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
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
Discovery Early Career Researcher Award - Grant ID: DE200101323
Funder
Australian Research Council
Funding Amount
$427,098.00
Summary
Structure guided mapping of protein interactions and their perturbation. Protein interactions are central to most biological processes, and significant effort has been devoted to trying to unravel these complicated networks. This project aims to develop new approaches to better understand these interactions, and the consequences of their perturbation. The main expected contributions will be: (i) methods to identify likely protein interaction sites using population conservation; (ii) computationa ....Structure guided mapping of protein interactions and their perturbation. Protein interactions are central to most biological processes, and significant effort has been devoted to trying to unravel these complicated networks. This project aims to develop new approaches to better understand these interactions, and the consequences of their perturbation. The main expected contributions will be: (i) methods to identify likely protein interaction sites using population conservation; (ii) computational approaches to assess the effects of any type of mutation on the interaction; and (iii) an understanding of how disruption of a specific interaction can affect the complicated biological network within a cell. Read moreRead less
Understanding somatic mutation in plants: new methods, new software, new data. Somatic mutations accumulate as plants grow, affecting everything from short-term ecological interactions to long-term evolutionary dynamics. These mutations have important consequences for plant industry and conservation, but because they are so hard to measure almost nothing is known about them. This project aims to develop new methods and software to detect, analyse, and compare the genome-wide history of somatic m ....Understanding somatic mutation in plants: new methods, new software, new data. Somatic mutations accumulate as plants grow, affecting everything from short-term ecological interactions to long-term evolutionary dynamics. These mutations have important consequences for plant industry and conservation, but because they are so hard to measure almost nothing is known about them. This project aims to develop new methods and software to detect, analyse, and compare the genome-wide history of somatic mutation in individual plants, providing an unprecedented level of detail into an important but understudied source of biological variation. By applying these methods to an iconic experimental population, This project aims to provide the first insights into the genome-wide causes and consequences of somatic mutation in plants.Read moreRead less
Discovery Early Career Researcher Award - Grant ID: DE150101117
Funder
Australian Research Council
Funding Amount
$327,000.00
Summary
The functional impact of new genes acquired through retrotransposition. Novel copies of genes often arise through retrotransposition of processed messenger RNAs. Many thousands of gene copies have arisen over evolutionary time and some of these have retained functionality while diverging from the parental gene leading to new paralogs under different regulatory regimes. Through analysis of whole-genome sequence data, we are now able to identify very recent gene copies that are not present in the ....The functional impact of new genes acquired through retrotransposition. Novel copies of genes often arise through retrotransposition of processed messenger RNAs. Many thousands of gene copies have arisen over evolutionary time and some of these have retained functionality while diverging from the parental gene leading to new paralogs under different regulatory regimes. Through analysis of whole-genome sequence data, we are now able to identify very recent gene copies that are not present in the reference genomes for various species, giving us the opportunity to explore the effects of new copies on the regulation of the original gene and the surrounding genomic environment into which the new copy is inserted. This project aims to address these important open questions through computational and biochemical approaches.Read moreRead less
Discovery Early Career Researcher Award - Grant ID: DE190100008
Funder
Australian Research Council
Funding Amount
$387,103.00
Summary
Exploring the evolution and ecology of non-photosynthetic Cyanobacteria. This project aims to contribute and expand our rudimentary understanding of non-photosynthetic Cyanobacteria by obtaining representative genome sequences using metagenomics. The dogma that all Cyanobacteria are photosynthetic has recently been challenged by the discovery of non-photosynthetic lineages. This project expects to obtain representative genome sequences using metagenomics to predict surface structures. The expect ....Exploring the evolution and ecology of non-photosynthetic Cyanobacteria. This project aims to contribute and expand our rudimentary understanding of non-photosynthetic Cyanobacteria by obtaining representative genome sequences using metagenomics. The dogma that all Cyanobacteria are photosynthetic has recently been challenged by the discovery of non-photosynthetic lineages. This project expects to obtain representative genome sequences using metagenomics to predict surface structures. The expected outcomes from this project includes providing insights into the function and evolution of non-photosynthetic Cyanobacteria and their viruses, and pure or enriched cultures to enable future studies.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
Discovery of Novel Bacteriophage with the Capacity to Modulate Gut Bacteria. This project aims to experimentally validate the largest ever collection of bacterial viruses (bacteriophages) within the gut microbiome. This project expects to generate new knowledge in the area of bacteriophage biology and genomics by using the innovative approaches of wet-lab and bioinformatic genome analyses. Expect outcomes of this project include the discovery of novel phages using bioinformatics, wet-lab validat ....Discovery of Novel Bacteriophage with the Capacity to Modulate Gut Bacteria. This project aims to experimentally validate the largest ever collection of bacterial viruses (bacteriophages) within the gut microbiome. This project expects to generate new knowledge in the area of bacteriophage biology and genomics by using the innovative approaches of wet-lab and bioinformatic genome analyses. Expect outcomes of this project include the discovery of novel phages using bioinformatics, wet-lab validation of their activity and characterisation of their potential to contribute new bacterial host metabolism. This should provide benefits, such as advancement to our understanding of bacteriophages, improved bioinformatic software, and a characterised collection of commercially valuable bacterial strains and phages.Read moreRead less
Transcription factor – enhancer – promoter based regulatory networks. This project aims to develop new understanding on how multicellular organisms (including humans) develop, and how mutations in distant regions of the genome can affect human traits. The way the human genome is interpreted by the cellular machinery is still a mystery. We have a reference sequence and know where the majority of coding genes are, but we are far from understanding how the genome is regulated to generate the divers ....Transcription factor – enhancer – promoter based regulatory networks. This project aims to develop new understanding on how multicellular organisms (including humans) develop, and how mutations in distant regions of the genome can affect human traits. The way the human genome is interpreted by the cellular machinery is still a mystery. We have a reference sequence and know where the majority of coding genes are, but we are far from understanding how the genome is regulated to generate the diversity of cell types in our bodies. Enhancer regions interact with proximal promoters to regulate gene expression level and tissue-specificity. This project aims to develop transcriptional regulatory network models using high throughput chromatin interaction data and expression perturbation to link promoter and enhancers genome-wide.Read moreRead less