The roundup of twittered updates for 2011-09-26

  • Reconstructing Fungal Tree of Life Using Phylogenomics & Investigation of Distribution of Yeast Prion-Like Proteins http://t.co/2YYXQGOo #
  • Cryptococcus gattii: where do we go from here? http://t.co/glWQLhnY #
  • In vitro antifungal activity of DNA topoisomerase inhibitors http://t.co/FFtHLpcA #
  • Phylogeny and species delimitation in the genus Coprinellus with special emphasis on the haired species http://t.co/K6onru9h #
  • Farnesol-induced cell death in the filamentous fungus Aspergillus nidulans http://t.co/oX4uRkSy #
  • Hsp90 governs dispersion and drug resistance of fungal biofilms http://t.co/lmMjjNIw #
  • Insight into structure and assembly of the nuclear pore complex by utilizing the genome of a eukaryotic thermophile http://t.co/iIOcJxNH #

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Nuclear Pore Complex studied in thermophilic fungus

ResearchBlogging.orgSometimes choosing a hot lover can make all the difference. In this case, choosing a thermophilic fungus was the right eukaryote for the job to purify stable proteins from the nuclear pore complex and test their interactions. Since high temperatures (60C as compared to what its relative Chaetomium globosum prefers, 24C) will denature proteins, this fungus has evolved the ability to still fold up proteins nicely at those high temperatures. Thus at more standard laboratory room temperature or below, these proteins should be really stable and easier to work with.  This manuscript (not OpenAccess sadly) includes the genome sequence of Chaetomium thermophilum sequenced with 454 FLX and XLR at 24X and assembled into 20 scaffolds – (8 chromosomes expected so they say – and I agree – this is quite good).The used the Celera assembler to make this final assembly for those of you taking notes at home on how to assemble your fungal genomes. The genome is available for download at the authors’s site or at GenBank. Their assembly is quite a bit smaller (28.3 Mb) than the related C. globosum (34.9) or Neurospora crassa genome (41Mb – though the authors use the old version and report 39.2; they also say “*based on the published genome (Galagan et al., 2003), although there is a newer assembly of N. crassa available from Broad, the newer assembly is not annotated for protein coding genes yet.” which is kind of weird because there is an annotated version here). I do wonder if the tendency of repeated elements to be collapsed in the assembly process resulted in a smaller assembly or if this really does have a smaller genome and less genes (~7k genes while Neurospora has ~10k).  Also worth noting that several other thermophilic fungi have been public for a while at the JGI too – Thielavia terrestris and Sporotrichum thermophile and our lab and others are investigating the genome content and how some genome properties like transposons have evolved in these lineages.

The thermophilic adaptation of this fungus has lead to stable proteins which can be studied more easily than mesophilic fungi. They have been able to determine how the nucleoporins (Nups) interact because of the biochemical and structural assays that are possible with the more stable protein complexes. This highlights the value of targeting an experimental system that has the properties needed and the simple and straightforward tactics needed to generate and use the genome sequence (the genome is but a minor note in the findings of this paper).  I can only wonder why none of my de novo genome assemblies go together as nicely as this one, but I’m excited to see this work present new insights into the biology of nuclear pore complexes.

Amlacher, S., Sarges, P., Flemming, D., van Noort, V., Kunze, R., Devos, D., Arumugam, M., Bork, P., & Hurt, E. (2011). Insight into Structure and Assembly of the Nuclear Pore Complex by Utilizing the Genome of a Eukaryotic Thermophile Cell, 146 (2), 277-289 DOI: 10.1016/j.cell.2011.06.039

Myco-bio-diesel

Previously I posted on an article on making biodiesel using the fungus Gliocladium roseum. Here is a new study reporting conversion of lipids to biodiesel using the basidiomycete Cryptococcus curvatus. There has been also other progress in this area where Mucor circinelloides can also be used to produce oils suitable for biodiesel production as reported in the paper and the press release – though it is a pathogenic fungus with interesting spore size dimorphism.

Thiru M, Sankh S, & Rangaswamy V (2011). Process for biodiesel production from Cryptococcus curvatus. Bioresource technology PMID: 21930373

Keystone Meeting on Fungal Pathogens

Upcoming 1st deadline for the Keystone Meeting on Fungal Pathogens, held in Santa Fe, NM January 2012. This looks to be a great gathering of scientists working on pathogens and fungal biology. The deadline for the abstracts is September 19. If you submit after this deadline it will cost more so don’t delay if you think you’d like to attend.

Please find attached an announcement and program for the first Keystone Symposia Meeting on Fungal Pathogens: From Basic Biology to Drug Discovery. The conference will be held January 15-20, 2012 in Santa Fe, New Mexico and is poised to be a milestone for the field. Please note the upcoming Abstract & Scholarship deadline of September 19, 2011.

The aim of this meeting is to bring together the academic, medical and pharmaceutical communities focused on fungal microbial pathogens of humans and other animals to illustrate common themes, and therapeutic, diagnostic and preventive strategies. Opportunities for interdisciplinary interactions will be significantly enhanced by the concurrent meeting on Drug Discovery for Protozoan Parasites, which will share the keynote session and two plenary sessions with this meeting. By bringing together leading experts on multiple pathogens from distinct scientific arenas, this meeting will surmount barriers that have emerged from more limited interactions between traditionally disparate organism-centric communities. The meeting will also provide an opportunity to obtain mentoring on issues spanning grant writing (workshop led by the NIH), career development, and publication in top-tier journals (workshop led by senior editors of top journals).

During free time in the afternoon, meeting participants will be able to enjoy skiing at the majestic Sangre de Cristo mountain range easily accessible by a complementary shuttle. The Convention Center is located within a few blocks of museums, art galleries, restaurants, and the Sante Fe marketplace, where local Indians exhibit and sell hand-crafted products. More details on the conference, activities and services can be found at the following link: http://www.keystonesymposia.org/Meetings/ViewMeetings.cfm?MeetingID=1164