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
Understanding and predicting small molecule binding to G protein-coupled receptors (GPCRs). The discovery of new treatments for serious diseases is a time consuming and expensive process. Our work involves developing and testing new computational modelling approaches with experimental validation for the understanding and prediction of how current and new drugs interact with their targets, and these methods can be extended for improved understanding of how other proteins work. Our approaches have ....Understanding and predicting small molecule binding to G protein-coupled receptors (GPCRs). The discovery of new treatments for serious diseases is a time consuming and expensive process. Our work involves developing and testing new computational modelling approaches with experimental validation for the understanding and prediction of how current and new drugs interact with their targets, and these methods can be extended for improved understanding of how other proteins work. Our approaches have the potential to increase the speed, reduce the cost and lead to the discovery of new treatments for serious crippling diseases such as anxiety, depression, diabetes, and obesity. 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
Theoretical Studies on the KcsA Potassium Channel and the L-type Calcium Channel. All electrical activities in the brain are regulated by opening and closing of ion channels. Thus, understanding their mechanisms is a fundamental problem in biology. The project is aimed at developing a theoretical model of two important types of ion channels. Using a supercomputer, we will first deduce the shape of the microstructure formed by a protein wall. Then, using a computer simulation technique, we will c ....Theoretical Studies on the KcsA Potassium Channel and the L-type Calcium Channel. All electrical activities in the brain are regulated by opening and closing of ion channels. Thus, understanding their mechanisms is a fundamental problem in biology. The project is aimed at developing a theoretical model of two important types of ion channels. Using a supercomputer, we will first deduce the shape of the microstructure formed by a protein wall. Then, using a computer simulation technique, we will construct a set of physical models of biological ion channels, which will correctly replicate experimental observations. Such a theory will link the structure and function of an ion channel through the fundamental principles of physics.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