Tag Archives: chytrid

Postdoc: UMichigan Fungal Genomics

The lab of Tim James in the Department of Ecology and Evolutionary Biology at the University of Michigan is looking to hire a postdoctoral fellow in the area of single cell and comparative genomics. The research is centered on understanding the phylogeny and molecular evolution of uncultured and poorly known fungi, including the Cryptomycetes, Zygomycetes, and Chytridiomycetes through genomic analyses. The ultimate goals of the project are to produce a well-resolved phylogeny of the basal branches of the fungal kingdom, to identify key evolutionary events associated with diversification and reproduction, and to use genomics to predict ecological roles of uncultured lineages. A major component of the work will be to develop or improve methods for sequencing fungal genomes and transcriptomes using single or few cells or genome assembly using metagenomic approaches. This work will involve collaborations with the ZyGOLife research network (zygolife.org) and the Joint Genome Institute (JGI). The projects are supported by NSF and two JGI Community Sequencing Projects.

The ideal candidate will be skilled in bioinformatics, molecular biology, and microbiology with an interest in fungi. Preference will be given to candidates with proficiency in both bioinformatics and molecular biology. Possible duties include environmental sampling, cell sorting (FACS, micromanipulation), microscopy, genome assembly and annotation, and comparative analyses of genome evolution. Opportunities for mentoring undergraduates or research associates will be provided. The initial appointment is for one year with a possibility of extension to a second year pending performance review.

Our lab (www.umich.edu/~mycology) pursues diverse projects in mycology, and the environment is conducive to development of a pathway to independence in academic research. The lab is in the Department of Ecology and Evolutionary Biology (http://www.eeb.lsa.umich.edu/eeb/index.html), which has strengths in phylogenetics, evolutionary genomics, and disease ecology.

Interested applicants should email Tim James (tyjames@umich.edu) with a CV, cover letter, and the names and contact information of three references.

Anticipated Start Date: Between Oct. 1, 2016 and Jan. 1, 2017.

The University of Michigan is a non-discriminatory/affirmative action employer. The Department of Ecology & Evolutionary Biology at the University of Michigan harbors multiple labs with a focus on evolutionary genetics (http://www.lsa.umich.edu/eeb).

Timothy Y. James
Associate Professor
Associate Curator of Fungi
Department of Ecology and Evolution
University of Michigan
Ann Arbor, MI 48109

Congratulations Joyce Longcore!

Joyce Longcore

Congratulations to Chytrid biologist Joyce Longcore from the University of Maine who was elected as one of 701 of the 2012 fellows of the American Association for the Advancement of Science. This is a very high honor and I’m delighted to see Joyce recognized for her many years working in this field which is often overlooked because there are a small number of researchers.

Joyce has been a hugely influential researcher in studies of chytrid diversity and biology. She is probably most well known for first describing the amphibian pathogenic chytrid Batrachochytrium dendrobatidis. In addition her lab keeps the stocks of the hundreds of chytrid isolates including Bd strains from all over the world, and is one of the few places that maintains these. I’ll mention she does this on a very limited budget (so don’t be bashful about ordering strains from her and helping pay for this important service), yet it provides a hugely valuable resource to the community studying this disease as keeping the chytrids in culture can sometimes be a finicky process, and deep frozen specimens are required to be revived and grown up in regular intervals of ~6 months (see published protocol from her lab).

Joyce completed her MS training under Fred Sparrow in 1964 at the University of Michigan, one of the great mycologists of the 20th century who worked on Chytrids and aquatic fungi (see Aquatic Phycomycetes). She worked on her Ph.D. in the late 1980s after raising children and later obtained her current position at the University of Maine in the School of Biology & Ecology. She has trained many students and researchers in the field on how to isolate and identify chytrids, and I’ll mention is still actively out in the field collecting more isolates, characterizing them and discovering many new species and many new orders of Chytrids to study the diversity and origins of these fascinating organisms.  She continues to be an important person in Mycological community and her research has had important implications in studies of biodiversity, amphibian decline, and phylogenetics and taxonomic studies of the kingdom Fungi.

Congratulations again Joyce!

(No I didn’t write any letters for her AAAS nomination, but I did wanted to make sure this important accolade gets out to the community, so these are just my thoughts at the time – js)


Fear of Fungi!

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

Amphibian skin bacteria shown to fight off Batrachochytrium dendrobatidis.

A year ago researchers at James Madison University discovered that, Pedobacter cryoconitis, a bacteria first found on the skin of red backed salamanders, was found to prevent the growth of the chytrid B. dendrobatidis, which is currently decimating frog populations.

(Mountain Yellow-Legged Frog from wikipedia)

The newest research on the subject is being presented this year at ASM by Brianna Lam who worked with other biologists from both San Francisco State University and JMU.

Lam’s research indicates that adding pedobacter to the skin of mountain yellow-legged frogs would lessen the effects of Batrachochytrium dendrobatidis (Bd), a lethal skin pathogen that is threatening remaining populations of the frogs in their native Sierra Nevada habitats.

Lam first conducted petri dish experiments that clearly showed the skin bacteria repelling the deadly fungus. She then tested pedobacter on live infected frogs, bathing some of them in a pedobacter solution. The frogs bathed in pedobacter solution lost less weight than those in a control group of infected frogs that were not inoculated.

In addition to the lab experiments, the JMU and SFSU researchers have studied the yellow-legged frogs in their natural habitats and discovered that some populations with the lethal skin disease survive while others go extinct. The populations that survived had significantly higher proportions of individuals with anti-Bd bacteria. The results strongly suggest that a threshold frequency of individuals need to have anti-Bd bacteria to allow a population to persist with Bd. (from Eureka alert)

The research above is really interesting and I am curious as to how the bacteria is actually killing the chytrid. The only other research I can think of where chytrids were being killed was a BBC news article that wrote about scientists bathing frogs in chloramphenicol.

Fungal Genetics 2007 details

I’m including a recapping as many of the talks as I remember. There were 6 concurrent sessions each afternoon so you have to miss a lot of talks. The conference was bursting at the seams as it was- at least 140 people had to be turned away beyond the 750 who attended.

If there was any theme in the conference it was “Hey we are all using these genome sequences we’ve been talking about getting”. I only found the overview talks that solely describe the genome solely a little dry as compared to those more focused on particular questions. I guess my genome palate is becoming refined.

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