and economic contribution, as a narrative incorporating the pre-, current and post-disruption era;
2. investigate and implement enhancements to the WRL MEY model based on verified stakehol ....The Program is required to enable the economics research required over the next 3-4 years by retaining the WRL Economist and engaging a WRL Data Analyst to :
1. undertake research and demonstrate the effects of COVID-19 and international trade disruptions on the industry’s financial wellbeing and economic contribution, as a narrative incorporating the pre-, current and post-disruption era;
2. investigate and implement enhancements to the WRL MEY model based on verified stakeholder feedback; • MEY modelling is based on (among other factors) expected longer-term beach prices for lobster achieved by fishers. Beach prices are themselves underpinned by prices achieved in domestic and export markets for live, frozen and other processed forms of western rock lobster, and supply chain costs — all of which have changed markedly over the past couple of years and have influenced the longer-term outlook considerably. o Domestic markets have absorbed higher volumes of Australian product over the past two years than in the previous ten, encouraging a pivot by processors to include more cooked, frozen and other processed product in the product portfolio. o Frozen and chilled product has also been demonstrated to have general acceptance in overseas markets, albeit at lower prices than achieved by similar live product. o Air and sea freight costs and reliability have been adversely compromised in the face of the continuing COVID-19 pandemic, with the medium-term outlook for freight costs expected to be a multiple of pre-COVID rates – affecting the relative attractiveness of domestic versus export markets. o Processors and marketers have explored alternative export markets and paths to market in the wake of political uncertainty and trade disruptions. There is a need to understand the implications of this market shift on the net beach prices achievable by fishers, which will be achieved through a better understanding of the changes in market access and supply chain costs (transport, live holding, handling, additional processing, freight forwarding by air and by sea). o Taken together, this suite of change constitutes a significant, and potentially longer-term, challenge to the western rock lobster industry that has high potential to bring about changes in industry structure.
3. research and implement mechanisms by which individual fishers / business owners can benchmark their businesses against relevant industry economic standards.
• Benchmarking aims to improve the internal performance of fishers' private business operations by providing each business with an opportunity to compare itself to the industry's performance • Benchmarking is not limited to economic metrics, including physical metrics such as fuel use that enable a more granular understanding of the carbon footprint of the fishing fleet. • The aim is to generate an understanding of the range of cost structures in the fishing fleet, to better inform the cost elements of MEY modelling for economic sustainability of the fishery.
4. investigate and implement enhancements to the WRL Global Trade Report.
• The pandemic and its ongoing turmoil, combined with trade disruptions to Australia’s live exports, has brought about a change in global lobster trade flows into the highest volume, highest value market – at Australia’s expense. o The resultant situation includes a loss of market share and value to alternative suppliers of live spiny lobster, other lobster species, and other high value crustaceans. o Consumer preferences have shown signs of changing in response to COVID and associated health policies, regulations and restrictions. During the course of the pandemic, consumption of rock lobster pivoted to at-home consumption, with some preference-shifting to frozen product, particularly in countries with aggressive health policies that enacted operating restrictions on restaurants and larger gatherings.
5. research and implement mechanisms by which WRL's Global Trade Report, MEY Model and Markets Dashboard would work together with DPIRD's Harvest Strategy to underpin TACC setting into the future, adding considerable benefit to government as the resource manager by supplying timely, independent, industry-oriented information to the consideration set
Objectives: 1. Enable the Global Trade Report the MEY Model and the Markets Dashboard to work together with the Harvest Strategy to underpin TACC setting and ensure the continued sustainability of the stock. 2. Demonstrate the effects of the SARSCoV2 pandemic and trade disruptions on the industry’s resilience, economic contribution and adaptation to changing market forces. 3. Develop benchmarks for use by fishers’ businesses against industry economic standards to enhance industry reslience and adaptation to trade disruptions. 4. Ensure usability of economics data by driving further integration of data sets, models and tools, and building into the digitization program. Read moreRead less
Molecular basis for susceptibility and immunity to Fusarium wilt disease. Fusarium wilt is a devastating disease of many important crop plants, including banana, cotton and tomato. There are significant gaps in our understanding of this disease that need to be addressed to enable better disease management. This project aims to identify and analyse tomato proteins targeted by Fusarium effector proteins (virulence factors), determine how corresponding tomato receptors (resistance proteins) recogni ....Molecular basis for susceptibility and immunity to Fusarium wilt disease. Fusarium wilt is a devastating disease of many important crop plants, including banana, cotton and tomato. There are significant gaps in our understanding of this disease that need to be addressed to enable better disease management. This project aims to identify and analyse tomato proteins targeted by Fusarium effector proteins (virulence factors), determine how corresponding tomato receptors (resistance proteins) recognise these effectors, and identify the signalling pathways and critical defence responses activated by these receptors. The intention is to close the gaps in our understanding and use the knowledge gained to develop new strategies for disease control by interfering with fungal pathogenicity and enhancing plant resistance.Read moreRead less