Unique epigenetic states in plant stem cell niches for safeguarding genome integrity. Plant stem cells are the foundation cells of all plant growth and development, including generation of the reproductive cells. Therefore, it is critical that stem cells defend against attacks that may damage the genome. A unique epigenetic state in plant stem cell niches has been discovered that may protect the genome from damage due to parasitic DNA elements. Using sophisticated genomics, genetics, and cellula ....Unique epigenetic states in plant stem cell niches for safeguarding genome integrity. Plant stem cells are the foundation cells of all plant growth and development, including generation of the reproductive cells. Therefore, it is critical that stem cells defend against attacks that may damage the genome. A unique epigenetic state in plant stem cell niches has been discovered that may protect the genome from damage due to parasitic DNA elements. Using sophisticated genomics, genetics, and cellular technologies, this project will investigate how stem cell epigenetic state is linked to genome defence, how environmental stresses can disrupt the defence system, and the role of the system in driving new genetic diversity. This knowledge is of high importance as agricultural crops enter an era of increasingly challenging conditions.Read moreRead less
Discovery Early Career Researcher Award - Grant ID: DE140101962
Funder
Australian Research Council
Funding Amount
$395,220.00
Summary
Functional epigenomics interrogation of DNA methylation dynamics during vertebrate development and evolution. DNA methylation (mC) is an epigenetic signal essential for the maintenance of correct gene expression patterns. To investigate the causal relationships between mC and transcription during vertebrate embryonic development and evolution, this project will perform high-resolution mC profiling at different stages of teleost, amphibian and mammalian development. Highly conserved and syntenic, ....Functional epigenomics interrogation of DNA methylation dynamics during vertebrate development and evolution. DNA methylation (mC) is an epigenetic signal essential for the maintenance of correct gene expression patterns. To investigate the causal relationships between mC and transcription during vertebrate embryonic development and evolution, this project will perform high-resolution mC profiling at different stages of teleost, amphibian and mammalian development. Highly conserved and syntenic, methylated sequences will then be used as baits in proteomics screens to identify novel 5mC 'readers'. The generation of genomic profiles of mC 'readers' and their integration with developmental mC maps will reveal transient epigenome dynamics during vertebrate embryogenesis and provide new insights into the conservation of these crucial developmental mechanisms.Read moreRead less
The roles and regulators of new plant cells linked to root transport. Plant genomics has moved to the single cell resolution, allowing precise investigations of previously hidden cell types and cell states that respond to environmental stress and that vary among differentially adapted plant populations. Here, we will extend our pioneering efforts that have mapped and discovered novel root cell types, to determine their salt and nutrient stress responses, and to elegantly dissect the underling ca ....The roles and regulators of new plant cells linked to root transport. Plant genomics has moved to the single cell resolution, allowing precise investigations of previously hidden cell types and cell states that respond to environmental stress and that vary among differentially adapted plant populations. Here, we will extend our pioneering efforts that have mapped and discovered novel root cell types, to determine their salt and nutrient stress responses, and to elegantly dissect the underling causal genetic variation. The unique cell markers and regulatory networks will be validated with tissue specific and transgenic tools that can work across a host of plant species to reveal adaptive cellular responses to harsh environmental conditions.Read moreRead less
The behaviour-genetics of NAPLAN data: Increasing power for complex analyses. This longitudinal behaviour-genetic study of the National Assessment Program – Literacy and Numeracy (NAPLAN) results at Grades 3, 5, 7 and 9 will continue to document the influence of genes and environmental factors on individual differences in school achievement. It aims to strengthen the longitudinal aspects of the data, allowing the project to identify sources of stability and change across the seven school years o ....The behaviour-genetics of NAPLAN data: Increasing power for complex analyses. This longitudinal behaviour-genetic study of the National Assessment Program – Literacy and Numeracy (NAPLAN) results at Grades 3, 5, 7 and 9 will continue to document the influence of genes and environmental factors on individual differences in school achievement. It aims to strengthen the longitudinal aspects of the data, allowing the project to identify sources of stability and change across the seven school years of the NAPLAN. It also aims to increase numbers in the low and high tails of the score distributions, creating a clearer picture of deficits like dyslexia and dyscalculia, and allow for firmer identification of gene-by-environment interactions. The project aims to further illuminate any differential effectiveness of schools and teachers on student outcomes, a topic of high public interest.Read moreRead less
A genomic approach to the mechanism of meiotic recombination in Neurospora. Recombination shuffles DNA sequences between homologous chromosomes during the reduction division in the life cycle of higher organisms. Along with mutation, it is a key process in evolution. Understanding of the molecular processes involved in recombination is largely based on yeast, which is intolerant of significant levels of sequence mismatch, limiting the resolution of analyses of normal recombination events. We hav ....A genomic approach to the mechanism of meiotic recombination in Neurospora. Recombination shuffles DNA sequences between homologous chromosomes during the reduction division in the life cycle of higher organisms. Along with mutation, it is a key process in evolution. Understanding of the molecular processes involved in recombination is largely based on yeast, which is intolerant of significant levels of sequence mismatch, limiting the resolution of analyses of normal recombination events. We have shown that Neurospora, like other less tractable multicellular eukaryotes, is tolerant of sequence mismatch, allowing high resolution analysis of individual recombination events. This project will build on fundamental advances we have already made in understanding how recombination occurs.Read moreRead less
Controlling the rate of transcription and translation of Rubisco transgenes effectively in higher-plant plastids. Genetic transformation of the circular genome of the plastids provides a containable means for modifying plant growth by manipulating photosynthesis. Although the transformation mechanism is precise, predicting the level of foreign gene expression is difficult because the amounts of messenger RNA and protein produced by foreign genes in plastids varies widely, even when the protein a ....Controlling the rate of transcription and translation of Rubisco transgenes effectively in higher-plant plastids. Genetic transformation of the circular genome of the plastids provides a containable means for modifying plant growth by manipulating photosynthesis. Although the transformation mechanism is precise, predicting the level of foreign gene expression is difficult because the amounts of messenger RNA and protein produced by foreign genes in plastids varies widely, even when the protein assembles without difficulty. This project will devise strategies for controlling this variability that will facilitate attempts to exploit plastid transformation for transplanting better versions of the photosynthetic CO2-fixing enzyme, Rubisco, into plants to improve their growth efficiency in terms of water, fertiliser and light use.Read moreRead less
Defining New Building Blocks for the Construction of Artificial Genetic Circuits. By characterising the components of a natural genetic switch, we will make available a set of well defined genetic building blocks for construction of rationally designed biological circuits. The ability to build such circuits would have significant economic benefit in areas such as metabolic engineering, to improve the efficiency of production of natural compounds from micro-organisms, and in biomedicine, for the ....Defining New Building Blocks for the Construction of Artificial Genetic Circuits. By characterising the components of a natural genetic switch, we will make available a set of well defined genetic building blocks for construction of rationally designed biological circuits. The ability to build such circuits would have significant economic benefit in areas such as metabolic engineering, to improve the efficiency of production of natural compounds from micro-organisms, and in biomedicine, for the controlled release of therapeutic compounds. The involvement of Honours and Ph.D students in this project will expose the next generation of Australian scientists to this emerging discipline. International collaboration leading to publications in high impact scientific journals will enhance Australia's scientific reputation.Read moreRead less
Linkage Infrastructure, Equipment And Facilities - Grant ID: LE160100002
Funder
Australian Research Council
Funding Amount
$1,040,000.00
Summary
Distributed Memory Cluster for the Intersect consortium of universities. Distributed memory cluster:
This project aims to establish a new supercomputing facility. The NSW research community has used high performance computing (HPC) to achieve major breakthroughs across a diverse range of disciplines including astrophysics, bioinformatics, environmental science, information technology and engineering. As the use of HPC increases, the application-specific needs of the research community become mo ....Distributed Memory Cluster for the Intersect consortium of universities. Distributed memory cluster:
This project aims to establish a new supercomputing facility. The NSW research community has used high performance computing (HPC) to achieve major breakthroughs across a diverse range of disciplines including astrophysics, bioinformatics, environmental science, information technology and engineering. As the use of HPC increases, the application-specific needs of the research community become more diverse, requiring greater flexibility as well as higher performance. The present facility is no longer internationally competitive, and is hampering progress in cutting edge research. The new cluster is designed to provide a greater than 10-fold increase in computing capability.Read moreRead less
Evolution and functional impact of gene silencing by hairpin derived RNAs. This project aims to study RNA-mediated gene silencing in genome evolution. RNA interference (RNAi) has been widely used as an experimental tool since its Nobel Prize-winning discovery in 1998, but little is known about endogenous RNAi or its evolution. This project uses bioinformatics, high-throughput sequencing and molecular approaches to study hpRNAs, a class of small interfering RNAs, their adaptive evolution across f ....Evolution and functional impact of gene silencing by hairpin derived RNAs. This project aims to study RNA-mediated gene silencing in genome evolution. RNA interference (RNAi) has been widely used as an experimental tool since its Nobel Prize-winning discovery in 1998, but little is known about endogenous RNAi or its evolution. This project uses bioinformatics, high-throughput sequencing and molecular approaches to study hpRNAs, a class of small interfering RNAs, their adaptive evolution across fly species and vertebrates, and their functional effect on testis morphogenesis and distortion of female/male sex-ratio. The project also studies splicing-dependent small RNAs and miRNA-target interaction. This research could have applications from animal development to human pathology.Read moreRead less
Evolutionary analyses of short-read sequences from pooled samples. This project aims to provide biologists with a means of making sound, statistical inferences about evolution by using next-generation data from mixed samples. When biologists make statements about history, they use evolutionary trees, frequently reconstructed from the genetic data of many individuals. Next-generation sequencing provides large amounts of genetic data at low cost, but biologists have difficulty using these data for ....Evolutionary analyses of short-read sequences from pooled samples. This project aims to provide biologists with a means of making sound, statistical inferences about evolution by using next-generation data from mixed samples. When biologists make statements about history, they use evolutionary trees, frequently reconstructed from the genetic data of many individuals. Next-generation sequencing provides large amounts of genetic data at low cost, but biologists have difficulty using these data for evolutionary research, particularly when they sample mixtures of DNA from many individuals. The anticipated value of this project is that it allows evolutionary biologists to capitalise on the benefits of next-generation sequencing, without sacrificing their ability to make reliable inferences about history.Read moreRead less