Defining how signalling pathways cooperate to regulate organ size. Control of organ size is essential for organ function and organism viability, and varies greatly across the animal kingdom. This project aims to understand how three important signalling pathways co-ordinately regulate organ size during development and also limit aberrant growth. By applying genomics, genetics and bioinformatics techniques, this project aims to discover a core set of growth genes that are regulated by different s ....Defining how signalling pathways cooperate to regulate organ size. Control of organ size is essential for organ function and organism viability, and varies greatly across the animal kingdom. This project aims to understand how three important signalling pathways co-ordinately regulate organ size during development and also limit aberrant growth. By applying genomics, genetics and bioinformatics techniques, this project aims to discover a core set of growth genes that are regulated by different signalling pathways and the mechanism by which transcription of these genes is repressed in order to eliminate faulty cells. Intended benefits are creation of jobs, new knowledge on fundamental principles of life and the stimulation of new research into organ size control.Read moreRead less
Can we exploit mRNA modifications to control protein expression? Genes are encoded by DNA but are transcribed into a message called RNA before they can be translated into protein. RNA can be chemically modified at a gene-specific level, and this modification has been central to the success of RNA vaccines against COVID-19. Despite the importance of these modifications in cellular life and in biotechnology, the role of the most abundant RNA modifications is unclear. This project will investigate ....Can we exploit mRNA modifications to control protein expression? Genes are encoded by DNA but are transcribed into a message called RNA before they can be translated into protein. RNA can be chemically modified at a gene-specific level, and this modification has been central to the success of RNA vaccines against COVID-19. Despite the importance of these modifications in cellular life and in biotechnology, the role of the most abundant RNA modifications is unclear. This project will investigate how we can exploit RNA modifications to modulate protein expression in a tractable single-celled organism with a small genome, Plasmodium. This information is important because understanding gene regulation is fundamental to all life, and the role of RNA modifications is emerging as integral to biotechnology.Read moreRead less
Asgard archaea: the first eukaryotic cells? . This project aims to uncover the role of unique microorganisms (Asgard archaea) in the origin of eukaryotes. These archaea may represent a ‘missing-link’ in eukaryotic evolution and are in abundance in the stromatolites in Shark Bay, Western Australia. Employing an innovative and interdisciplinary approach of cutting-edge molecular biology and high-resolution microscopy, this project expects to generate insights into fundamental aspects of evolution ....Asgard archaea: the first eukaryotic cells? . This project aims to uncover the role of unique microorganisms (Asgard archaea) in the origin of eukaryotes. These archaea may represent a ‘missing-link’ in eukaryotic evolution and are in abundance in the stromatolites in Shark Bay, Western Australia. Employing an innovative and interdisciplinary approach of cutting-edge molecular biology and high-resolution microscopy, this project expects to generate insights into fundamental aspects of evolution and cell biology. Expected outcomes include the discovery of unique branches of life and the proposal of new models for the emergence of eukaryotes. This research should allow for benefits across a spectrum of environmental and social gains, including improved ties with Indigenous communities.Read moreRead less
Sequencing and assembling microbial community metagenomes in real-time. This project aims to assemble metagenomes directly from environmental samples using nanopore sequencing. Short-read approaches to metagenomics cannot assemble mixed genomes from an environmental sample, so focus on describing which species and genes are present. Long-read nanopore sequencing enables the assembly of full genomes of multiple species in a sample. Assembling complete genomes in important resources such as water ....Sequencing and assembling microbial community metagenomes in real-time. This project aims to assemble metagenomes directly from environmental samples using nanopore sequencing. Short-read approaches to metagenomics cannot assemble mixed genomes from an environmental sample, so focus on describing which species and genes are present. Long-read nanopore sequencing enables the assembly of full genomes of multiple species in a sample. Assembling complete genomes in important resources such as water and soil should lead to deeper understanding of the dynamics, variation and transfer of genetic material within these resources’ microbial communities, strategies to manage microbial diversity, and improved productivity and long-term sustainability for these resources.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
The genetic architecture of colour polymorphism and speciation. Speciation, the process by which populations diverge and become distinct, is the engine that drives biodiversity and Darwin's 'mystery of mysteries'. Speciation is accelerated in species with multiple, discrete, coexisting colour forms; yet the genetic mechanisms underpinning this pattern are not known. This project aims to identify the genes underlying different colour forms and how they are distributed across the genome. The proj ....The genetic architecture of colour polymorphism and speciation. Speciation, the process by which populations diverge and become distinct, is the engine that drives biodiversity and Darwin's 'mystery of mysteries'. Speciation is accelerated in species with multiple, discrete, coexisting colour forms; yet the genetic mechanisms underpinning this pattern are not known. This project aims to identify the genes underlying different colour forms and how they are distributed across the genome. The project plans to test the prediction that these same areas of the genome show marked divergence between lineages that are in the process of becoming distinct species. Doing so may contribute significantly to our understanding of speciation, underlying genetic mechanisms, and genes generating colour variation in vertebrates.Read moreRead less
Diatom lipids to reveal sea-ice history in remote Antarctic regions. This project aims to understand seasonal Antarctic sea-ice extent using molecular, geochemical, elemental and genomic characteristics of specific marine phytoplankton (diatoms). Little is known of the seasonal sea-ice variation and the position of the summer sea-ice extent a million years before satellite records, but this information is critical to determining air-sea gas exchange and ecosystem food web regulation. This projec ....Diatom lipids to reveal sea-ice history in remote Antarctic regions. This project aims to understand seasonal Antarctic sea-ice extent using molecular, geochemical, elemental and genomic characteristics of specific marine phytoplankton (diatoms). Little is known of the seasonal sea-ice variation and the position of the summer sea-ice extent a million years before satellite records, but this information is critical to determining air-sea gas exchange and ecosystem food web regulation. This project will unite geochemical and biological approaches to provide the data to improve past Antarctic ecosystem and climate models where sea-ice data is missing. Studying diatom biomarkers in deep sea cores from Australia’s Southern Ocean will redefine knowledge of Antarctic climate and provide data necessary to improve global ecosystem and climate models.Read moreRead less
Evolution and specificity of alternative splicing in plants. This project aims to elucidate fundamental principles of alternative splicing, a basic mechanism that plays a vital role in several biological processes across all organisms. Plants are highly effective in adapting to varied environmental, seasonal and climatic conditions and this project aims to uncover how alternative splicing contributes to regulation of gene expression in response to developmental and environmental cues. Uncovering ....Evolution and specificity of alternative splicing in plants. This project aims to elucidate fundamental principles of alternative splicing, a basic mechanism that plays a vital role in several biological processes across all organisms. Plants are highly effective in adapting to varied environmental, seasonal and climatic conditions and this project aims to uncover how alternative splicing contributes to regulation of gene expression in response to developmental and environmental cues. Uncovering the underlying mechanisms of alternative splicing will not only advance fundamental knowledge, but also has the potential to provide tools and technologies through which sensitivities of plants to environmental stress can be potentially manipulated to benefit agriculture.Read moreRead less
Genome dynamics following plastid endosymbiosis. Plastid endosymbiosis events (enslavement of an algal cell inside of a host cell to form a plastid) are difficult to pinpoint because the genomic data required for a broad array of species are rarely available. Furthermore, the classical method used to infer endosymbiotic gene transfers is being criticised. This project will elucidate the origin of chlorarachniophyte and dinoflagellate plastids and characterise the genome dynamics following endosy ....Genome dynamics following plastid endosymbiosis. Plastid endosymbiosis events (enslavement of an algal cell inside of a host cell to form a plastid) are difficult to pinpoint because the genomic data required for a broad array of species are rarely available. Furthermore, the classical method used to infer endosymbiotic gene transfers is being criticised. This project will elucidate the origin of chlorarachniophyte and dinoflagellate plastids and characterise the genome dynamics following endosymbiosis. It uses densely sampled genome data obtained with high-throughput sequencing technologies. Simulation studies will be used to evaluate methods for inferring endosymbiotic gene transfer and alignment-free methods will be used to improve phylogenomic pipelines.Read moreRead less
Unlocking the secrets of metabolic variation in a highly diverse bacterium. This project aims to explore metabolic diversity of Klebsiella pneumoniae, a bacterium relevant to the agricultural, veterinary, medical and biotechnology industries. It is expected to reveal significant insights into the biology of this diverse organism via an innovative combination of DNA sequence analyses and metabolic modelling. Expected outcomes include 4500 novel metabolic models and a novel population metabolic fr ....Unlocking the secrets of metabolic variation in a highly diverse bacterium. This project aims to explore metabolic diversity of Klebsiella pneumoniae, a bacterium relevant to the agricultural, veterinary, medical and biotechnology industries. It is expected to reveal significant insights into the biology of this diverse organism via an innovative combination of DNA sequence analyses and metabolic modelling. Expected outcomes include 4500 novel metabolic models and a novel population metabolic framework. This should provide major benefits for understanding bacterial ecology and evolution, and for future studies seeking to optimise industrial processes or prevent disease. It will also directly contribute to building Australia’s capacity in computational biology- a key driver of biotechnology innovation.Read moreRead less