All posts by Jason Stajich

Assistant Professor at UC Riverside

FGI Chytrid annotations available

The public release of the Batrachochytrium dendrobatidis automated annotation from the Broad/FGI has been made available.

“This project is part of the Fungal Genome Initiative at the Broad Institute and was funded by NHGRI. This release contains a set of 8,794 predicted genes, BLAST databases, precomputed BlastX and HMMer analyses, alternative gene predictions, tRNA predictions, and RFAM features.

The annotation can be accessed through the project website:
http://www.broad.mit.edu/annotation/genome/batrachochytrium_dendrobatidis

We would like to thank Franz Lang and Mary Berbee for sharing their B. dendrobatidis EST sequences and contributing a cDNA library for end-sequencing.”

Mystery in the mechanism of yeast speciation

A paper in PLoS Genetics studied what happens when individual chromosomes of S. cerevisiae are replaced with a homologous copy its sister species, S. paradoxus. Previous work from Ken Wolfe’s lab interpreted the differential loss of genes after the whole genome duplication in the Saccharomyces lineage played a role in speciation among the yeast species. Surprisingly (or not, depending on how you interpret the previous work) Greig did not find any lethality in haploid F1 offspring from a diploid synthetically constructed individuals. Certainly this is not the last word but it represents a nice experimental screen to identify interacting genotypes. What would be interesting in followup work would be more subtle dissection of epistatic interactions among the genes on the different chromosomes to score phenotypes other than complete inviability. This might help understand what pathways are operating differently.

Continue reading Mystery in the mechanism of yeast speciation

Fungi for bioremediation

Saprophytic fungi degrade organic matter to release carbon, nitrogen, and other elements locked up in complexes. There is interest in better degradation of recalictrant ligin and cellulose plant matter as part of a bioenergy program. Some fungi are able to break down these plant molecules that would otherwise remain behind when left to digestion by bacteria.

Continue reading Fungi for bioremediation

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.

Wikis for genome (re)annotation

Steven Salzberg (who is nominated for the Franklin award at bioinformatics.org) has an opinion piece in Genome Biology proposing wiki technology to help solve the problem of genome annotations getting out of date.
Continue reading Wikis for genome (re)annotation

Evolving a new pathway

A paper* this week from the Huffnagle lab argues that even though the human pathogenic fungus Cryptococcus neoformans can produce an oxylipin similar to prostaglandin, the authors were unable to identify any homologous cyclooxygenase genes in the genome. They showed through LC-MS-MS on supernatants from C. neoformans cells grown on arachidonic acid that molecules with activity similar to prostaglandin E2 are synthesized. BLAST searches of the genome could not identify any similar genes to cyclooxygenase genes including the PPo genes from Aspergillus which contain catalytic domains similar to mammalian cyclooxygenases.

So did C. neoformans evolve a new way to synthesize this enzyme which may act as a hormone and affect the host’s immune system? My cursory searches against other basidiomycete genomes did turn up homologs to these PPo genes in Ustilago and Coprinus so perhaps the enyzmes in the pathway have changed in the Cryptococcus lineage. Perhaps searches with protein structure of cyclooxygenases could pick up functionaly similar genes which would serve as good candidates which have little sequence similarity to the cannonical protein determined in humans.

* Paid access required for 6 months.

Neurospora crassa

Here is an image of Neurospora crassa I took today in my first attempt at squashes. These are from strains that Dave Jacobson grew up with his constructs so I can’t take any credit other than playing with the microscope next door. Now my first attempt came out badly, so this is actually Dave’s prep as well. And these got dry so they aren’t as nices as they could be. For much nicer images, see N.B. Raju’s.

All that said, I hope these quick images give a hint at the extremely cool structures these fungi produce. These 8-chain ascospores are the result of meoisis that took place inside the perithecia (which was squeezed gently to release the rosettes [or not too gently in my case]).

N.crassa rosetteN.crassa Histone GFP

( I was previous confused about the sample and had labeled this N. tetrasperma which has 4-chained ascospores [tetra] while this sample is crassa which has 8).

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.

Gut check

Ever wonder what goes on in a cow’s multi-chambered stomach? Probably not. I did think about it a little more after a trip to a teaching farm during grad school where we saw a cow with a fistula. This hole provides access to the cows stomach so that samples can be drawn of the community living in the gut and understand how the bovine stomach can digest the recalcitrant cellulose of grasses.

Of course all kinds of lovely things live in the dark, anaerobic environment. In fact there is a delicately balanced community of species. When cows are fed corn instead of grass this affects the rumen acid content and allows pathogenic E. coli like O:157 to survive. So far I don’t seen any JGI proposal for sequencing of the gut communities of rumens, but maybe that should be proposed.

Rumen fungi are probably not on your keyword list, but these fungi are extremomophiles living in highly anaerobic environment. A paper in Microbiology details an analysis of the genome of the anaerobic fungus Orpinomyces.

Splicing machinery and introns

Splicing of pre-messenger RNA is necessary to remove introns and create well formed and translateable mRNA, but the purpose of introns still remains a mystery. One idea is they provide a role in the error checking machinery, or Nonsense Mediated Decay (NMD), by providing way-points during translation. A protein is deposited at the exon junction complex (EJC) which indicates a splicing event has occurred. During translation, if the ribosome encounters a premature stop (or termination) codon (PTC) and then sees one of these EJC way-points, it signals the corrupted message for degradation.

NMD_PTC

Several predictions come out of these models including the lack of introns in the 3′ UTR and that the average length of exons should be correlated with the window that the proofreading mechanism can operate on. These are discussed in several papers out of Mike Lynch’s lab including (Lynch and Connery 2003), (Lynch and Kewalramani, 2003), (Lynch and Richardson, 2002) and recently (Scofield et al, 2007).

Efforts to understand the splicing machinery, particularly in S. cerevisiae have led to the discovery of numerous genes that code for proteins that make up the spliceosome. Some of these include small RNAs as well as protein coding genes. The SR proteins are serine-arginine rich proteins that regulate splicing and are found in almost all eukaryotes including most fungi (even those with few introns, such as S. cerevisiae). SR proteins play a role in splicing and in nuclear export (Masuyama et al, 2004, Sanford et al, 2004) indicating that a coupling of these processes may explain why genes with introns tend to be more highly expressed. The evolution of the spliceosomal family of genes is also interesting because the families appear to diversify in some eukaryotes perhaps where there are more elaborate splicing and regulatory action (Barbosa-Morais et al, 2006).

There is some debate as to whether splicing occurs after the pre-mRNA is completely synthesized or if it happens as transcription is occurring. Work on this has shown that both spliceosomal assembly can co-occur with polymerase during transcription, as well as evidence that most splicing (in yeast) is post-transcriptional (Tardiff et al, 2006). It is argued that the two steps occur together to maximize efficiency and fidelity (Das et el, 2006, Moore et al, 2006), but perhaps affinities are species-specific and have evolved to correlate with intron densities?

[Note: This post has links to non-open access journal articles. At this point I am still referring to these even if they are not all readable by everyone, because they contain some data that is only available there. I will strive to focus more narrowly on only papers that are available as open access through pubmed central or directly through open-access journals.]