Famed ecologist Paul Ehrlich addressed an audience at UT as part of the Baker Center Interdisciplinary Group on Energy and Environmental Policy series.
Archives for August 2011
EEB grad student Premal Shah (now a postdoc in the Plotkin lab at the U. of Pennsylvania) and his adviser, Associate Prof. Mike Gilchrist, recently published a paper in the Proceedings of the National Academy of Sciences on “Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift.”
Abstract: The genetic code is redundant with most amino acids using multiple codons. In many organisms, codon usage is biased toward particular codons. Understanding the adaptive and nonadaptive forces driving the evolution of codon usage bias (CUB) has been an area of intense focus and debate in the fields of molecular and evolutionary biology. However, their relative importance in shaping genomic patterns of CUB remains unsolved. Using a nested model of protein translation and population genetics, we show that observed gene level variation of CUB in Saccharomyces cerevisiae can be explained almost entirely by selection for efficient ribosomal usage, genetic drift, and biased mutation. The correlation between observed codon counts within individual genes and our model predictions is 0.96. Although a variety of factors shape patterns of CUB at the level of individual sites within genes, our results suggest that selection for efficient ribosome usage is a central force in shaping codon usage at the genomic scale. In addition, our model allows direct estimation of codon-specific mutation rates and elongation times and can be readily applied to any organism with high-throughput expression datasets. More generally, we have developed a natural framework for integrating models of molecular processes to population genetics models to quantitatively estimate parameters underlying fundamental biological processes, such a protein translation.
Brandon Matheny and Neale Bougher (Department of Conservation, Western Australia) have received a grant from the Australian Biological Resources Study, in conjunction with matching funds from the Western Australia Naturalists’ Club, Inc., to add a systematic volume to the Fungi of Australia series. The subject of the volume will be the Inocybaceae of Australia, a family of ectomycorrhizal fungi particularly diverse in temperate regions of Australia.