Twitter Updates for 2010-05-31

  • Breeding for better tasting tomatoes, from @NPR #
  • RT @idjoly: Follow #globalwheat tweets by @KamounLab @CIMMYT and @globalrust (am I missing someone tweeting from there?) #
  • Role for methylation & exon definition? Relationship btwn nucleosome positioning & DNA methylation /via @nutrigenomics #
  • A public resource for metabolic pathway mapping of Aspergillus fumigatus Af293. #
  • Cytochrome P450 monooxygenases involved in anthracene metabolism by the white-rot basidiomycete P. chrysosporium. #
  • Proteome profiling & functional classification of intracellr prots from conidia of human-pathogenic fungus A.fumigatus #
  • Transcriptome sequencing and comparative transcriptome analysis of the scleroglucan producer Sclerotium rolfsii #
  • Characterization of the temperature-sensitive mutations un-7 and png-1 in Neurospora crassa #
  • The MAT locus & sex repro of Crypto heveanensis: insights into the evolution of sex-determining chrom regions in fungi #
  • Natural functions of mycotoxins and control of their biosynthesis in fungi #
  • ene silencing of transgenes inserted in the Aspergillus nidulans alcM and/or alcS loci #
  • N crassa zinc transporter gene in transgenic N. tabacum enhances plant Zn accumulation without co-transport of Cd #
  • Characterization of yeasts colonizing in healthy individuals #
  • An extracellular ice-binding glycoprotein from an Arctic psychrophilic yeast. #
  • The evolution of sex: a perspective from the fungal kingdom #
  • Genomic Plasticity of the Human Fungal Pathogen Candida albicans #
  • Population structure of Pneumocystis jirovecii isolated from immunodeficiency virus-positive patients #

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Busy, but here are some links

Dear Hyphal Tip reader-

I’m having a hard time making enough to blog about interesting papers at length, but to spell you I am putting up twitter msgs about papers that have interesting abstracts and are worth a followup look.  You’ll see these in the boringly titled “Weekly Twitter Updates” on Monday morning with a round up links from the week’s twitterings by @fungalgenomes.  If you are like me, sometimes just a survey of some interesting titles is enough to introduce a new paper that might be worth reading but you don’t have time to read a whole long post about a paper anyways.  Hopefully there will be some more time this summer to catch up on papers that could be blogged about.  I also plan on reorganizing some more of the links to accessible genome data and database resource to make it easier to mine and download this information.  With so many projects that are no longer specifically funded or directed by sequencing centers since every lab can pretty much do a fungal genome now, it is hard for the list to realistically expect to keep it  up to date without other contributors to it.

I’m also open and interested in other people with mycological interests providing short blogged reviews on papers or fungal genome database resources, but I understand the pull between spending time writing things that “count” (ie published, peer reviewed papers & reviews), getting work done, and blogging.

Other things here are afoot with work developing databases for fungal genome data, a bunch of new data loads for gbrowse tools that is competing with my time teaching and the work to get initial lab projects running that are takes up lots of time.  I co-submitted a couple of CSP proposals and tried to support other fungal groups’ proposals with some letters.  In the meantime I’ll keep blogging about what comes across my plate and hope to see you at a conference this summer or online.

Twitter Updates for 2010-05-24

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CSP: Letter of support time!

Several groups working on Fungi are submitting proposals to the JGI Community Sequencing Program.  Several proposals relating to the JGI’s interest in an encyclopedia of fungal genomes sequencing genomes of ascomycete and basidiomycete yeasts, filamentous ascomycetes, basidiomycetes,  and early diverging fungi are being put forward.  If you haven’t been contacted by these community members but would like to write a letter of support in these areas, please get in touch as the deadline for the proposals in early next week. There are also other proposals going in for Neurospora mutant strain resequencing, more Fusarium species, transcriptomes of mycorrhizal fungi, and other topics.  If you are are a user of data from any of the previous fungal projects that you know how important these resources are in both comparative genomics and molecular biology work, so support to get additional sequences generated will benefit many in the community.

I don’t know if it is appropriate for me to post the text of the solicitation for letters here, differing to the privacy of the groups submitting proposals, but if you want to help out the community by writing a letter showing that you would benefit from these resources, I can try to put you in touch.

Dynamics of amphibian pathogen infection cycles
Two papers out this week on the population dynamics and epidemiology of the chytrid pathogen of amphibians, Batrachochytrium dendrobatidis (Bd). This is work from the Vredenburg and Briggs labs that includes several decade-long studies of frog declines and the prevalence of Bd.

See Vance in action swabbing a frog

In the Briggs et al paper, they describe a 5-year study on the fungal load in surviving populations of frogs in Sierra Nevada mountain lakes.  They find that adult frogs that have low enough fungal load escape chytridiomycosis and can actually lose and regain infection. They propose that fungal load dynamics are the reason behind differential survival of various populations of mountain frogs. They conclude that:

“Importantly, model results suggest that host persistence versus extinction does not require differences in host susceptibility, pathogen virulence, or environmental conditions, and may be just epidemic and endemic population dynamics of the same host–pathogen system.”

So they propose that differences in the populations that are coming down with the disease is due only to “density-dependent host–pathogen dynamics” not that some populations are resistant. They go on to provide a detailed model of persistence if the host and pathogen, chance of reinfection, and survival of the host which is derived from the long-term study data.  There are many more interesting findings and models proposed in the paper. It also further reinforces (for me) the need to know more about the molecular basis of the host-pathogen interactions and more about how the fungus persists without a host, lifestyle of how it overwinters, and the details of the microbe-host interactions, and the infection dynamic when zoospores disperse from infected frogs.

The Vrendenburg et al paper adresses the dynamics of population decline in the mountain yellow-legged frogs over a periods of 1-5 and 9-13 year study in 3 different study sites at different sampling intervals.  The authors were able to catalog the species decline and conduct skin swabbing to assess Bd prevalence. They found that the fungus spread quickly as it could detected in virtually all the lakes over the course of a year starting with a 2004 survey. The dramatic declines of frog populations in these lakes followed in the years subsequent to the initial detection. This sadly predicts that most if not all of the mountain lakes will go extinct for the frogs as the current tadpoles develop into frogs in the next 3 years and then fall victim to Bd. Based on their sampling work, the authors were also able to correlate what fungal burden predicted a subsequent decline – in populations where more the ~10,000 zoospores were detected in a swab from frog skin, then the frog population was about to experience a sharp decline.  The take-home from this work is that finding ways to keep the intensity of fungal infections down could provide a meaningful intervention that could prolong the viability of the population.

Briggs, C., Knapp, R., & Vredenburg, V. (2010). Enzootic and epizootic dynamics of the chytrid fungal pathogen of amphibians Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0912886107

Vredenburg, V., Knapp, R., Tunstall, T., & Briggs, C. (2010). Dynamics of an emerging disease drive large-scale amphibian population extinctions Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0914111107

Still time to sign up for the Gordon Conference

A message from the Fungal Cellular & Molecular Biology chairs:

Fellow Fungal Biologists,

We have only 6 weeks until the Cellular and Molecular Fungal Biology Gordon Conference! We have 11 spots for speakers that will be filled based on poster abstracts and we’re especially interested in giving postdocs and grad students the chance to present. If you want to be considered for a talk, be sure you’ve submitted your poster title and abstract online by MONDAY, MAY 10. To update your poster title and abstract follow the link in the email you received from the Gordon Conference notifying you of your acceptance to the meeting. We also still have a few open slots for meeting participants, so if others in your lab are interested in coming, let them know to sign up.

Looking forward to a great meeting!

Michelle Momany and John Taylor Co-Chairs CMFB GRC