Few organisms are as well understood at the genetic level as Saccharomyces cerevisiae. Given that there are more yeast geneticists than yeast genes and exemplary resources for the community (largely a result of their size), this comes as no surprise.
Yes, Ecology can improve Genomics
Posted on October 5th, 2007 by sharpton · 1 Comment
Few organisms are as well understood at the genetic level as Saccharomyces cerevisiae. Given that there are more yeast geneticists than yeast genes and exemplary resources for the community (largely a result of their size), this comes as no surprise.
Categories: bioinformatics · comparative · functional · gene function · gene knockout · genome · genome annotation · genome sequencing · molecular evolution · saccharomyces · yeast
Gene knockouts in Candida parapsilosis
Posted on September 18th, 2007 by Jason Stajich · 1 Comment
A recent paper "Targeted gene deletion in Candida parapsilosis demonstrates the role of secreted lipase in virulence", from the Nosanchuk lab at Yeshiva University, shows the role of secreted lipases in virulence of this pathogen.
Categories: candida · functional · gene function · gene knockout · human pathogen · pathogens
Exploring a global regulator of gene expression in Aspergillus
Posted on June 25th, 2007 by Jason Stajich · No Comments
When first discovered, the gene LaeA was thought to be a master switch for silencing of several NRPS secondary metabolite gene clusters in Aspergillus. NRPS and PKS are important genes in filamentous fungi as they produce many compounds that likely help fungi compete in the ecological niche mycotoxins (e.g. aflatoxin, gliotoxin)...
Categories: NRPS · aspergillus · gene cluster · gene function · gene regulation · microarray · secondary metabolite
Mechanism of riboswitch controlling mRNA splicing
Posted on June 11th, 2007 by Jason Stajich · No Comments
A exciting research paper "Control of alternative RNA splicing and gene expression by eukaryotic riboswitches" published in Nature details the mechanism of how riboswitches work in Neurospora crassa. While riboswitches have been found and studied in bacteria there has not been extensive work showing how they work in fungi. In bacteria the riboswitch acts as the direct interacting sensor that switches gene
Categories: gene function · neurospora · riboswitch
Yeast genome: Known knowns, and known unknowns
Posted on May 20th, 2007 by Jason Stajich · 1 Comment
From Genetics this week a review discusses Why are there still 1000 Uncharacterized Yeast genes? Poor Yeast - so many more genes have no known function, while S. pombe has nearly 100% coverage in functional annotation. I'll also point out that the 1000 genes refers to protein-coding genes, not ncRNA genes which may mean that there is alot more that is unknown.
Categories: gene function · genome annotation · saccharomyces · yeast
That was a lot of work
Posted on April 3rd, 2007 by sharpton · No Comments
I've never worked with Magnaporthe grisea, the fungus responsible for rice blast, one of the most devastating crop diseases, but I do know that its life cycle is complicated and that knocking out roughly 61% of the genes in the genome and evaluating the mutant phenotype to infer gene function is not trivial. In their recent letter to Nature, Jeon et al did what many
Categories: functional · fungi · gene function · genome · genome annotation · magnaporthe · plant pathogen