March 2008 « The Hyphal Tip

Check out some Space Microbiology including lichens - http://bit.ly/cWEa9M /via genrepair http://bit.ly/c3WKmP 3 days ago
At least all are sequenced. Armed & Dangerous: Plant Diseases that threaten food security http://bit.ly/dx3qrY /via @plantdisease @KamounLab 5 days ago
The JGI Mucor circinelloides CBS277.49 v2 Genome Portal is now on the public JGI website: http://www.jgi.doe.gov/Mucor/ 1 week ago
RT @doe_jgi: Naegleria gruberi video on JGI's SciVee (http://tr.im/QCZn) features Simon Prochnik and UC Berkeley's Lillian Fritz-Laylin 1 week ago
Cool! PLoSGenetics: Allelic Exchange of Pheromones and Their Receptors Reprograms Sexual Identity in C. neoformans http://bit.ly/bBLueH 2 weeks ago
More updates...

Mold farm?

By Jason Stajich, on March 31st, 2008

Bret has a mold farm of Aspergillus fumigatus in Flight of the [...]

Of frogs and fungi

By Jason Stajich, on March 26th, 2008

Nature news articles on the frog decline (doi:10.1038/452394a) and Batrachochytrium dendrobatidis (doi: [...]

A paper in Current Genetics describes the discovery of Repeat Induced Polymorphism (RIP) in two Euriotiales fungi. RIP has been extensively studied in Neurospora crassa and has been identified in other Sordariomycete fungi Magnaporthe, Fusiarium. This is not the first Aspergillus species to have RIP described as it was demonstrated in the biotech workhorse Aspergillus oryzae. However, I think this study is the first to describe RIP in a putatively asexual fungus. The evidence for RIP is only found in transposon sequences in the Aspergillus and Penicillium. A really interesting aspect of this discovery is RIP is thought to only occur during sexual stage, but a sexual state has never been observed for these fungi. [...]

(re)Annotating GenBank

By Jason Stajich, on March 22nd, 2008

Tom Bruns, Martin Bidartondo and 250 others sent a letter to Science describing the current problems with fixing annotation in GenBank. There is an entertaining accompanying news article that interviews several people about the problem of updating annotation and species assigned to sequences in the database. In particular the problem for mycologists that many fungi found from metagenomic approaches are only identified through molecular sequences and having the wrong species associated with a sequence can be difficult when studying community ecology composition. This problem is not limited to fungi by any means, but recent reports find as many as 20% of fungal Intergenic Spacer (ITS) sequences are mis-attributed to the wrong species.

There’s a nice quote in the news article from Steven Salzberg talking about the difficulties in getting sequences, especially from big centers, updated. I’m sure he is thinking of many examples, like reclassifying some Drosophila sequence [...]

Throw away that field guide, just use echolocation

By Jason Stajich, on March 21st, 2008

This isn’t fungal, but sounds pretty cool – ability to identify plants by echolocation.

Yovel, Y., Franz, M.O., Stilz, P., Schnitzler, H., Bourne, P.E. (2008). Plant Classification from Bat-Like Echolocation Signals. PLoS Computational Biology, 4(3), e1000032. [...]

Ireland’s blight and Puccinia update

By Jason Stajich, on March 17th, 2008

Hyphoid logic points out that it is appropriate to discuss about the oomycete Phytophthora infestans on St. Patrick’s Day and mentions a NYT article “The fungus that conquered Europe” that is worth a look.

It is also worth thinking about another blight, well rust, that is spreading through the middle east and could threaten wheat crops worldwide. New Scientist has excellent coverage of [...]

Aspergillus comparative transcriptional profiling

By Jason Stajich, on March 12th, 2008

Researchers from Technical University of Denmark published some interesting results from comparing expression across the very distinct Aspergillus species.

Kudos also goes to making it Open Access. I am posting a few key figures below the fold because I can! They grew the fungi in bioreactors fermenting glucose or xylose. After calibrating the growth curves they were able to sample the appropriate time points for comparison of gene expression across these three species. They found a set of genes commonly expressed.

Fun with estimating divergence times

By Jason Stajich, on March 11th, 2008

Estimating divergence times is notorious difficult and the field can be downright rancorous with some being accused of reading tea leaves and chicken entrails – interesting reading for personalities as much as the different scientific approaches. There are several different approaches to trying to estimate a divergence time among species, using [...]

Botany Photo of the Day: Chytrid

By Jason Stajich, on March 11th, 2008

Toko Mori from the Berbee Lab at UBC has an excellent post at the Botany Photo of the day describing a Chytrid that feeds on the algae Vaucheria sessilis. Botany Photo of the Day: Chytriomyces [...]

B. dendrobatidis strain JAM81 released

By Jason Stajich, on March 6th, 2008

The following is an announcement to the B.dendrobatidis and fungal community at large from Alan Kuo at JGI. This is the JAM81 strain (Jess Morgan collected from a frog in the California Sierra Nevada). The JEL423 (Joyce Longcore, collected in Panama) strain genome sequence and annotation is available from the Broad [...]

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