Automated bioinformatic analysis of vertical and lateral gene transmission among microbial genomes. Genetic information is transmitted "vertically" from parents to offspring within species. Biologists have long assumed that this mechanism, extrapolated far into the past, explains the distribution of genes among genomes, thus the potential properties of all phenomes. But genome sequences show that some, perhaps many, genes have been transmitted "laterally" between species. We are building a uniqu ....Automated bioinformatic analysis of vertical and lateral gene transmission among microbial genomes. Genetic information is transmitted "vertically" from parents to offspring within species. Biologists have long assumed that this mechanism, extrapolated far into the past, explains the distribution of genes among genomes, thus the potential properties of all phenomes. But genome sequences show that some, perhaps many, genes have been transmitted "laterally" between species. We are building a unique automated computer-based system to find all instances of lateral transmission in all microbial genomes, using rigorous methods. Our results will be important both fundamentally and practically, e.g. in explaining sets and dynamics of phenomic traits, and quantifying background levels of "natural genetic engineering".Read moreRead less
Linkage Infrastructure, Equipment And Facilities - Grant ID: LE0989334
Funder
Australian Research Council
Funding Amount
$400,000.00
Summary
An integrated high-performance computational platform powering systems biology investigation. Systems biology is the study of the organism as a whole and provides a deeper understanding of biological processes than is possible by studying components separately. Recognised as essential for biological research, we propose to establish an advanced computational platform to study these processes at a systems level. Its hardware and specialised software will allow Australian researchers to examine co ....An integrated high-performance computational platform powering systems biology investigation. Systems biology is the study of the organism as a whole and provides a deeper understanding of biological processes than is possible by studying components separately. Recognised as essential for biological research, we propose to establish an advanced computational platform to study these processes at a systems level. Its hardware and specialised software will allow Australian researchers to examine complex pathways involved in animal and human health and disease, as well as in biotechnology and environmental processes. It will provide unique capabilities not currently available in Australia, and help Australian researchers remain internationally competitive in breakthrough science and frontier technologies.Read moreRead less
The genomic programming of complex organisms. The project will have far-reaching consequences in medicine, agriculture, biotechnology, engineering, information science and associated industries. It will provide a platform for the rationalization of genetic epidemiology and genetic improvement programs, the development of a wide range of new diagnostics and therapies, the development of new core technologies and practical approaches in genetics and genetic diversity, a framework for advanced gen ....The genomic programming of complex organisms. The project will have far-reaching consequences in medicine, agriculture, biotechnology, engineering, information science and associated industries. It will provide a platform for the rationalization of genetic epidemiology and genetic improvement programs, the development of a wide range of new diagnostics and therapies, the development of new core technologies and practical approaches in genetics and genetic diversity, a framework for advanced genetic engineering, the development of new principles and systems for information storage and transmission, and the design of artificial systems capable of self-referential assembly in other environments.Read moreRead less
Special Research Initiatives - Grant ID: SR0354610
Funder
Australian Research Council
Funding Amount
$10,000.00
Summary
Australian Bioinformatics Grid Network. OzBioGrid will be an open source, collaborative, bioinformatics environment supporting Australian biotechnology and life science researchers on the Grid. Researchers will be able to use distributed resources including databases, computational power and analytical tools, and to collaborate remotely, using customized work environments. With hubs in Brisbane, Canberra and Melbourne, and nodes elsewhere, OzBioGrid will build on Australia's high performance co ....Australian Bioinformatics Grid Network. OzBioGrid will be an open source, collaborative, bioinformatics environment supporting Australian biotechnology and life science researchers on the Grid. Researchers will be able to use distributed resources including databases, computational power and analytical tools, and to collaborate remotely, using customized work environments. With hubs in Brisbane, Canberra and Melbourne, and nodes elsewhere, OzBioGrid will build on Australia's high performance computing capacity. It will greatly enhance Australia's research capability by networking ARC and other centres of excellence, major national research facilities, independent researchers, biotechnology companies, bioinformatics research centres, public databases. It will be linked to bio-grid initiatives overseas. Read moreRead less
Quantifying the Tree of Life's Diversity with the Paleobiology Database. The Paleobiology Database is the Internet's key source of scientific data on the fossil record. It records names and classification of fossil organisms and the ages, locations, and environments of the places that yield these fossils. It has often been used to estimate the number of species existing at different points in geological time. Macquarie will house the Database as it is expanded to record evolutionary relations ....Quantifying the Tree of Life's Diversity with the Paleobiology Database. The Paleobiology Database is the Internet's key source of scientific data on the fossil record. It records names and classification of fossil organisms and the ages, locations, and environments of the places that yield these fossils. It has often been used to estimate the number of species existing at different points in geological time. Macquarie will house the Database as it is expanded to record evolutionary relationships of many species. This information will help to estimate dates of origination for major groups such as mammals and birds. It will also help to show whether mass extinctions tend to target old groups with few surviving species, which will help to predict which groups will survive the current mass extinction.Read moreRead less
Structure and function of novel transporters in alphaproteobacteria. First, detailed knowledge of a set of membrane transporters and the way their activity might be inhibited, will have implications for the treatment of human disease. Second, excellent outcomes are provided for the training of postgraduate students and research staff. This project entails cutting edge technology, and the transfer of technical capabilities not currently available in Australia. Third, our studies on non-pathogenic ....Structure and function of novel transporters in alphaproteobacteria. First, detailed knowledge of a set of membrane transporters and the way their activity might be inhibited, will have implications for the treatment of human disease. Second, excellent outcomes are provided for the training of postgraduate students and research staff. This project entails cutting edge technology, and the transfer of technical capabilities not currently available in Australia. Third, our studies on non-pathogenic species of alpha-proteobacteria provides for a timely advance in our knowledge of their biology: other species of alpha-proteobacteria were amongst the first organisms trialled for biological weapons by the USA and the former Soviet Union, and those pathogenic species are rated as Class 3 organisms.Read moreRead less
Parametric Brain Imaging via Modeling and Analysis of Electroencephalographic Signals. Parameters of brain function and physiology will be spatially imaged with high time resolution via their effects on electroencephalographic (EEG) signals, a form of imaging that is impossible with existing methods. This will be achieved by improving existing physiologically-based models of the generation of EEGs and developing analysis tools based on fitting of model predictions to multielectrode EEG data. T ....Parametric Brain Imaging via Modeling and Analysis of Electroencephalographic Signals. Parameters of brain function and physiology will be spatially imaged with high time resolution via their effects on electroencephalographic (EEG) signals, a form of imaging that is impossible with existing methods. This will be achieved by improving existing physiologically-based models of the generation of EEGs and developing analysis tools based on fitting of model predictions to multielectrode EEG data. The results will be used to probe spatiotemporal features of EEGs in normal subjects to explore the underlying fundamental mechanisms and to infer novel parameter variations of practical relevance.Read moreRead less
Molecular machines that drive microbial pathogens. We will provide a comprehensive understanding of molecular machines situated at the surface of bacteria. This ground-breaking research will provide excellent outcomes in the training of research students and staff: this project entails frontier technology, and the transfer of technological capabilities not currently available in Australia. Our study on a non-pathogenic species of bacteria is timely too for National security: related species of b ....Molecular machines that drive microbial pathogens. We will provide a comprehensive understanding of molecular machines situated at the surface of bacteria. This ground-breaking research will provide excellent outcomes in the training of research students and staff: this project entails frontier technology, and the transfer of technological capabilities not currently available in Australia. Our study on a non-pathogenic species of bacteria is timely too for National security: related species of bacteria were amongst the first organisms trialed as biological weapons, and the pathogenic species remain rated as Class 3 organisms by the Centers for Disease Control.Read moreRead less
Mitochondrial biogenesis: the evolution of molecular machines. Benefits from this research program fall into two discrete types. Firstly, excellent outcomes are provided for the training of postgraduate students and research staff. This project entails cutting edge technology, and the development of skills not common in Australia. Secondly, detailed knowledge will be gained of molecular machines and the way in which they may differ in human cells and in the cells of human cell parasites, with im ....Mitochondrial biogenesis: the evolution of molecular machines. Benefits from this research program fall into two discrete types. Firstly, excellent outcomes are provided for the training of postgraduate students and research staff. This project entails cutting edge technology, and the development of skills not common in Australia. Secondly, detailed knowledge will be gained of molecular machines and the way in which they may differ in human cells and in the cells of human cell parasites, with implications for the treatment of human disease.Read moreRead less
Reducible complexity in the molecular machines of humans and bacteria. Firstly, we will provide detailed knowledge of the surface membrane proteins of an important class of bacteria, the alpha-proteobacteria. Secondly, excellent outcomes are provided for the training of postgraduate students and research staff: this project entails frontier technology, and the transfer of technological capabilities not currently available in Australia. Thirdly, our studies on non-pathogenic species of alpha-prot ....Reducible complexity in the molecular machines of humans and bacteria. Firstly, we will provide detailed knowledge of the surface membrane proteins of an important class of bacteria, the alpha-proteobacteria. Secondly, excellent outcomes are provided for the training of postgraduate students and research staff: this project entails frontier technology, and the transfer of technological capabilities not currently available in Australia. Thirdly, our studies on non-pathogenic species of alpha-proteobacteria is timely for National security: species of alpha-proteobacteria were amongst the first organisms trialled as biological weapons by the USA and the former Soviet Union, and these pathogenic species remain rated as Class 3 organisms by the Centers for Disease Control. Read moreRead less