Understanding prokaryotic small proteins from context. Prokaryotic small proteins are increasingly recognised to play important biological roles but have been largely overlooked due to the lack of adequate tools to study them. This project aims to develop new methods to identify and predict the functions of small proteins from microbial communities by studying sequence patterns in their genomes. These predicted functions will be confirmed in the laboratory, leading to a catalogue of newly charac ....Understanding prokaryotic small proteins from context. Prokaryotic small proteins are increasingly recognised to play important biological roles but have been largely overlooked due to the lack of adequate tools to study them. This project aims to develop new methods to identify and predict the functions of small proteins from microbial communities by studying sequence patterns in their genomes. These predicted functions will be confirmed in the laboratory, leading to a catalogue of newly characterised small proteins from a diverse range of habitats and geographies. By creating new ways to study the role of small proteins in the global microbiome, we will provide the foundational knowledge required to leverage these proteins for use in biotechnology. Read moreRead less
Genome evolution & adaptation of the multinuclear wheat stripe rust fungus. Animals and plants package their genomes into a single nucleus within each cell. In contrast, millions of fungal species accommodate multiple nuclei containing individual haploid genomes. It is currently unknown what the evolutionary implications are for this unusual genome division into multiple nuclei. Here we explore the evolutionary consequences of genome division into multiple nuclei for the first time by applying c ....Genome evolution & adaptation of the multinuclear wheat stripe rust fungus. Animals and plants package their genomes into a single nucleus within each cell. In contrast, millions of fungal species accommodate multiple nuclei containing individual haploid genomes. It is currently unknown what the evolutionary implications are for this unusual genome division into multiple nuclei. Here we explore the evolutionary consequences of genome division into multiple nuclei for the first time by applying cutting edge genome biology tools and algorithms. The economically significant study system is the devastating wheat stripe rust fungus. This pathogen costs Australian farmers over $100 million a year. New understanding is expected to lead to better disease management, reduced fungicide applications, and increased yields.Read moreRead less
Discovery Early Career Researcher Award - Grant ID: DE230100178
Funder
Australian Research Council
Funding Amount
$453,913.00
Summary
Fast, lightweight and live nanopore sequencing analysis. This project aims to address limitations in nanopore sequencing (latest emerging technology in genomics) by applying advanced computational methods. This project expects to create new knowledge in bioinformatics and computer science through innovative approaches that leverage the live data streaming capability of nanopore devices to deliver results rapidly, or in real-time. Expected outcomes include improved, highly efficient analysis meth ....Fast, lightweight and live nanopore sequencing analysis. This project aims to address limitations in nanopore sequencing (latest emerging technology in genomics) by applying advanced computational methods. This project expects to create new knowledge in bioinformatics and computer science through innovative approaches that leverage the live data streaming capability of nanopore devices to deliver results rapidly, or in real-time. Expected outcomes include improved, highly efficient analysis methods and designs for future creation of custom computer hardware for nanopore analysis. This will facilitate widespread adoption of nanopore technology in bioscience research and applied domains (health, agriculture, ecology, biosecurity and forensics), including for portable in-the-field applications. Read moreRead less
Statistical Methods for Next Generation Genome-Wide Association Studies. This project aims to develop cutting-edge statistical methods to analyse large genomic datasets and identify genetic variants associated with inter-individual differences in various human traits. Knowledge of trait-associated DNA variants is instrumental in understanding how natural selection has shaped human traits. By integrating genomic data from diverse and underrepresented populations, this project further expects to c ....Statistical Methods for Next Generation Genome-Wide Association Studies. This project aims to develop cutting-edge statistical methods to analyse large genomic datasets and identify genetic variants associated with inter-individual differences in various human traits. Knowledge of trait-associated DNA variants is instrumental in understanding how natural selection has shaped human traits. By integrating genomic data from diverse and underrepresented populations, this project further expects to contribute to the equitable use of genomic technologies in humans, regardless of geographical origins. Expected outcomes of this research include novel analysis methods and software tools, which should broadly and significantly benefit gene discovery in other species, including those of agricultural relevance.Read moreRead less
Next generation high throughput lipidomics using adaptive modelling. This project aims to develop a unique high-throughput method to capture the lipidomic profile of human plasma suitable for large human population screening. Lipids are fundamental to every biological system, but our understanding of their regulation in humans have been largely superficial. By incorporating a new lipidomics approach, with genomic data, this project aims to expand our understanding of human biology by identifying ....Next generation high throughput lipidomics using adaptive modelling. This project aims to develop a unique high-throughput method to capture the lipidomic profile of human plasma suitable for large human population screening. Lipids are fundamental to every biological system, but our understanding of their regulation in humans have been largely superficial. By incorporating a new lipidomics approach, with genomic data, this project aims to expand our understanding of human biology by identifying regulators of lipid metabolism. The large diversity in humans necessitate sufficient sample sizes to identify true genetic regulators, but to date techniques capturing phenotypic data (lipids) have been largely limited. It is anticipated that this study will identify new regulators of lipid metabolism in humans.Read moreRead less
Accelerating pulse breeding using machine learning. Advances in genomics and high throughput phenotyping are generating vast quantities of data that can be applied for crop improvement, however the lack of computational analysis tools and approaches limits the full exploitation of this data. Pulse legumes are currently under utilised in Australian agriculture due to poor adaptation, however they offer significant benefits both for soil improvement and the production of high protein crops. This p ....Accelerating pulse breeding using machine learning. Advances in genomics and high throughput phenotyping are generating vast quantities of data that can be applied for crop improvement, however the lack of computational analysis tools and approaches limits the full exploitation of this data. Pulse legumes are currently under utilised in Australian agriculture due to poor adaptation, however they offer significant benefits both for soil improvement and the production of high protein crops. This project will develop machine learning (ML) tools for the analysis of pulse legume crop traits and their association with genomic variation to accelerate the breeding of high performance pulse legumes for Australian growers.Read moreRead less
Discovery Early Career Researcher Award - Grant ID: DE240100301
Funder
Australian Research Council
Funding Amount
$440,000.00
Summary
Reducing uncertainty in prediction of leaf respiration in a changing world. This project aims to advance our understanding of responses of carbon dioxide (CO2) release by leaf (leaf respiration) to sustained changes in CO2 and temperature. Leaf respiration in terrestrial forests releases yearly CO2 that is two to four times higher than CO2 emitted by human activities, but its response to climate change is not well understood. The project expects to generate new knowledge on mechanisms underlying ....Reducing uncertainty in prediction of leaf respiration in a changing world. This project aims to advance our understanding of responses of carbon dioxide (CO2) release by leaf (leaf respiration) to sustained changes in CO2 and temperature. Leaf respiration in terrestrial forests releases yearly CO2 that is two to four times higher than CO2 emitted by human activities, but its response to climate change is not well understood. The project expects to generate new knowledge on mechanisms underlying responses of leaf respiration to these climate change variables, separately and combined. Expected outcome is to deliver criteria that enable dynamic changes in leaf respiration to be predicted in climate models. Results should benefit improved forecast of feedback between Australian forests' carbon cycling and climate.Read moreRead less
Early Career Industry Fellowships - Grant ID: IE230100263
Funder
Australian Research Council
Funding Amount
$477,037.00
Summary
Improve genomic testing tools for fertility traits in beef cattle. Fertility is a key driver of productivity and profitability for beef industry; however, a substantial industry challenge is poor fertility and the difficulty and expense of measuring fertility in remote Australia. By integrating multiple omics datasets and fifty thousand fertility phenotypes recorded on beef cattle, the project will identify sequence variation, including structural variants, that underpin genetic variation in cat ....Improve genomic testing tools for fertility traits in beef cattle. Fertility is a key driver of productivity and profitability for beef industry; however, a substantial industry challenge is poor fertility and the difficulty and expense of measuring fertility in remote Australia. By integrating multiple omics datasets and fifty thousand fertility phenotypes recorded on beef cattle, the project will identify sequence variation, including structural variants, that underpin genetic variation in cattle fertility. Our industry partner, which genotypes hundreds of thousands of cattle a year, will produce new genotype arrays and novel low-cost sequencing approaches including these variants, enabling selection that could potentially increase herd reproductive rate by 4%, returning $40M per annum to the farmers.Read moreRead less
Horizontal convection at ocean-relevant proportions. This project aims to determine the role of buoyancy differences from solar radiation and vertical confinement. Flows created by lateral variation in heat or buoyancy are poorly understood when the horizontal length greatly exceeds the height, precisely the conditions relevant to industry and understanding the role of horizontal convection in Earth's oceans and in turn the delicate current system that maintains Earth's temperate climate. This p ....Horizontal convection at ocean-relevant proportions. This project aims to determine the role of buoyancy differences from solar radiation and vertical confinement. Flows created by lateral variation in heat or buoyancy are poorly understood when the horizontal length greatly exceeds the height, precisely the conditions relevant to industry and understanding the role of horizontal convection in Earth's oceans and in turn the delicate current system that maintains Earth's temperate climate. This project proposes computational and experimental efforts to probe the ultimate regime of heat transport in very shallow horizontal convection, benefiting humankind through improvements to future ocean and climate modelling efforts.Read moreRead less
Gravity Current Driven Smoke Dispersion In a Stratified Ambient. Smoke from bushfires transported by gravity currents, and known to occur nationwide, caused the shutdown of businesses, education and events in Canberra in 2019. Recent scientific investigations have shown that the speed of propagation and concentration of smoke in these three-dimensional gravity currents have a long term ‘memory’ of their initial configuration. In this project, high-fidelity computational and experimental techniq ....Gravity Current Driven Smoke Dispersion In a Stratified Ambient. Smoke from bushfires transported by gravity currents, and known to occur nationwide, caused the shutdown of businesses, education and events in Canberra in 2019. Recent scientific investigations have shown that the speed of propagation and concentration of smoke in these three-dimensional gravity currents have a long term ‘memory’ of their initial configuration. In this project, high-fidelity computational and experimental techniques will be used to elucidate the fundamental mechanisms of gravity current entrainment and propagation. This knowledge will set a strong foundation to improve operational forecasts of smoke transport that will allow government agencies to better respond to the negative impact of these complicated flows.Read moreRead less