Candida White-Opaque switching

Blogging on Peer-Reviewed ResearchA paper in PLoS Biology from Sandy Johnson’s lab entitled “Interlocking Transcriptional Feedback Loops Control White-Opaque Switching in Candida albicans discusses phenotype switching in the human pathogenic fungus Candida albicans. Why is the important?

“White-opaque switching is an epigenetic phenomenon, where genetically identical cells can exist in two distinctive cell types, white and opaque. Each cell type is stably inherited for many generations, and switching between the two types of cells occurs stochastically and rarely—roughly one switch in 10^4 cell divisions”

white-opaque coloniesThere is also a review by Kira O’Day to discuss the implications of the findings. Understanding this sort of developmental and epigenetic signaling is important to better know how fungi adjust and interact with their environment. However, the authors do conclude that White-Opaque switching is exclusive to Candida albicans so aspects of this research only directly applicable to studies in this system. Phenotype switching is an active area of research for Candida biologists – some nice micrographs and SEM of the different cell morphologies can be seen at Prof. Joachim Morschhäuser’s page (and linked to the right).

Continue reading Candida White-Opaque switching

Mucor circinelloides genome update

I recently heard through the grapevine that the Mucor ircinelloides genome 4X assembly was completed by JGI and a BLAST server is available if you contact the authors. Mucorales (previously Zygomycota which is not monophyletic) includes previously sequenced Rhizopus oryzae and Phycomyces blakesleeanus which we’ve blogged about before.

Continue reading Mucor circinelloides genome update

Yeast resequencing update

Ed Louis at Nottingham sent out an email today outlining plans for publishing analyses of the Saccharomyces Genome Resequencing Project.  They are in process of analyzing the data and ask that people respect their use of the data, but also invite collaborations and companion papers.

“If anyone has done or plans on doing a global analysis with a tight clean result which you think should be included in the overview paper, please contact us [Richard Durbin and Ed Louis; emails available through above links]. The analysis would have to be complete by 14 December and you would have to be willing to have the details transparently displayed on the web pages associated with the project.”

Contact your represenative: Vote in the Senate on NIH Funding

This was sent along from the GSA. It is important to contact your represenative about the Vote in the Senate on NIH Funding.

The Senate is expected to vote on the Fiscal Year 2008 Labor, Health and Human Services and Education (L-HHS) appropriations bill the week of October 15.

For the NIH, the Senate bill provides $29.9 billion, $250 million more than the House-passed L-HHS bill and $1.2 billion more than the President’s FY08 request. President Bush has threatened to veto the L-HHS bill because the House and Senate bills are $12 billion and $10 billion, respectively, more than the President proposed in his FY08 budget.

Strong, bipartisan support of the Senate bill is our best hope in the Congress to achieve a meaningful increase for the NIH. Otherwise the NIH will be forced to make further cuts in research as it has for the past few years.

Exploring CUG codon evolution in Candida

A recent PLoS One article “A Genetic Code Alteration Is a Phenotype Diversity Generator in the Human Pathogen Candida albicans” finds some pretty dramatic changes in gene expression and phenotypes by replacing the tRNAs for CUG back to Leucine (Leu; in the standard genetic code) from their meaning of Serine (Ser) in these Candida species. The CUG codon transition in some Candida spp has been of interest since it is an example of a recent change in the genetic code and provides a comparative system to study the mechanism and genome changes of how a genetic code shift is manifested.

Continue reading Exploring CUG codon evolution in Candida

Bay Area Seminar(s): Jonathan Eisen

For those within reach of Bay Area, Jonanthan Eisen (who recently posted about 3-day Biology and Mathematics in the Bay Area meeting) will be presenting at Bay Area BioSystematists meeting on Oct 16. I had the pleasure of presenting in the series last month in a 3-way forum with Nancy Moran and Dan Pollard.

Below is the BABS announcement: Continue reading Bay Area Seminar(s): Jonathan Eisen

Yes, Ecology can improve Genomics

Blogging on Peer-Reviewed ResearchFew 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. What is curious is the large number of yeast genes for which we’ve been unable to characterize. Of the ~6000 genes currently identified in the yeast genome, 1253 have no verified function (for the uninclined, this is roughly 21% of the yeast proteome). Egads! If we can’t figure this out in yeast, what hope do we have in non-model organisms?Lourdes Peña-Castillo and Timothy R. Hughes discuss this curious observation and its cause in their report in Genetics.

Continue reading Yes, Ecology can improve Genomics

Next gen sequencing technology

Nature has an overview of what goes in and out of next generation sequencers with an interview with a smiling Chad Nusbaum from the Broad Institute. Most of these have been out and about for a while, but it seems that the hayride/bandwagon is starting to pick up more steam as GT‘s Genome Scan has several posts about sequencing referencing J. Craig V, George Church, and the Nature news article (not free).

Note that Solexa is no longer the cool name – “Genome analyzer” being the name for the machine that was previously called Solexa 1G. I’m holding out hope for funnier names in the future. I do feel that ABI’s choice of SOLiD is more exciting than 310/3700/3730 that is as inspiring as HAL9000.

But I mean if your technology is called pyrosequencing, I am hoping Roche will come up with a firey or at least smoldering play on words if they rename 454 again (GS FLX for now).

Little Coprinus mushroom pictures

Coprinus cinereus (renamed Coprinopsis cinerea) growing in the lab. The genome was sequenced, assembled into chromosomes, and annotated and we are working on the final analysis of it to describe some of the interesting biology about this little Coprophilic fungus. I’m excited to put up a few of my pictures of the tiny mushrooms growing in the lab (although others have better ones). A few more days and I might have better shots.

Coprinus cinereus Coprinus

Coprinus

Update: Chris Ellison in the Taylor Lab sent this post from Cornell Mushroom Blog which has a video of Coprinus comatus (shaggy mane) fungi deliquescing.