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
Radical change in the architecture of a nucleus: loss of typical DNA organisation systems in dinoflagellates. The genetic blueprint of all higher cells is stored in the cell nucleus, and proteins called histones provide the filing system for compactly stacking and organising the cell's DNA. One group of organisms, the dinoflagellate algae, have lost this histone system. This project will provide insight into their alternative DNA management systems.
Elucidating the genetic basis of newly evolved metabolic functions in yeast. Elucidating the genetic basis of newly evolved metabolic functions in yeast. This project intends to research how complex metabolic pathways originate and evolve. This project will use cutting edge genome sequencing and molecular techniques to elucidate the heritable genetic basis of Baker’s yeast, which has been the selectively evolved to use xylose as a sole carbon source: something vital for second generation biofuel ....Elucidating the genetic basis of newly evolved metabolic functions in yeast. Elucidating the genetic basis of newly evolved metabolic functions in yeast. This project intends to research how complex metabolic pathways originate and evolve. This project will use cutting edge genome sequencing and molecular techniques to elucidate the heritable genetic basis of Baker’s yeast, which has been the selectively evolved to use xylose as a sole carbon source: something vital for second generation biofuel production that wild yeast cannot do. This project will combine detailed molecular characterisation of highly adapted yeast strains with a novel "molecular palaeontology" approach to trace the evolutionary process and identify functionally significant loci under selection. Detailed characterisation of this trait will accelerate the development of future yeast strains and test fundamental evolutionary theories.Read moreRead less
Discovery Early Career Researcher Award - Grant ID: DE190100085
Funder
Australian Research Council
Funding Amount
$414,864.00
Summary
Elucidating a novel mechanism for coping with harmful mutations. This project aims to improve our understanding of the complex regulatory mechanisms that increase genetic and phenotypic robustness. Survival of organisms depends on their ability to cope with genetic variation. A novel process of genetic compensation has recently been identified, producing a normal phenotype in a homozygous mutant, that would be expected to have deleterious effects. This project will reveal how compensation is ach ....Elucidating a novel mechanism for coping with harmful mutations. This project aims to improve our understanding of the complex regulatory mechanisms that increase genetic and phenotypic robustness. Survival of organisms depends on their ability to cope with genetic variation. A novel process of genetic compensation has recently been identified, producing a normal phenotype in a homozygous mutant, that would be expected to have deleterious effects. This project will reveal how compensation is achieved by examining the molecular pathways that are activated following genetic mutation. This project is expected to strengthen Australian reputation in evolutionary genetics, and in turn enhance our understanding of how organisms adapt to changing environments.Read moreRead less
Discovery Early Career Researcher Award - Grant ID: DE140101728
Funder
Australian Research Council
Funding Amount
$395,220.00
Summary
The regulation and evolution of posttranscriptional gene networks. The ability of cells to regulate gene expression is key for organism development, adaptation to new environments and evolutionary changes that shape the diversity of life on Earth. This project studies the RNA binding proteins called PUFs which are central for gene expression in diverse organisms. Using cutting-edge new generation systems biology approaches, this project will study how PUF proteins regulate genes to enable metabo ....The regulation and evolution of posttranscriptional gene networks. The ability of cells to regulate gene expression is key for organism development, adaptation to new environments and evolutionary changes that shape the diversity of life on Earth. This project studies the RNA binding proteins called PUFs which are central for gene expression in diverse organisms. Using cutting-edge new generation systems biology approaches, this project will study how PUF proteins regulate genes to enable metabolic adaptation, differentiation of cell types and the evolution of new gene expression outputs in distinct biological species. The outcomes will include new insights into the regulation and evolution of posttranscriptional gene networks. Read moreRead less
The role of RNA editing by the brain-specific enzym ADAR3 in learning and memory. Higher-order cognition sets us apart from other species but how this is achieved is still under debate. The project will test the idea, strongly supported by recent genomic analyses, that subtle changes in the sequences of RNA in response to environmental stimuli underpin this extraordinary ability.
Discovery Early Career Researcher Award - Grant ID: DE120102763
Funder
Australian Research Council
Funding Amount
$375,000.00
Summary
The contribution of histone post-translational modifications to eukaryotic evolution. By comparing the complete DNA sequence of closely related species, it is possible to identify changes in DNA that account for the diversity between these species. The project will use this approach to ask whether DNA changes that influence how DNA itself is packaged into cells have contributed to the evolution of new yeast species.
Exploiting Sexual Differences In Germline Biology To Resolve The Causes Of Germline Mutation
Funder
National Health and Medical Research Council
Funding Amount
$315,914.00
Summary
Mutagenesis during the production of sex cells is a fundamental biological process and the cause of inherited human disorders. These disorders span the entire spectrum of diseases that have a genetic component, such as autoimmune diseases and cancers, therefore influencing all age groups. A better understanding of the mechanisms underlying this process is a priority since it is the essential knowledge required for understanding all of the factors that contribute to this array of debilitating dis ....Mutagenesis during the production of sex cells is a fundamental biological process and the cause of inherited human disorders. These disorders span the entire spectrum of diseases that have a genetic component, such as autoimmune diseases and cancers, therefore influencing all age groups. A better understanding of the mechanisms underlying this process is a priority since it is the essential knowledge required for understanding all of the factors that contribute to this array of debilitating diseases, and for devising effective preventative and diagnostic measures. To attain this understanding necessitates establishing the mechanistic origins of germline mutagenesis. Two basic approaches are employed to understand this process. The first assesses the incidence of mutation in pedigrees. This identifies the spectrum of risk mutations underlying the specific disease surveyed. Because other biological processes also influence these observations, the results from this approach do not reflect the underlying germline mutation spectra and are therefore not translatable between diseases. As mutations are rare events, it is prohibitive to obtain sufficient observations to resolve the underlying mechanisms. The second approach employs comparative genomic data, and uses differences in germline biology to estimate sex-biased effects. This comparative approach benefits from the accumulation of mutations over vast periods of time. The approach has not, however, been applied to diagnose the mechanistic origins of mutations. In this project, we will apply the enormous volume of comparative sequencing data to relate components of the mutagenic spectrum with sexual differences in germline biology. The project will differentiate between different types of mutations, and their association with specific processes will be established. The results will be a determination of the relative contributions of different mechanisms of mutation to germline mutagenesis.Read moreRead less
The early marsupial embryo - a missing link in vertebrate development. Most of our knowledge of early development comes from one species, the mouse, but it is not known how similar it is to other mammals or even other vertebrates such as birds and reptiles. Using a marsupial model, the tammar wallaby, the project aims to identify mechanisms that are fundamental to mammals and those that are more evolutionarily plastic.