The genome sampling in the Eurotiomycota clade just keeps getting better. The new J. Crag Venter Institute (TIGR) deposited WGS Assemblies of the human pathogens Penicillium marneffei and Talaromyces stipitatus. P. marneffei is a thermally dimorphic fungus endemic to South-East Asia found in bamboo rats. It is studied by a number of labs and the genome will aid in many of the studies including the population structure through MLST studies.
I don’t know if you’ve heard, but bee colonies are disappearing! Colony collapse disorder, as this phenomenon is better known, worries bee-keepers, agriculturalists and insect admirers all over: over 25% of the commerical bee colonies have disappeared since last fall. Normally, when a commerical hive collapses, honey is left behind in the box and wild bees set up shop on top of this free resource. But it seems that wild bees are also suffering, as honey filled boxes remain bee-less.
Researchers are scrambling to determine the cause of this bee die-off. Given the agricultural implications of losing one of nature’s best pollinators, time is of the essence. All sorts of hypotheses have been suggested, from pesticides or pathogens to solar flares and cell phones, but little evidence has been accumulated (mostly due to the fact that bee bodies are rarely found).
Fortunately, a recent breakthrough occured at UCSF. Joe DiRisi’s group found, in collaboration with other researchers, that Nosema ceranae (a microsporidian) had invaded several dead bees that had been found in the wild. There are several bee pathogens in the fungi (e.g. Ascosphera apis, whose genome was recently sequenced), but the discovery of Nosema infection is notable given that Nosema apis was the cause of widespread colony collapse disorder in Spain during the mid-nineties.
So is this pathogen the cause of the widespread colony die off? The jury is still out. But this represents some of the best evidence to date that fungi may be playing a role in this unfortunate event.
A while back, Jason blogged briefly on a New Scientists article about the rise of a new Puccinia graminis strain, Ug99, that is spreading through West African wheat fields at an enormous rates. It looks like this story is growing in the scientific conciousness, as Science is now running an article on the spread of this wheat pandemic.
The article has a nice bit of background regarding the rise of the disease. It seems that it is spreading so quickly for due to its relatively broad host range compared to other strains. While scientists have been working to derive resistant wheat varieties, Puccinia has successfully foiled their recent attempts by mutating to acheive resistance to the plant expressed Sr24.
To boot, this strain has been found in Yemen, allowing its spores to hitch a ride along the winds that blow north along the Indian Ocean, putting much of the global bread basket at risk (I imagine that the last thing the middle east needs right now is a wheat shortage). The last time a rust spread through this area, it caused 1 billion dollars in damage. Given the extensive host range of this variety, experts predict that damages will exceede at least three times this amount.
Fortunately, researchers in Ethiopian have derived two wheat strains that may be resistant to Ug99. However, it can take several years to get these wheat strains in the ground and, ultimately, no one is certain that Ug99 won’t cleverly find a way to adapt resistance. We should keep our ears to the rail on this one: it could be a big problem.
I’m including a recapping as many of the talks as I remember. There were 6 concurrent sessions each afternoon so you have to miss a lot of talks. The conference was bursting at the seams as it was- at least 140 people had to be turned away beyond the 750 who attended.
If there was any theme in the conference it was “Hey we are all using these genome sequences we’ve been talking about getting”. I only found the overview talks that solely describe the genome solely a little dry as compared to those more focused on particular questions. I guess my genome palate is becoming refined.
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.
We’re at Asilomar mtg for Fungal Genetics 2007. We’ll try and blog a bit about the interesting talks and data.Â I’m curious how many fungal geneticists are in fact reading blogs like these and if this medium will work for idea dissemination.
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.
An 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.