By Jason Stajich, on February 23rd, 2008
Definitely worth listening to the RadioLab show episode “So-Called Life”. The second act describes some “MIT bioengineering kids” who engineered sweet smelling E.coli. I’m sure some of them interviewed hang out at OWW, like Reshma. The sound effects for gene exchange and “The BioEngineers song” at the end of the 2nd act is definitely worth listening [...]
By Jason Stajich, on February 21st, 2008
David Carter at the Sanger Centre emailed a message that new assemblies of Saccharomyces strain resequencing project have been posted including a new three-way alignment of S. bayanus-S.paradoxus-S.cerevisiae. This updates the Dec 2007 [...]
By sharpton, on February 18th, 2008
Though less Fungal (and more fungal, if you’ll grant me that) than most of the stories we cover, a recent analysis of the Diplonema papillatum mitochondria genome sequence is interesting nonetheless. The genome consists of over 100 chromosomes, each roughly 6 kilobasepairs (kbp) or 7 kbp in size. However, each chromosome contains only a short (less than 500 bp) gene encoding region. It appears that genes are scrambled, where modular genetic units are dispersed across many chromosomes. Curiously, despite having discontigous genes, cDNA sequencing identifies contiguous and properly ordered mRNA. So just how are scrambled genes expressed and asssembled?
By Jason Stajich, on February 17th, 2008
PZ Meyers has a post summarizing of an older paper from Elliot Meyerowitz (2002) that comapares plant and animal development. In particular there is are some major themes summarized about how plants and animals form patterns and cell to cell signaling as part of development. What’s missing is what we’ve learned about within group comparisons where there are multiple lineages of single-celled and [...]
By Jason Stajich, on February 17th, 2008
What delineates species boundaries in fungi? Much work has been done on biological and phylogenetic species concepts in fungi. Some concepts are reviewed in Taylor et al 2006 and in Taylor et al 2000, and applications can be seen in several pathogens such as Paraccocidiodies, Coccidioides, and the model filamentous (non-pathogenic) fungus
By Jason Stajich, on February 13th, 2008
I had the pleasure of meeting Phil Ross, a SF area artist, last night at the BABS Darwin Day Celebration. He has been growing fungi in a variety of different ways to make living art in an project called ‘Pure Culture‘. He is using Ganoderma lucidum (a Polyporales fungus, which is
By Jason Stajich, on February 11th, 2008
The UniProtKB/Swiss-Prot team is curating fungal proteins in their databases and reportedly have curated more than 20,000 fungal proteins in Release 54.8 of [...]
By Jason Stajich, on February 9th, 2008
I’m not at AGBT, but Jonathan and Anthony both have coverage of Pacific Biosciences’s new sequencing technology that uses detection of DNA polymerase activity to determine sequence. I believe some of the details are in the paper “Selective aluminum passivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide [...]
By Jason Stajich, on February 8th, 2008
A review in Plant Cell from Darren Soanes and colleagues summarizes some of the major findings about evolution of phytopathogenic fungi gleaned from genome sequencing highlighting 12 fungi and 2 oomycetes. By mapping evolution of genes identified as virulence factors as well as genes that appear to have similar patterns of diversification, we can hope to derive some principals about how phytopathogenic fungi have evolved from saprophyte [...]
By Jason Stajich, on February 5th, 2008
Dettman, Anderson, and Kohn recently published a paper in BMC Evolutionary Biology on reproductive experimental evolution in two Neurospora crassa populations evolved under different selective conditions. This is a great study that complements work published last year in Nature on experimental evolution in Saccharomyces cerevisiae populations. Neurospora populations were evolved under high salt and low temperature and were started from either high diversity (interspecific crosses, N. crassa vs N. intermedia) or low diversity (intraspecific cross, two N. crassa isolates D143 (Louisiana, USA)and D69 (Ivory Coast)) as described in Figure 1. The experimentally evolved populations were then tested for asexual and sexual fitness (they were taken through complete meiotic cycle throughout the experiment to avoid insure there was selection on the sexual reproduction pathway.
