Mathematical Methods for Next Generation Sequencing. The emergence of a new generation of high throughput genomic sequencing technologies is providing unprecedented opportunities for biological research. Hidden within the huge amounts of data generated by this technology is information about the expression and regulation of genes, and the complex functional purpose of non-coding, so called 'junk', DNA. Development of mathematical and statistical tools is essential to interpreting these data. The ....Mathematical Methods for Next Generation Sequencing. The emergence of a new generation of high throughput genomic sequencing technologies is providing unprecedented opportunities for biological research. Hidden within the huge amounts of data generated by this technology is information about the expression and regulation of genes, and the complex functional purpose of non-coding, so called 'junk', DNA. Development of mathematical and statistical tools is essential to interpreting these data. The proposed research will enhance Australia's reputation for developing novel quantitative techniques at the cutting edge of modern biology. The proposed project has a broad range of potential applications in biotechnology, particularly in the medical and agricultural industries.Read moreRead less
Phyloinformatics and biodiversity: developing bioinformatic tools for understanding the dynamics of extinction and invasion within species assemblages. DNA sequence data provides an exciting new way to study biodiversity, because the genome of each organism records its evolutionary history. By analysing DNA sequences co-existing species, we can reconstruct the ecological and evolutionary history of a biological community. This allows us to track biodiversity changes over time, and examine how th ....Phyloinformatics and biodiversity: developing bioinformatic tools for understanding the dynamics of extinction and invasion within species assemblages. DNA sequence data provides an exciting new way to study biodiversity, because the genome of each organism records its evolutionary history. By analysing DNA sequences co-existing species, we can reconstruct the ecological and evolutionary history of a biological community. This allows us to track biodiversity changes over time, and examine how the state of a species assemblage determines which species are lost through extinction or gained through the invasion of exotic species. Understanding the factors that govern changes in biodiversity over time is essential for planning for future conservation in the face of a rapidly changing environment. Read moreRead less
Old brains, new data - early evolution of structural complexity in the vertebrate head. Of the all the complex structures biology has provided, the evolution of the vertebrate brain and its sensory organs is perhaps the most enigmatic. The fossil record occasionally provides a chance to trace this evolution, but only with the use of novel X-ray scanning techniques can these secrets be detailed in three dimensions. Exploiting the exceptional fossil record from Australia and China, this team will ....Old brains, new data - early evolution of structural complexity in the vertebrate head. Of the all the complex structures biology has provided, the evolution of the vertebrate brain and its sensory organs is perhaps the most enigmatic. The fossil record occasionally provides a chance to trace this evolution, but only with the use of novel X-ray scanning techniques can these secrets be detailed in three dimensions. Exploiting the exceptional fossil record from Australia and China, this team will for the first time collect a vast comparative data base which will yield clues on the early evolution of the ear, eye and brain. Read moreRead less
Can efficient algal variants of the photosynthetic CO2-fixing enzyme, Rubisco, be folded and assembled in functional forms in higher-plant plastids? We have shown that it is possible to alter the photosynthetic phenotype of a plant predictably and profoundly by engineering the plastid genome to replace the plant's CO2-fixing enzyme, Rubisco, with a bacterial homolog. Thus it may be possible to replace the plant enzyme with more efficient algal Rubiscos that would allow plants to grow with less l ....Can efficient algal variants of the photosynthetic CO2-fixing enzyme, Rubisco, be folded and assembled in functional forms in higher-plant plastids? We have shown that it is possible to alter the photosynthetic phenotype of a plant predictably and profoundly by engineering the plastid genome to replace the plant's CO2-fixing enzyme, Rubisco, with a bacterial homolog. Thus it may be possible to replace the plant enzyme with more efficient algal Rubiscos that would allow plants to grow with less light, less water or less fertiliser. Before such desirable changes to the plant phenotype can be realised, some complex issues of modification, folding and assembly of Rubisco subunits need to be resolved. This proposal addresses them.Read moreRead less
Epigenetic silencing in vertebrates: evolution and function from the bottom-up. The primary benefits are contribution to Australia's knowledge base and raising the profile of functional genomics in Australia, with the research priority of Frontier Technologies for Building and Transforming Australian Industries and priority goals in Breakthrough Science and Frontier Technologies. This project focuses on important biological questions surrounding gene regulation and sex chromosome evolution. Inte ....Epigenetic silencing in vertebrates: evolution and function from the bottom-up. The primary benefits are contribution to Australia's knowledge base and raising the profile of functional genomics in Australia, with the research priority of Frontier Technologies for Building and Transforming Australian Industries and priority goals in Breakthrough Science and Frontier Technologies. This project focuses on important biological questions surrounding gene regulation and sex chromosome evolution. International attention has already resulted in genome characterization of Australian icons (wallaby, Tasmanian devil and platypus), more research on these, and other Australian animals, will further highlight the importance of Australian fauna and impact positively on our scientific profile.Read moreRead less
Gene Patents in Australia: Options for Reform. Controversies over the upsurge in gene patenting, access to pharmaceuticals, biopiracy, and ownership of genetic resources, lead many to question whether patent law is appropriate for biotechnology. Do patents thwart access to beneficial technologies such as drugs, research tools and new crops, while hampering policy options for health care and agriculture? This project addresses the urgent need for a comprehensive study of the impact of biotech pat ....Gene Patents in Australia: Options for Reform. Controversies over the upsurge in gene patenting, access to pharmaceuticals, biopiracy, and ownership of genetic resources, lead many to question whether patent law is appropriate for biotechnology. Do patents thwart access to beneficial technologies such as drugs, research tools and new crops, while hampering policy options for health care and agriculture? This project addresses the urgent need for a comprehensive study of the impact of biotech patenting, critically reviewing overseas developments, setting biotechnology in the broader policy context of intellectual property law, and empirically analysing patterns rather than relying on the anecdotal and piecemeal studies that dominate this area.Read moreRead less
Epigenetic integration of genomic and environmental information in honey bees. Environmental factors such as nutrition, drugs or childhood neglect alter gene activity without a change to the DNA code and may result in a range of conditions such as cancer, obesity and mental illness. Such epigenetic phenomena are driven by subtle and poorly understood modifications of the genome known as DNA methylation. Our aim is to study the link between DNA methylation and environmental influences. We aspire ....Epigenetic integration of genomic and environmental information in honey bees. Environmental factors such as nutrition, drugs or childhood neglect alter gene activity without a change to the DNA code and may result in a range of conditions such as cancer, obesity and mental illness. Such epigenetic phenomena are driven by subtle and poorly understood modifications of the genome known as DNA methylation. Our aim is to study the link between DNA methylation and environmental influences. We aspire to understand how environmental signals trigger the reprogramming of transcriptional control of genetic networks that lead to contrasting phenotypic and behavioural outcomes using the honey bee modelRead moreRead less
Analysing and modelling molecular rate variation among nuclear and mitochondrial genomes. My research will have important practical benefits for bioinformaticians and evolutionary biologists, because existing analytical methods will be rigorously tested and new tools will be developed. Australia has a comparatively high concentration of researchers in this field, so my research will foster domestic collaboration and import international expertise. The research will provide important insights int ....Analysing and modelling molecular rate variation among nuclear and mitochondrial genomes. My research will have important practical benefits for bioinformaticians and evolutionary biologists, because existing analytical methods will be rigorously tested and new tools will be developed. Australia has a comparatively high concentration of researchers in this field, so my research will foster domestic collaboration and import international expertise. The research will provide important insights into the rates and patterns of genetic changes associated with domestication, and into variation in evolutionary rates among the primate ancestors of humans. In addition to developing new software, which will be made publicly available, I will develop new evolutionary models to supplement existing software packages. Read moreRead less
Origin and evolution of genes on the human X chromosome. Two groups of functionally related genes are found on the human X chromosome in disproportionately high numbers. I will test whether an uneven distribution of genes is common in mammalian genomes, or whether the human X is special. I will test hypotheses of how the gene groups arose on the human X by comparing their location and expression patterns in other mammals, and other vertebrates. It will then be clear whether the ancestral autosom ....Origin and evolution of genes on the human X chromosome. Two groups of functionally related genes are found on the human X chromosome in disproportionately high numbers. I will test whether an uneven distribution of genes is common in mammalian genomes, or whether the human X is special. I will test hypotheses of how the gene groups arose on the human X by comparing their location and expression patterns in other mammals, and other vertebrates. It will then be clear whether the ancestral autosome was ?chosen?, whether it ?selfishly? accumulated these genes, or whether the function of genes changed in response to selective pressures.Read moreRead less
Realistic models of permeation in ion channels. Ion channels are formed by proteins in cell membranes and provide pathways for fast and controlled flow of selected ions. This activity generates action potentials in nerves and muscles that forms the basis of all movement, sensation and thought processes. Recent determination of the crystal structure of channel proteins has enabled construction of models that can relate channel function to its structure--necessary for understanding their operati ....Realistic models of permeation in ion channels. Ion channels are formed by proteins in cell membranes and provide pathways for fast and controlled flow of selected ions. This activity generates action potentials in nerves and muscles that forms the basis of all movement, sensation and thought processes. Recent determination of the crystal structure of channel proteins has enabled construction of models that can relate channel function to its structure--necessary for understanding their operation and seeking cures for diseases caused by their malfunction. This project aims to develop accurate ion-protein-water interactions for permeation models based on stochastic and molecular dynamics simulations using both classical and quantum mechanical methods.Read moreRead less