Coccidioides in the news

The NY Times has an article on the high rate of Coccidioides incidence at the state prison in Pleasant Valley, California. The infection rate has been documented by Pappagianis et al in an in-depth study of Coccidioidomycosis in the California state prisons. The disease has stalled some plans for constructing a new prison the edge of the San Joaquin Valley so the state is definitely taking note.

Cocci map
Also see Figure here with prettier links.

Thanks Liz!

Remembering Marcy Speer

Suzanne Leal wrote a very touching tribute in PLoS Genetics to Marcy Speer who passed away this summer.  Marcy was one of the reasons I went to grad school at Duke and was a wonderfully generous and brilliant scientist, mother, and friend.  I had the great opportunity to know her both when I worked at the CHG during and after college (where she would later become the director) and in her leadership role in my grad Program in Genetics (and Genomics) at Duke.  Her smile and bright outlook is missed but her scientific legacy will continue to influence a great many.

More updates on Saccharomyces resequencing project at Sanger

I’ve paraphrased an email sent by David Carter to folks interested in Saccharomyces resequencing project.

The latest version of the SGRP data is on the web site and ftp site. This release is somewhat provisional, and motivated more by the fact that we have a paper deadline coming up than by any claim to finality. It should be quite a bit better than what was there before, but doesn’t have a correct treatment of transposons.

You can get the data by starting here:
http://www.sanger.ac.uk/Teams/Team71/durbin/sgrp/datadoc.shtml

There is also a new version of the browser:
http://www.sanger.ac.uk/Teams/Team71/durbin/sgrp/browser.shtml

There are a few new features in the browser which [David] is going to document over the next couple of days.

Major new features of the data are that there should be much better consistency between alignments; Solexa/Illumina data has been incorporated for the strains that had it; and the S. paradoxus alignments are based on a new assembly that created a few weeks ago and which covers about 95% of the genome; a description is at
http://www.sanger.ac.uk/Teams/Team71/durbin/sgrp/spara_assembly.shtml

Willi Hennig Superstar

Willi HennigThe Willi Hennig Society, homebase for all good cladists, has subsidized the license fee for TNT so that it is now a freely available program (although it is not open-source). TNT implements phylogenetic analysis under parsimony with a fast tree searching algorithm. I believe TNT was one of the software tools that CIPRES was targeting for optimization as well so this may reflect some of that work.

From EvolDir.

Flaxseed antifungals

Blogging about Peer-Reviewed ResearchCareful eating those old noodles left in the fridge, lots of fungi probably have made a home in the starch rich environment. But can food be inoculated with some inherent antifungal properties to help it last longer. A recent paper in the Intl Journal of Food Microbiology “Fungistatic activity of flaxseed in potato dextrose agar and a fresh noodle system.” describes work to test whether flaxseed can stop fungi from growing as a potential food preservation agent. Strains of Penicillium chrysogenum, Aspergillus flavus,moldy noodles Fusarium graminearum, and other Penicillium sp isolated from moldy noodles were used in a test assay for fungistatic activity of flaxseed. Flaxseed has a whole host of health benefits that have lead to is use in many foods, cereals, and baked goods. The authors test to see what type of antifungal properties flaxseed has as well to test if it can provide a role in food preservation and be edible (or even healthy). Some other edible antifungals include spices like cinnamon, cloves, and mustard. These authors have also investigated the stability of the antifungal properties of flaxseed in another paper.

Onygenales genome cluster

I’m excited about our projects to tackle the evolution of the Onygenales fungi.

I just remembered to look and see what was going on with the Blastomyces genome sequencing at WashU.  I checked and the Blastomyces dermatitidis genome sequence assembly version 3 was released in October 2007 and ESTs via 454 and ABI technologies are all available from WUSTL Genome Sequencing Center.

With the Broad Institute release this week of the Paracoccidioides genome sequence, the 10 Coccidioides strain genomes + 1 C. posadasii strain from JCVI/TIGR, 3 strains of Histoplasma capsulatum (both WUSTL and Broad), and the in-progress dermatophyte for Trichophyton and Microsporum sequences that are being generating through the FGI at Broad we have incredible genome coverage of this group of dermatophyte, keratin loving, and often animal pathogenic fungi.

I know I’ve been accused of being too positive announcing these things, but I do think analyses here are going to be as rich for comparisons as any old 12 flies.

Evolutionary morphology of mushroom-forming fungi

Blogging about Peer-Reviewed ResearchDave Hibbett wrote a great article for Mycological Research that describes the current state of systematics and evolutionary studies of morphology in mushroom-forming Agaricomycete fungi. His article, dedicated to the late, great mycologist Orson K Miller, Jr and entitled “After the gold rush, or before the flood? Evolutionary morphology of mushroom-forming fungi (Agaricomycetes) in the early 21st century” describes the how classification and systematics has changed in the last two hundred years and macromorphology to the more than “108,000 nucleotide sequences of ‘homobasidiomycetes’, filed under 7300 unique names.”

The article contains some beautiful pictures many of which are taken from some of the eminent mycological photographers and mycologists Michael Wood and Taylor Lockwood.

Continue reading Evolutionary morphology of mushroom-forming fungi