Black Death Genomics And The Evolution Of Pathogen Virulence
Funder
National Health and Medical Research Council
Funding Amount
$525,412.00
Summary
The Black Death was one of the most lethal plagues of antiquity and changed the course of human history. We will reconstruct and analyse the evolution of its causative agent – the bacterium Yersinia pestis – sampled from human skeletal remains dating back to the Black Death and beyond. We will determine the mutations that changed the virulence of plague epidemics through time, enabling a unique insight into the most dramatic example of pathogen emergence that has ever been available for study.
Epigenetic regulation in bacteria. This project aims to understand the effect of DNA modification on gene regulation in the bacterial organism Escherichia coli, which causes urinary tract infection worldwide. High-throughput DNA sequencing technologies mean one can determine the entire genetic blueprint of a bacterium – its genome – accurately, quickly and cheaply. Single-molecule real-time sequencing provides a complete read-out of a bacterial genome (genetic data) and chemical modifications of ....Epigenetic regulation in bacteria. This project aims to understand the effect of DNA modification on gene regulation in the bacterial organism Escherichia coli, which causes urinary tract infection worldwide. High-throughput DNA sequencing technologies mean one can determine the entire genetic blueprint of a bacterium – its genome – accurately, quickly and cheaply. Single-molecule real-time sequencing provides a complete read-out of a bacterial genome (genetic data) and chemical modifications of the DNA (epigenetic data). Epigenetic data can affect regulation: how genes are switched off and on. This project seeks to harness the power of single-molecule DNA sequencing, together with state-of-the-art genomic and molecular approaches, to better understand the impact of DNA modification on gene regulation in the model bacterial organism, Escherichia coli. This work will support advanced training in bioinformatics and microbiology and improve our understanding of regulation in all bacteria.Read moreRead less
Smarter fermentations through starter culture genomics. Australia makes over $1 billion dollars worth of cheese each year, however fermentation can be adversely affected by virus (phage) attack or sub-optimal strain mixtures. The latest genomics and molecular biology approaches will be used to characterise and optimise starter culture strains leading to improved flavour, quality and efficiency in cheese making.
To eat or not to eat? How symbiotic bacteria manipulate the phagocytic behaviour of their eukaryotic host. Bacteria often live in close association with eukaryotic cells, ranging from simple amoeba to humans. This project will identify key factors that control their interactions and will yield important information on the evolution of beneficial or harmful relationships.
Coral-associated viruses: pathogens, mutualists and agents of evolution? Corals host numerous organisms, of which viruses are the least studied. The aim of this project is to characterise the viruses associated with corals and to obtain a detailed understanding of the critical roles that viruses play in coral health, coral bleaching and adaptation of corals to climate change.
Understanding protein-nucleic-acid interaction networks in cold-adapted archaea. The aim of this project is to learn how microorganisms can function effectively in naturally cold environments. Results will determine how important cellular processes occur when microorganisms grow in the cold, and hence why they are able to maintain a natural balance in ecosystems such as Antarctica.
Archaeal dark matter and the origin of eukaryotes. This project aims to investigate the highly controversial origin of eukaryotes and thus all multicellular life within Archaea, a domain of single-celled microorganisms. Resolving eukaryotic origins has long been hampered by an inability to cultivate archaea from the environment. This project aims to develop a novel high-throughput single-cell genomics approach to recover archaeal genomes, thus bypassing the cultivation step. The genomes will con ....Archaeal dark matter and the origin of eukaryotes. This project aims to investigate the highly controversial origin of eukaryotes and thus all multicellular life within Archaea, a domain of single-celled microorganisms. Resolving eukaryotic origins has long been hampered by an inability to cultivate archaea from the environment. This project aims to develop a novel high-throughput single-cell genomics approach to recover archaeal genomes, thus bypassing the cultivation step. The genomes will contribute to a comprehensive taxonomic framework which will facilitate the evaluation of evolutionary relationships between the eukaryotic and archaeal domains. This may uncover previously unknown archaea with novel metabolic capabilities.Read moreRead less
MOLECULAR APPROACHES TO OVERCOME SCABIES AND ASSOCIATED DISEASE. Scabies causes childhood pyoderma predisposing to severe disease in later life. It is a major increasing health burden in Indigenous people of Northern Australia. Drug resistance is developing in mites and bacteria. The lack of clinical material has hampered molecular research and this work will use comparative genomics of parasitic and free living mites and microbiome analysis to understand fundamental aspects of mite biology and ....MOLECULAR APPROACHES TO OVERCOME SCABIES AND ASSOCIATED DISEASE. Scabies causes childhood pyoderma predisposing to severe disease in later life. It is a major increasing health burden in Indigenous people of Northern Australia. Drug resistance is developing in mites and bacteria. The lack of clinical material has hampered molecular research and this work will use comparative genomics of parasitic and free living mites and microbiome analysis to understand fundamental aspects of mite biology and pathogenesis. The understanding of proteins that are essential for mite survival and interfere with host defences will allow the informed design of peptide inhibitors as a new strategy to develop alternative treatment options.Read moreRead less
The dynamics of evolution: How horizontal gene transfer drives the diversification and adaptation of complex, bacterial communities. The genetic exchange between populations is a prerequisite for the long-term evolution of bacteria, however its short-term dynamics are largely unexplored. This project aims to define the temporal dynamics of gene transfer and how it shapes the genetic composition of entire bacterial communities. Using innovative DNA sequencing technologies and bioinformatics, This ....The dynamics of evolution: How horizontal gene transfer drives the diversification and adaptation of complex, bacterial communities. The genetic exchange between populations is a prerequisite for the long-term evolution of bacteria, however its short-term dynamics are largely unexplored. This project aims to define the temporal dynamics of gene transfer and how it shapes the genetic composition of entire bacterial communities. Using innovative DNA sequencing technologies and bioinformatics, This project aims to offer a significant new understanding of the short-term diversification of communities and how different evolutionary forces shape bacterial function. It will show how bacterial systems can adapt to new environmental conditions and the effect on essential ecosystem functions.Read moreRead less
Discovery Early Career Researcher Award - Grant ID: DE170100428
Funder
Australian Research Council
Funding Amount
$368,968.00
Summary
Diversity and evolution of methanogens. This project aims to discover methane-metabolising microorganisms and link their metabolic capabilities to cryptic parts of the carbon cycle. To date, only a small fraction of microbial diversity has been characterised, so there are significant gaps in our understanding of carbon cycling, while the metabolic capabilities of undiscovered and widely distributed microorganisms involved in methane metabolism remain unknown. This project will study these microo ....Diversity and evolution of methanogens. This project aims to discover methane-metabolising microorganisms and link their metabolic capabilities to cryptic parts of the carbon cycle. To date, only a small fraction of microbial diversity has been characterised, so there are significant gaps in our understanding of carbon cycling, while the metabolic capabilities of undiscovered and widely distributed microorganisms involved in methane metabolism remain unknown. This project will study these microorganisms’ metabolic pathways using DNA sequencing, bioinformatics and cultivation techniques. By understanding these microorganisms’ metabolisms, researchers expect to assess how they affect global carbon cycling and climate change.Read moreRead less