The Hyphal Tip http://fungalgenomes.org/blog Digesting the fungal genomes Sat, 04 Sep 2010 17:26:24 +0000 en hourly 1 http://wordpress.org/?v=abc 37.865026-122.285901fungalcompgenomicshttp://feedburner.google.comSubscribe with My Yahoo!Subscribe with NewsGatorSubscribe with My AOLSubscribe with BloglinesSubscribe with NetvibesSubscribe with GoogleSubscribe with PageflakesSubscribe with PlusmoSubscribe with The Free DictionarySubscribe with Bitty BrowserSubscribe with NewsAlloySubscribe with Live.comSubscribe with Excite MIXSubscribe with Yourminis.comSubscribe with Attensa for OutlookSubscribe with WebwagSubscribe with netomat HubSubscribe with Podcast ReadySubscribe with FlurrySubscribe with WikioSubscribe with Daily Rotation A new kind of monograph – online http://feedproxy.google.com/~r/fungalcompgenomics/~3/ThaIQRAwDa0/ http://fungalgenomes.org/blog/2010/09/a-new-kind-of-monograph-online/#comments Sat, 04 Sep 2010 17:26:24 +0000 Jason Stajich http://fungalgenomes.org/blog/?p=1706 C. pruinosa

A critical part of understanding and documenting the diversity is formal descriptions of species and their relatives. This can be a laborious task and is usually captured in the form of a monograph of a species where a group of species are described in careful detail along with the phylogenetic relationships of them.  This has served as the basis for documentation of the the natural history and morphological descriptions of species.  The information is typically presented in the form of a book that goes to a library or your shelf which can be pulled down and poured over when trying to determine traits for a group of organisms.  Books are great but sharing images and the

Ryan Kepler, a PhD student at Oregon State, is writing a monograph about the ever so cool Cordyceps fungi which have intimate and quite manipulative relationship with insects. However, he’s doing it as an electronic monograph that he is publishing on the web. This is a great way to share this technical and visual information. By publishing it online he is making it searchable and so that it can be a living document that can be updated over time. He’s also willing to publish it as he goes along so the current version is a starting point, but will continue to mature as he completes his PhD thesis work and has input from other experts in the field. I really like that the is publishing it early on and truly embracing an open science approach to presenting his descriptions of the species and their relationships. This is akin to other efforts putting information about species on the web, from the Encyclopedia of Life to Mushroom observer, but I really like that this is a site dedicated to capturing the expert level information that Ryan is gathering as part of this thesis in a searchable and interactive form.

Cordyceps are an interesting group of fungi not only because of their insect association, but their variety of colors and morphologies. The ability to manipulate their insect hosts also suggests a wide variety of secondary metabolites are probably produced by these fungi to enable them to change behavior of infected individuals.

Will be great to see this resource mature and also additional monographs and species descriptions to embrace an online and freely available form. I suspect there could be a (tiny) market for better web software here for making this easier so that one doesn’t have to be or have an expert web development team to deploy these for individual projects.

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  • Conserved Fungal LysM Effector Ecp6 Prevents Chitin-Triggered Immunity in Plants. http://bit.ly/bgkSvl & blogged review http://bit.ly/9Mjnun #
  • Blog post on 'Ants found to use multiple antibiotics as "weed" killers' http://bit.ly/9FuYgr reviewing the paper http://bit.ly/dpKtZN #
  • Sordaria macrospora, a model organism to study fungal cellular development. http://bit.ly/bdQwJm #
  • A novel class of peptide pheromone precursors in ascomycetous fungi http://bit.ly/dsWQqX #
  • High variability in MAT linked region in the dry rot fungus Serpula lacrymans caused by frequency-dependent selection? http://bit.ly/9YtvW7 #
  • Small RNA repertoire gen by plant/fungal-like machinery and effected by a metazoan-like Argonaute in T gondii. http://bit.ly/9mwhbL #
  • U.maydis Clp1 Protein Orchestrates Pheromone and b-Dependent Sig Pways to Coordinate Cell Cycle & Pathogenic Developmt. http://bit.ly/cx6LZL #
  • Identification of PEX33, a novel component of the peroxisomal docking complex in the filamentous fungus N. crassa. http://bit.ly/bbK6al #
  • The new definitive Cryptococcus book from Heitman et al comes out in October, order yours now from #ASM http://bit.ly/avK6uP #

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  • Job:Comparative Transcriptomics of Symbiosis in Amanita in Pringle lab at Harvard – http://bit.ly/du7RiG http://bit.ly/afSiGo #

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  • Friend or Foe – a sweet story: Francis Martin reviews Parrent et al's paper on GH32 (invertase) distribution in fungi – http://bit.ly/9qcgmx #
  • RT @yeastgenome: SGD is now on Twitter! Stay tuned for news and updates – we're here if you want to 'ascus' anything! #

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  • A fun blog post & paper review on Cordyceps entitled "fungal parasites & zombie ants" http://bit.ly/a3FoYA #

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  • A deviation from the bipolar-tetrapolar mating paradigm in an early diverged basidiomycete http://bit.ly/dAeCft #
  • Fitness-Associated Sexual Reproduction in a Filamentous Fungus (A. nidulans) http://bit.ly/ar6o5g #
  • Evolutionary Genetics: Desperate Times Call for More Sex (A. nidulans). http://bit.ly/c5HN7g #
  • RT @dritoshi: Comprehensive comparative analysis of strand-specific RNA sequencing methods http://htn.to/g5zEp7 #

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  • TFs in light & circadian clock signaling networks revealed by genome-wide mapping of direct targets for Neurospora WCC http://bit.ly/9ML9Nr #

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  • R. de Vries: Database of fungal growth profiles and linking to CAZY gene family copy number. http://www.fung-growth.org/ #IMC9 #
  • RT @aemonten: Article title WIN!!: "Plant twitter: ligands under 140 amino acids enforcing stomatal patterning" http://bit.ly/bSxAhw #
  • Genome-wide characterization of methylguanosine-capped and polyadenylated small RNAs in the rice blast fungus M oryzae http://bit.ly/ceoNyi #
  • Genetic and molecular characterization of a cryptochrome from the filamentous fungus Neurospora crassa null http://bit.ly/a02VU2 #
  • Genome-wide investigation of reproductive isolation in Neurospora: identifying regions by microarray-based mapping http://bit.ly/d09hkv #
  • Myosin Motor Domain of Chitin Synthase V Is Dispensable for Vesicle Motility but Required for Virulence in U. maydis. http://bit.ly/ab2hXo #

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  • Edinburgh is teeming with mycologists – will see what 1760 of us in one place looks like. #IMC9 /via @hyphaltip #

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  • An updated list of fungal genomes incorporating more of JGI in progress list. Will migrate to a db in future I suspect. http://bit.ly/aQrupM #

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    ]]>     http://fungalgenomes.org/blog/2010/07/imc-yah/feed/ 0 http://fungalgenomes.org/blog/2010/07/imc-yah/     The roundup of twittered updates for 2010-07-28 http://feedproxy.google.com/~r/fungalcompgenomics/~3/uo6MmU7SXIo/ http://fungalgenomes.org/blog/2010/07/the-roundup-of-twittered-updates-for-2010-07-28/#comments Wed, 28 Jul 2010 15:00:00 +0000 Jason Stajich http://fungalgenomes.org/blog/2010/07/the-roundup-of-twittered-updates-for-2010-07-28/
  • Isolation and morphological and metabolic characterization of common endophytes in annually burned tallgrass prairie http://bit.ly/b6Uz7m #
  • A circadian rhythm regulating hyphal melanization in Cercospora kikuchii http://bit.ly/9Em853 #
  • Sexual reproduction in aflatoxin-producing Aspergillus nomius http://bit.ly/b8pmKZ #
  • Functional genomic profiling of Aspergillus fumigatus biofilm reveals enhanced production of the mycotoxin gliotoxin. http://bit.ly/baujOh #
  • Neurospora illuminates fungal photoreception http://bit.ly/cPOKya #
  • Architecture of the wood-wide web: Rhizopogon spp. genets link multiple Douglas-fir cohorts. http://bit.ly/d3DbbX #
  • Exploiting the determinants of stochastic gene expression in Scerevisiae for genome-wide prediction of expression noise http://bit.ly/bDeHP2 #

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  • NIFA press release on recent effector study in Cell shows how RXLR effectors use lipids to enter cells http://bit.ly/bItnTm #
  • RT @aemonten: Tinkering Evolution of Post-Transcriptional RNA Regulons: Puf3p in Fungi as an Example http://bit.ly/crurtm #

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  • J. Heitman's review Cell Host & Mic "Evolution of Euk Microbial Pathogens via Covert Sexual Reprod http://tinyurl.com/37m4v96 via @KamounLab #

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  • Amphibians wiped out before they are discovered. Fungal disease drives the loss of 30 species in Panama. http://bit.ly/bK3XAR #
  • Epidemic dx decimates amphibian abundance, species diversity, & evolutionary history in highlands of central Panama http://bit.ly/atcOdF #

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  • A unique wheat disease resistance-like gene governs effector-triggered susceptibility to necrotrophic pathogens http://bit.ly/dmNWBv #
  • Shedding of the Mucin-Like Flocculin Flo11p Reveals a New Aspect of Fungal Adhesion Regulation http://bit.ly/aZjANf #
  • Cytochrome P450 enzymes in the fungal kingdom http://bit.ly/bOUG8C #
  • 3 mycorrhizal genes in the common ancestor of land plants suggests key role of mycorrhizas in the colonization of land http://bit.ly/bYaoyI #
  • RT @Darwin2009: Evolutionary ecology of mycorrhizal functional diversity in agricultural systems http://ow.ly/2dqDk #

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  • Our Pythium genome ppr (incl @stajichlab @KamounLab). The fight against crop pathogens http://bit.ly/9cKAAN #bmcblog http://bit.ly/bIXuMR #

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  • (fixed) Review in EukCell: Next Gen Sequencing application to euk microorganisms & biological questions. http://bit.ly/cTuBzb #

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  • The septal pore cap is an organelle that functions in vegetative growth & mushroom formation of S.commune. http://bit.ly/aOyhQ5 #
  • Comparative analysis of secreted protein evolution using ESTs from 4 poplar leaf rusts (Melampsora spp.). http://bit.ly/dcR4GK #
  • Noncanonical transcript forms in yeast and their regulation during environmental stress. http://bit.ly/9GvCBd #
  • Comp expression in C. neoformans finds novel role of Ras & cAMP in env stress response & antifungal drug sensitivity. http://bit.ly/dyYppM #
  • An excellent review in EukCell of Next Gen Sequencing application to euk microorganisms and biological questions. http://bit.ly/cTuBzb (fixed link) #
  • How to annotate the non-coding regions of the genome, by Mark Gerstein et al http://bit.ly/bXivws via @nutrigenomics via @NatureRevGenet: #

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  • RT @doe_jgi: Greater enzyme variety for breaking down plant mass found in genome of wood-decay fungus S. commune: http://go.usa.gov/O8a #
  • RT @doe_jgi Split-gill fungus is the third wood-decaying fungus sequenced by DOE JGI. Learn what the first two were at http://go.usa.gov/O8a #
  • RT @mike_challen: Genome sequence of S commune — now in Nature Biotechnology http://bit.ly/bEUk0c — Congratulations to the Schizo team #
  • Conidia but not yeast of fungal pathogn H capsulatum trigger Type I interferon innate immune resp in murine macrophages http://bit.ly/bwIiS9 #

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