Few fungi+host papers

Posted on June 22, 2012 by Jason Stajich

Three papers on some cool fungi that interact with hosts and I recommend them for a good read.

One is coverage of by Ed Yong on rice blast (Magnaporthae orzyae) on paper from Nick Talbot and Gero Steinberg‘s lab on appressorium development in Science this week.

A paper from my lab on role of an expansion of copy number of a chitin-binding domain in the amphibian pathogen B. dendrobatidis.

New Scientist also provides a nice summary of tripartite symbiosis paper on Metarhizium, insects, and plants from Mike Bidochka’s lab.

Fear of Fungi!

Posted on April 12, 2012 by Jason Stajich

The cover of Nature today highlights an article from Matthew Fisher and colleagues on the major impact that Fungi as emerging infectious diseases are playing on threatening diversity of ecosystems and agricultural productivity.

Fisher, M., Henk, D., Briggs, C., Brownstein, J., Madoff, L., McCraw, S., & Gurr, S. (2012). Emerging fungal threats to animal, plant and ecosystem health Nature, 484 (7393), 186-194 DOI: 10.1038/nature10947

Still time to sign up for EMBO Comparative Genomics meeting

Posted on June 20, 2011 by Jason Stajich

[via Teun Boekhout]

This year looks like another great lineup of speakers for the EMBO Comparative Genomics of Microorganisms: ‘Understanding the Complexity of Diversity’ 15-20 Oct 2011 Sant Feliu de Guixols, Spain.

Andrew Allen	J. Craig Venter Institute	US
Anders Blomberg	Göteborg University	SE
Chris Bowler	École Normale Supérieure	FR
Gertraud Burger	University of Montreal	CA
Bernard Dujon	Institut Pasteur	FR
Toni Gabaldón	CRG, Barcelona	ES
Ursula Goodenough	Washington University	US
Michael Gray	Dalhousie University	CA
Joseph Heitman	Duke University	US
Christiane Hertz-Fowler	University of Liverpool	UK
Regine Kahmann	Max Planck Institute	DE
Patrick Keeling	University of British Columbia	CA
Nicole King	UC, Berkeley	US
Edda Klipp	Humboldt University	DE
Veronique Leh Louis	University of Strasbourg	FR
Jan Pawlowski	University of Geneva	CH
Jure Piskur	Lund University	SE
Tom Richards	University of Exeter	UK
Andrew J. Roger	Dalhousie University	CA
David Roos	University of Pennsylvania	US
Iñaki Ruiz-Trillo	University of Barcelona	ES
Joseph Schacherer	University of Strasbourg	FR
Artur Scherf	Institut Pasteur	FR
Joey Spatafora	Oregon State University	US
Nicholas Talbot	University of Exeter	UK
Kevin Verstrepen	University of Leuven	BE
Eric Westhof	University of Strasbourg	FR
Patrick Wincker	Genoscope	FR
Ken Wolfe	Smurfit Institute of Genetics	IE
Alexandra Z. Worden	University of California	US

Some comments from former participants:

Comments from 2009 meeting

Overall rating

Based on responses from 80% of participants:

Excellent 50%; Very Good 44%; Good 6%.

Comments:

It is hard to improve the meeting. It’s a good mixture of conference and workshop with a lot of input from expert of adjacent field.

I strongly support the idea the meeting is organized in the future at a regular basis.

Very high quality, open minded with presentations ranging from pure genomics to implementation in the field of ecology; plenty of novelties. Plenty of time to discuss and to establish potential collaborations

I hope to have the possibility to go in the future to this meeting. We learn a lot, and also the size is well, the students have the possibility to talk of discuss with senior

Great work!

Thanks to the organizers for an extremely interesting and productive meeting.

Great meeting. This is a unique meeting because it brings together a group of scientists that dont normally interact with each other. Thus, great opportunities for cross-interactions. This meeting has the potential to fill a very unique niche. I enjoyed meeting new people from diverse fields. I plan to attend again and encourage my colleagues to do so.

This meeting was a great match to my interests but also challenged me to think outside of my normal sphere. I applaud the organizers and the participants in making this a useful meeting.

The meeting was very well organized and at a very good location. I enjoyed it very much.

I hope this meeting continues as it was a valuable forum for the field of comparative genomics.

This meeting is unique in its broad organism focus. Please keep supporting it.

Origins and evolution of pathogens

Posted on February 8, 2010 by Jason Stajich

An article in PLoS Pathogens by Morris et al describe a hypothesis about the evolution and origins of plant pathogens applying the parallel theories to the emergence of medically relevant pathogens. The authors highlight the importance of understanding the evolution of organisms in the context of emerging pathogens like Puccinia Ug99 for our ability to design strategies to protect human health and food supplies. Both bacterial and fungal pathogens of plants are discussed but I (perhaps unsurprisingly) focus on the fungi here. Continue reading →

New species of Cryptococcus found in seawater

Posted on December 14, 2008 by Jason Stajich

A paper in IJSEM describes a new species in the Cryptococcus basidiomycete yeast lineage. The name is proposed as Cryptococcus keelungensis sp. nov. for a strain isolated from the sea surface microlayer. Its identity as a Cryptococcus sp was determined by sequencing of 26S rDNA D1/D2 and ITS loci and molecular phylogenetics. This is quite diverged from the human pathogen Cryptococcus neoformans and C. gattii as the new species falls in the order Filobasidiales while C. neoformans is classified in the order Tremellales. Interestingly, based on the phylogeny in the paper it seems to be relatively close to newly discovered Cryptococcus himalayensis.

Bats beware of white nose

Posted on August 18, 2008 by Jason Stajich

An outbreak of a fungal infection called “white-nose syndrome” is killing bats in the Northeastern US. This New Scientist article mentions the outbreak briefly and an NPR story and recent Boston Globe story also gives it some coverage. Sounds like we still don’t know much about the causal agent or how it is killing the bats at this time, but some researchers, including Elizabeth Buckles at Cornell University, Vishnu Chaturvedi at NY State Dept of Health, and Jon Reichard at Boston University are working on it.

This is of course old news if you read what Hyphoid Logic has been saying.

That there is a previously undescribed cold loving fungus sounds very interesting, there have been some recent discoveries of psychrophilic fungi like Cryptococcus laurentii and Rhodotorula himalayensis so it would be interesting to learn more when the researchers publish some of these results.

Some more links

Thanks Kathyrn B for reminder about this story.

Phytophthora work highlighted

Posted on April 22, 2008 by Jason Stajich

A link to the story about Matteo Garbelotto‘s work on Phytophthora ramorum and showing that the source in California is likely from ornamentals from a nursery. The work is to appear soon in Molecular Ecology but alas is not available yet.

A recent paper on updated Phytophthora phylogeny from Jamie Blair and co-authors is also out in FGB. They used genome sequences to determine additional markers for multi-locus sequencing and then sequenced and built trees from 82 taxa.

Some links

Posted on March 3, 2008 by Jason Stajich

I’ve been too busy to post much these last few days, but here are a few links to some papers I found interesting in my recent browsing.

FOLy: an integrated database for the classification and functional annotation of fungal oxidoreductases potentially involved in the degradation of lignin and related aromatic compounds – so a database of these enzymes from several different fungi including some of the white rot fungi. I’ll be curious to see how the brown rot fungus Postia‘s genome complement compares.
Evolution of host resistance in a toxin-producing bacterial–fungal alliance. Some more fungal-bacterial symbosis work in Rhizopus that follows on previous work that shows that the bacterial make a toxin that is anti-mitotic, so how does this not affect the host fungus? The authors use a phylogenetics and character state reconstruction to argue that ancestral fungi were sensitive to the toxin (rhizoxin) but that the extant resistant taxa all derive from a single ancestor. So I guess the resistance only evolved once is another way to say that.
New extremophile fungi: Psychrophilic basidiomycete yeast were isolated from Himalayan lake soil and is another Cryptococcus species. I wonder what Neil and his psychro-phile thinking would do with these?

Schmitt, I., Partida-Martinez, L.P., Winkler, R., Voigt, K., Einax, E., DÃ¶lz, F., Telle, S., WÃ¶stemeyer, J., Hertweck, C. (2008). Evolution of host resistance in a toxin-producing bacterialâ€“fungal alliance. The ISME Journal DOI: 10.1038/ismej.2008.19

LEVASSEUR, A. (2008). FOLy: an integrated database for the classification and functional annotation of fungal oxidoreductases potentially involved in the degradation of lignin and related aromatic compounds. Fungal Genetics and Biology DOI: 10.1016/j.fgb.2008.01.004

Shivaji, S., Bhadra, B., Rao, R.S., Pradhan, S. (2008). Rhodotorula himalayensis sp. nov., a novel psychrophilic yeast isolated from Roopkund Lake of the Himalayan mountain ranges, India. Extremophiles DOI: 10.1007/s00792-008-0144-z

Tracking honeybee decline

Posted on September 6, 2007 by Jason Stajich

An early access to article in Science A Metagenomic Survey of Microbes in Honey Bee Colony Collapse Disorder (direct link since DOI is not updated yet) using the current favorite buzzword, metagenomics, of course, describes some early work to try and discover what is killing the honeybees. It is early access and non-free and ScienceExpress is not part of our subscription here so I’ve not actually had a chance to read it yet, but the gist of the reporting about it suggest that a virus is to blame. This is in line with what Joe DeRisi and collaborators found using their Virus chip based on some news reports earlier this year, but no scientific article yet to follow this up.

Some links to today’s SFChronicle article and an article “Stung” from the New Yorker in August that alluded to this Science article.

Melaninized fungi use ionizing radiation for energy

Posted on May 29, 2007 by Jason Stajich

Blogging about Peer-Reviewed Research A recent paper in PLoS One entitled Ionizing Radiation Changes the Electronic Properties of Melanin and Enhances the Growth of Melanized Fungi describes some pretty amazing results that have gotten some press lately. The lead author, Dr Dadachova, spoke on NPR’s Science Friday last week about how melanized fungi are able to use ionizing radiation for energy as seen in the enhanced growth in their experiments.

While this is the first report of such as result, the fact that innovation occurs wherever there is free energy is not surprising. As mentioned by Arturo Casadevall this story in the spring when he was gave a seminar at Berkeley, marine organisms that live near undersea hydrothermal vents have been able to photosynthesize the infrared light emitted from the vent. He discussed the radiation utilization of melanized fungal work at the end of his talk, and said that it has been an epic process to get it published — that this work had been in review for four years at several high profile journals, but I guess that it was controversial enough to not be accepted there. I guess Nature and Science get it now since they wrote news briefs…

Continue reading →

The Hyphal Tip

Digesting the fungal genomes

Category Archives: microbe