Tag Archives: news

Fungal Genetics 2007 summary

A Fungal Genetics 2007 summary.
Wow. What a meeting! I am still exhausted and not just because of the very late Saturday night dancing at the close of the conference. I will just say anyone who thinks scientists are boring people should witness the passion researchers have for their science and in sharing it with other people. Not to mention that some know how to put on their dancing shoes and let loose. Because of the atmosphere at the Asilomar conference center, it really did feel like I was at a super fun science camp that culminated with a rock band and dancing in the big hall.

I am also digesting the science from the talks and social interactions with a variety of people enthusiastic about mycology, genomes, and evolution (which could be a conference unto itsself). There were presentations on a lot of really great topics, from symbiosis between mycorhizal fungi and plants (Laccaria bicolor) to cell wall structure in Cryptococcus. I got to meet so many people who are making an impact in the fungal community both in their research and in the resources provide online. I will try and re-cap so I can remember everything I saw.

Continue reading Fungal Genetics 2007 summary

Full(er) length methods sections in Nature papers

Nature is reporting that it is now going to expand the methods section in print and online versions of its papers. This will also include a 300 word summary of the methods in the print version as well as a full length methods section in the online version which is not a supplemental methods document.

Nature also uses the news piece to remind us that the author formated version of the paper can be submitted to pubmed central (6 months after publication) (well only for NIH supported pubs though – see comments exchange on Jonathan’s blog) and that can include the full length methods.

This seems to be all around a GOOD THING. I’ve always heard complaining about how the glossy publications skimp on actually providing enough evidence to reproduce the results (“telegraphic tradition” in Naturespeak). The best thing is if this means methods are actually peer-reviewed. I don’t really know that they are. You can download the supplemental materials but it isn’t clear to me that someone has actually reviewed it and made sure that a) methods are clearly explained and indicates a reproduceable protocol, b) is typographically proofread.

Fungi on the radio

NPR imageAn NPR story on former Taylor Lab postdoc and current Harvard professor Anne Pringle airs tonight. They followed her, Ben, and Frank around collecting Amanita phalloides in Point Reyes in December. Poor Anne’s voice is going as she had a cold, but as usual she does a great job expressing her unbridled passion for mycology and biology.

The NPR newscast right after the report also has two briefs on medicinal research with fungi.

Whole genome tiling arrays

A recent paper describes the discovery of 9 new introns in Saccharomyces cerevisiae by Ron Davis’s group at Stanford, using high density tiling arrays from Affymetrix. The arrays are designed for both strands allow the detection of transcripts transcribed from both strands. The arrays were also put to work by the Davis and Steinmetz labs to create a high density map of transcription in yeast and for polymorphism mapping from the Kruglyak lab.

PNAS Yeast Transcriptional map

Whole genome tiling arrays have also been employed in other fungi. For example, Anita Sil’s group at UCSF constructed a random tiling array for Histoplasma capsulatum and used it to identify genes responding to reactive nitrogen species. A similar approach was used in Cryptococcus neoformans to investigate temperature regulated genes using random sequencing clones.

As the technology has become cheaper, it may become sensible to use a tiling array to detect transcripts rather than ESTs when attempting to annotate a genome. In the Histoplasma work transcriptional units could be identified from hybridization alone. Some of the algorithms will need some work to correct incorporate this information, and the sensitivity and density of the array will influence this. These techniques can be part of a resequencing approaches or fast genotyping progeny from QTL experiments when the sequence from both parents is known (or at least enough of the polymorphims for the genetic map).

What is superior about the current Affymetrix yeast tiling array is the inclusion of both strands. This allows detection of transcripts from both strands. Several anti-sense transcripts in yeast have been discovered recently including in the IME4 locus through more classical approaches, but perhaps many more await discovery with high resolution transcriptional data from whole genome tiling arrays.