Comments for The Hyphal Tip http://fungalgenomes.org/blog Digesting the fungal genomes Sun, 09 Nov 2008 12:23:37 +0000 http://wordpress.org/?v=abc hourly 1 Comment on Bat White-nose syndrome brevia by Alex http://fungalgenomes.org/blog/2008/10/bat-white-nose-syndrome-brevia/comment-page-1/#comment-4776 Alex Sun, 09 Nov 2008 03:13:27 +0000 http://fungalgenomes.org/blog/?p=802#comment-4776 I don't know if reptiles and amphibians pollinate anything, but having a plague on bats and bees simultaneously indicates a common origin connected with pollination. I would be looking at butterfly, hummingbird, and other pollinator populations for similar crashes in the works. Bats, reptiles, and amphibians eat a lot of insects though, and are especially important in protecting food-bearing plants from rampant insect populations. Another category of important food-protecting insect-eaters would be many fish, small birds, and spiders. I would also look at parasites, like mites, that could be common among bees, bats, etc. Looking at the dead bodies is one way to find a solution, but anticipating crashes in animal populations with similar ecological functions may lead to the uncovering of the root cause -- probably emanating from an enlarging hole in the world's ecology. I would hazard this guess: acid rain. Soil acidity has risen almost everywhere in the world, and as climate becomes more volatile and species wander in new ranges, species that are stressed by acid soil conditions will fall to diseases and competitors. Fish and amphibians, with such sensitive skin and close contact with water, have been shown the greatest stress under these conditions. Parasite and insect populations previously checked by these species then can attack bees, bats, and others. I would also look to migratory birds carrying contagions across the hemispheres as they freeze and thaw in more volatile ways. Geomyces pannorum could be associated with acid soils, and migration from arctic permafrost soils. http://aem.asm.org/cgi/content/full/73/18/5817?view=long&pmid=17660302 I don't know if reptiles and amphibians pollinate anything, but having a plague on bats and bees simultaneously indicates a common origin connected with pollination. I would be looking at butterfly, hummingbird, and other pollinator populations for similar crashes in the works. Bats, reptiles, and amphibians eat a lot of insects though, and are especially important in protecting food-bearing plants from rampant insect populations. Another category of important food-protecting insect-eaters would be many fish, small birds, and spiders. I would also look at parasites, like mites, that could be common among bees, bats, etc.

Looking at the dead bodies is one way to find a solution, but anticipating crashes in animal populations with similar ecological functions may lead to the uncovering of the root cause -- probably emanating from an enlarging hole in the world's ecology.

I would hazard this guess: acid rain. Soil acidity has risen almost everywhere in the world, and as climate becomes more volatile and species wander in new ranges, species that are stressed by acid soil conditions will fall to diseases and competitors. Fish and amphibians, with such sensitive skin and close contact with water, have been shown the greatest stress under these conditions. Parasite and insect populations previously checked by these species then can attack bees, bats, and others. I would also look to migratory birds carrying contagions across the hemispheres as they freeze and thaw in more volatile ways.

Geomyces pannorum could be associated with acid soils, and migration from arctic permafrost soils.
http://aem.asm.org/cgi/content.....d=17660302

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]]> Comment on Lichen genome projects and the power shift prompted by next-gen sequencing by Matt http://fungalgenomes.org/blog/2008/10/lichen-genome-projects-and-the-power-shift-prompted-by-next-gen-sequencing/comment-page-1/#comment-4771 Matt Tue, 04 Nov 2008 05:40:46 +0000 http://fungalgenomes.org/blog/?p=819#comment-4771 Here's a link for free access to the Genome Technology article: http://www.genome-technology.com/issues/2_19/webreprints/150422-1.html Here's a link for free access to the Genome Technology article:

http://www.genome-technology.c.....422-1.html

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]]> Comment on Jobs in fungal genomics by Bridget http://fungalgenomes.org/blog/2008/10/jobs-in-fungal-genomics/comment-page-1/#comment-4770 Bridget Mon, 03 Nov 2008 22:54:17 +0000 http://fungalgenomes.org/blog/?p=797#comment-4770 Thanks for this! I am looking. Keep me in mind if you run across anything "perfect." See you in Feb still? Thanks for this! I am looking. Keep me in mind if you run across anything "perfect." See you in Feb still?

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]]> Comment on Tracking honeybee decline by Bat White-nose syndrome brevia http://fungalgenomes.org/blog/2007/09/tracking-honeybee-decline/comment-page-1/#comment-4767 Bat White-nose syndrome brevia Fri, 31 Oct 2008 20:57:13 +0000 http://fungalgenomes.org/blog/2007/09/tracking-honeybee-decline/#comment-4767 [...] diseases there are series of recent fungal-associated disease of animal populations including honeybees perhaps from a virus and a microsporidium, frogs and amphibians via Batrachochytrium dendrobatidis, [...] [...] diseases there are series of recent fungal-associated disease of animal populations including honeybees perhaps from a virus and a microsporidium, frogs and amphibians via Batrachochytrium dendrobatidis, [...]

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]]> Comment on Haunted Woods by Bat White-nose syndrome brevia http://fungalgenomes.org/blog/2007/07/haunted-woods/comment-page-1/#comment-4766 Bat White-nose syndrome brevia Fri, 31 Oct 2008 07:02:43 +0000 http://fungalgenomes.org/blog/2007/07/haunted-woods/#comment-4766 [...] frogs and amphibians via Batrachochytrium dendrobatidis, and white-nose syndrome. Diseases like Cryptococcus gattii are also examples of pathogens that may be able to infect healthy animals and humans. It seems [...] [...] frogs and amphibians via Batrachochytrium dendrobatidis, and white-nose syndrome. Diseases like Cryptococcus gattii are also examples of pathogens that may be able to infect healthy animals and humans. It seems [...]

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]]> Comment on Of frogs and fungi by Bat White-nose syndrome brevia http://fungalgenomes.org/blog/2008/03/of-frogs-and-fungi/comment-page-1/#comment-4765 Bat White-nose syndrome brevia Fri, 31 Oct 2008 07:02:28 +0000 http://fungalgenomes.org/blog/2008/03/of-frogs-and-fungi/#comment-4765 [...] A Brevia piece in Science today describes efforts to describe the causal agent in white-nose syndrome (WNS) in bats which appears to be contributing to bat decline. According to the authors, previous work had described an uncharacterized fungus associated with bats that showed signs of being sick with WNS. This is an emerging pathogen as the samples described in this paper were from Spring 2008. Phylogenetic analysis of the rDNA (and presumably ITS) sequence of fungal isolates from diseased bats placed it as a Geomyces spp, in the Helotiales order (in the Leotiomycetes if you are wondering what are the closest sequenced fungal genomes for this species). Other Geomyces spp are also psychrophiles and found colonizing the skin of animals in cold climates (it must be hard to make a living). The authors suggest the finding of this fungal species on bats is consistent with its involvement in disease. The authors also make the parallel to chytridiomycosis, an emerging pathogen of amphibians that is contributing to the worldwide amphibian decline. [...] [...] A Brevia piece in Science today describes efforts to describe the causal agent in white-nose syndrome (WNS) in bats which appears to be contributing to bat decline. According to the authors, previous work had described an uncharacterized fungus associated with bats that showed signs of being sick with WNS. This is an emerging pathogen as the samples described in this paper were from Spring 2008. Phylogenetic analysis of the rDNA (and presumably ITS) sequence of fungal isolates from diseased bats placed it as a Geomyces spp, in the Helotiales order (in the Leotiomycetes if you are wondering what are the closest sequenced fungal genomes for this species). Other Geomyces spp are also psychrophiles and found colonizing the skin of animals in cold climates (it must be hard to make a living). The authors suggest the finding of this fungal species on bats is consistent with its involvement in disease. The authors also make the parallel to chytridiomycosis, an emerging pathogen of amphibians that is contributing to the worldwide amphibian decline. [...]

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]]> Comment on Attend Fungal Genetics 2009! by Registration opens for 25th Fungal Genetics http://fungalgenomes.org/blog/2008/09/attend-fungal-genetics-2009/comment-page-1/#comment-4760 Registration opens for 25th Fungal Genetics Mon, 27 Oct 2008 16:02:29 +0000 http://fungalgenomes.org/blog/?p=632#comment-4760 [...] Attend Fungal Genetics 2009! [...] [...] Attend Fungal Genetics 2009! [...]

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]]> Comment on Trichoderma reesei genome paper published by P. chrysogenum genome http://fungalgenomes.org/blog/2008/05/trichoderma-reesei-genome-paper-published/comment-page-1/#comment-4759 P. chrysogenum genome Wed, 01 Oct 2008 00:02:24 +0000 http://fungalgenomes.org/blog/?p=325#comment-4759 [...] industrial fungal genome papers have seen publication in Nature Biotechnology (Aspergillus niger, Trichodermera reesei, and Phanerochaete [...] [...] industrial fungal genome papers have seen publication in Nature Biotechnology (Aspergillus niger, Trichodermera reesei, and Phanerochaete [...]

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]]> Comment on Not one, but two Aspergillus niger genome sequences by P. chrysogenum genome http://fungalgenomes.org/blog/2007/01/not-one-but-two-aniger-genome-sequences/comment-page-1/#comment-4758 P. chrysogenum genome Wed, 01 Oct 2008 00:01:35 +0000 http://fungalgenomes.org/blog/2007/01/not-one-but-two-aniger-genome-sequences/#comment-4758 [...] - Most of the industrial fungal genome papers have seen publication Nature Biotechnology (Aspergillus niger, Trichodermera reesei, and Phanerochaete [...] [...] - Most of the industrial fungal genome papers have seen publication Nature Biotechnology (Aspergillus niger, Trichodermera reesei, and Phanerochaete [...]

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]]> Comment on Fungal genome assembly from short-read sequences by Mark Chaisson http://fungalgenomes.org/blog/2008/06/fungal-genome-assembly-from-short-read-sequences/comment-page-1/#comment-4755 Mark Chaisson Sat, 27 Sep 2008 04:45:41 +0000 http://fungalgenomes.org/blog/?p=492#comment-4755 Came across this forum while googling.  I'm not so surprised about the inferior results of EULER with 20X coverage.  Some work is done behind the scenes now to deal with this.  Some of the problems should go away both with EULER and Velvet when 50+ base reads are used since many gaps happen due to the not quite uniform sampling that happens.   Came across this forum while googling.  I'm not so surprised about the inferior results of EULER with 20X coverage.  Some work is done behind the scenes now to deal with this.  Some of the problems should go away both with EULER and Velvet when 50+ base reads are used since many gaps happen due to the not quite uniform sampling that happens.  

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]]> Comment on Escaping the dung pile quickly: Speedy Pilobolus spores by Hayley Kilroy http://fungalgenomes.org/blog/2008/09/escaping-the-dung-pile-quickly-speedy-pilobolus-spores/comment-page-1/#comment-4739 Hayley Kilroy Wed, 17 Sep 2008 15:26:33 +0000 http://fungalgenomes.org/blog/?p=685#comment-4739 The video set to music can be viewed here: http://www.youtube.com/watch?v=TrKJAojmB1Y The video set to music can be viewed here: http://www.youtube.com/watch?v=TrKJAojmB1Y

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]]> Comment on Escaping the dung pile quickly: Speedy Pilobolus spores by migg http://fungalgenomes.org/blog/2008/09/escaping-the-dung-pile-quickly-speedy-pilobolus-spores/comment-page-1/#comment-4738 migg Wed, 17 Sep 2008 07:43:42 +0000 http://fungalgenomes.org/blog/?p=685#comment-4738 The movie with opera soundtrack is fantastic too http://www.youtube.com/watch?v=Y4n0b5rMqE0   The movie with opera soundtrack is fantastic too
http://www.youtube.com/watch?v=Y4n0b5rMqE0
 

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]]> Comment on A word about databases by Amy http://fungalgenomes.org/blog/2008/07/a-word-about-database/comment-page-1/#comment-4735 Amy Wed, 17 Sep 2008 03:22:57 +0000 http://fungalgenomes.org/blog/?p=555#comment-4735 hear, here! hear, here!

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]]> Comment on Melaninized fungi use ionizing radiation for energy by Fungi on Science Friday http://fungalgenomes.org/blog/2007/05/melaninized-fungi-use-ionizing-radiation-for-energy/comment-page-1/#comment-4728 Fungi on Science Friday Fri, 12 Sep 2008 21:29:54 +0000 http://fungalgenomes.org/blog/2007/05/melaninized-fungi-use-ionizing-radiation-for-energy/#comment-4728 [...] Arturo Casadevall who has been a leader and pioneer in Cryptococcus research including recent work on its ability to use ionizing radiation as an energy source. [...] [...] Arturo Casadevall who has been a leader and pioneer in Cryptococcus research including recent work on its ability to use ionizing radiation as an energy source. [...]

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]]> Comment on Papers on our desk by John Logsdon http://fungalgenomes.org/blog/2008/08/papers-on-our-desk/comment-page-1/#comment-4725 John Logsdon Mon, 08 Sep 2008 23:06:28 +0000 http://fungalgenomes.org/blog/?p=621#comment-4725 Sex on the brain, eh? Those same papers have been recently on my desk, too! (now where did they go?...) Sex on the brain, eh? Those same papers have been recently on my desk, too! (now where did they go?...)

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]]> Comment on Sarah Palin and the fungus (a story according to Jonathan) by Jason Stajich http://fungalgenomes.org/blog/2008/09/palin-and-the-fungus/comment-page-1/#comment-4724 Jason Stajich Mon, 08 Sep 2008 18:46:28 +0000 http://fungalgenomes.org/blog/?p=644#comment-4724 <p>Likely derived from the phrase commonly heard when a farmer discovers a fruit infected with the disease....</p> <p>Not really <a href="http://en.wikipedia.org/wiki/Botryotinia_fuckeliana" rel="nofollow">B. fuckelina</a> was named for <a href="http://en.wikipedia.org/wiki/Karl_Wilhelm_Gottlieb_Leopold_Fuckel" rel="nofollow">Dr Fuckel</a></p>

Likely derived from the phrase commonly heard when a farmer discovers a fruit infected with the disease....

Not really B. fuckelina was named for Dr Fuckel

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]]> Comment on Sarah Palin and the fungus (a story according to Jonathan) by Jonathan Eisen http://fungalgenomes.org/blog/2008/09/palin-and-the-fungus/comment-page-1/#comment-4723 Jonathan Eisen Mon, 08 Sep 2008 18:19:16 +0000 http://fungalgenomes.org/blog/?p=644#comment-4723 I am so so so glad someone decided to use the fuckeliana name and not cinerea ... I am so so so glad someone decided to use the fuckeliana name and not cinerea ...

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]]> Comment on Sex in fungi: MAT locus cloned from a Zygomycete by Papers on our desk http://fungalgenomes.org/blog/2008/01/sex-in-fungi-mat-locus-cloned-from-a-zygomycete/comment-page-1/#comment-4701 Papers on our desk Wed, 03 Sep 2008 00:49:28 +0000 http://fungalgenomes.org/blog/2008/01/sex-in-fungi-mat-locus-cloned-from-a-zygomycete/#comment-4701 [...] Casselton, LA. Fungal sex genes - searching for the ancestors. doi: 10.1002/bies.20782. A review of recent findings about the Zygomycete MAT locus. [...] [...] Casselton, LA. Fungal sex genes - searching for the ancestors. doi: 10.1002/bies.20782. A review of recent findings about the Zygomycete MAT locus. [...]

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]]> Comment on Papers on our desk by anonymous http://fungalgenomes.org/blog/2008/08/papers-on-our-desk/comment-page-1/#comment-4690 anonymous Fri, 29 Aug 2008 18:59:20 +0000 http://fungalgenomes.org/blog/?p=621#comment-4690 This review on transcription factors in fungi may be of interest: Transcription factors in fungi Ekaterina Shelest FEMS Microbiology Letters Volume 286 Issue 2 (September 2008) DOI: 10.1111/j.1574-6968.2008.01293.x http://www3.interscience.wiley.com/journal/121377720/abstract This review on transcription factors in fungi may be of interest:
Transcription factors in fungi
Ekaterina Shelest
FEMS Microbiology Letters
Volume 286 Issue 2 (September 2008)
DOI: 10.1111/j.1574-6968.2008.01293.x
http://www3.interscience.wiley.....0/abstract

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]]> Comment on Cochliobolus genome released by Bookmarks about Genome http://fungalgenomes.org/blog/2008/07/cochliobolus-genome-released/comment-page-1/#comment-4689 Bookmarks about Genome Tue, 26 Aug 2008 23:45:27 +0000 http://fungalgenomes.org/blog/?p=548#comment-4689 [...] - bookmarked by 4 members originally found by freeriod on 2008-08-08 Cochliobolus genome released http://fungalgenomes.org/blog/2008/07/cochliobolus-genome-released/ - bookmarked by 6 members [...] [...] - bookmarked by 4 members originally found by freeriod on 2008-08-08 Cochliobolus genome released http://fungalgenomes.org/blog/.....-released/ - bookmarked by 6 members [...]

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