Postdoc: Univ of Minnesota Fungal Genomics

Postdoctoral Position – Fungal Genomics and Metabolomics
University of Minnesota, St. Paul, MN

Position description:

A postdoctoral position focused on comparative genomics, metabolomics, and regulatory mechanisms of secondary metabolites in fungi is available in the Bushley lab. This project will focus on population genomics of fungi (Fusarium, Tolypocladium spp.) to investigate regulation and evolution of secondary metabolite genes, clusters, and metabolites. The project will
adopt an interdisciplinary approach that integrates next-generation genome sequencing and assembly, comparative genomics, and RNA-Seq experiments with analyses of chemical products. Genome resequencing will examine the roles of structural variation, transposition, selection, genome methylation, and other evolutionary processes in driving the diversification of secondary metabolite genes and clusters. Strain specific differences in metabolite expression will be investigated under a variety of different media conditions and data will be integrated to develop and analyze metabolic and regulatory networks involved in controlling secondary metabolism.

Minimum requirements:
A Ph.D. in molecular biology and genetics, mycology, genomics, chemistry, biochemistry, or related fields. The ideal candidate will have existing skills in two or more of the following: experience in sequencing and analysis of next-generation sequence data, bioinformatics and comparative genomics, molecular biology, mass spectrometry, NMR, and a willingness to learn new techniques. The initial appointments is for 1 year, with an opportunity for renewal for a second year. The position is available beginning in June 2014. Start date is flexible. Salary range $38,000 – $43,000 depending on experience, plus health benefits.

To apply:
Any questions regarding the position should be directed to kbushley@umn.edu. Informal inquiries are welcome. Applicants must apply through the University of Minnesota Office of Human Resources website (http://employment.umn.edu/applicants/Central?quickFind=119828) and include a CV, a cover letter detailing research interests and experience, and contact information for three references. Screening of applicants will begin May 15 until a suitable candidate is found.

Kathryn Bushley
Assistant Professor
University of Minnesota
Department of Plant Biology
822 BioSci Bldg
1445 Gortner Avenue
St. Paul, MN 55108

Meeting wrapup from ECFG12 in Seville

I recently returned from a successful ECFG12 in Seville, Spain held at the end of March. Some of us flew into Madrid first and took the high speed train to Seville (about 2 1/2 hours) which was a great way to relax and get out of planes after a transatlantic flight. We boarded the train in Madrid and stepped off in Seville. Very fast trains

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The countryside at 200km/hr

The  satellite meetings held before the conference include organism-specific conferences including Neurospora, Fusarium, Dothiedeomycetes, and Colleotrichum and AsperFest

ECFG Sattelite meetings

The conference content was excellent – I am reminded whenever I go to a fungal genetics meeting how fast paced the field has become with the application of genomics and genetics driving studies of cell biology, evolution, and industrial uses of fungi.

It was quite fun to see many of my long term collaborators and colleagues who work in this field. I am also especially interested to see many “non model” systems becoming more tractable with the tools that can be developed based on genome sequencing, transformation techniques, and a growing research community. The separation of “model system” work from applied or medically less clear to me .

This included symbiosis and fungal “communication” or interactions with other organisms such as Hypocreales fungi that are insect associated, as well Dan Vanderpool and his project working on Ophistoma fungi associated with beetles, some interesting Lichen genomics from environmentally sampled thalli from work from Toby Spribille.  Work presented by Jessie Uehling from work by collaboration with the Labbé  (ORNL) and Vilgalys (Duke) labs included a description of endohyphal symbiotic bacteria associated with Mortierella elongata fungus (a “zygomycete” early diverging lineage) which is associated with tree roots.

I unfortunately missed some of the concurrent session that was happening at the same time but some interesting talks in “Unconventional gene regulation” that I would have liked to hear more about.

I also got to hear good work presented in the session on Fungal development and genomics where Minou Nowrousian spoke on Pyronema genome and developmental biology, Francis Trail‘s talk on Fusarium fruiting body development.

I also enjoyed the session I spoke in, organize by Hanna Johannesson and Toni Gabaldón which included great overviews on application of phylogenomics and genomes to fungal biology. This ranged from Hanna on evolution of sex chromosomes in Neurospora tetrasperma,  Saccharomyces and the (amazing) power of yeast genetics and molecular biology (Maitreya Dunham, @dunhamlab) to mycorrhizal fungal genomics (Francis Martin, @fmartin1954), Toni (@gabaldonlab) and the PhylomeDB project but also the analysis of the WGD in Saccharomyces which suggests an alternative scenario for the duplication that may have arisen through allopolyploidization (hybridization between two species) rather than autopolyploidization. Several other great talks in our session including Jaqueline Hess on variation in Amanita genomes, Sarah Schmidt on identifying  AVR2 gene in Fusarium oxysporum.

The plenary sessions were plentiful with highlights across the fungal genetics spectrum. From Phycomyces biology (which has had much of its main origins and efforts in Spain) to Magnaporthe (@talbotlabexeter). Many more interesting work highlighted in the program and links to the abstract book are available. I expect a published report on the meeting will come in the future. Overall I really enjoyed the chance to mix more European and international colleagues and talk about the virtues of football and tapas!

Some of us spent a few more days after the meeting to enjoy Spain or meet with friends. For example Zack and I planned some great Neurospora experiments over tapas and sightseeing.  Hope to be back to Madrid and Spain again soon.

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Eels and shrimp tapas
Eels and shrimp tapas

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Fungal Ecology Evolution Metagenomics Postdoc (University of Illinois)

A postdoctoral position is available in the department of Plant Biology, in the School of Integrative Biology, at the University of Illinois in Urbana-Champaign. PIs Astrid Ferrer (aquatic mycologist), Katy Heath (plant and microbe evolution), and Jim Dalling (plant and fungal community ecology) are looking for a highly motivated postdoc to work on a NSF-funded Dimensions of Biodiversity project aimed at understanding the ecological and genetic controls on fungal community assembly and decomposition function in tropical wood-decomposing aquatic fungi. Both the Heath and Dalling labs are lively, highly-collaborative environments with students and postdocs working on a range of topics in ecology and evolution of plants, bacteria, and fungi.

The duties of the project postdoc will include preparing libraries for metagenomic sequencing of aquatic fungi communities from environmental DNA samples, RNAseq of cultured fungi in response to various environmental treatments, downstream bioinformatic and statistical analyses, and writing manuscripts based on these results.

Expertise in some or all of the following areas is desired: Molecular biology, (meta)genomics, bioinformatics, statistical analysis, ecology, evolution.

Strong candidates will also possess the following attributes:

  • A strong publication record from their PhD (papers published, in press, or submitted).
  • Creativity, independence, and the desire to learn new things.
  • Excellent communication skills, both written and oral.

All candidates must have received a Ph.D. in a relevant field. The position is available for 2 years, with the first year as a probationary period, and will include a competitive salary and full benefits.

Application review will begin May 1, 2014 and will continue until the position is filled. Start date is flexible, with a rough target date of August 2014. All materials should be submitted to the PIs below for consideration. Applications should include a brief cover letter, curriculum vitae, a brief description of past research accomplishments and future research goals (under two pages), and the names and contact information for three references.

Contact Dr. Katy Heath regarding the position or application process. For further information about the Heath lab, visit the lab webpage accessible at: http://www.life.illinois.edu/heath

Yale EEB Postdoc in Microbial Evolutionary Ecology

Yale Postdoctoral Position in Microbial Evolutionary Ecology.

A two- to three-year postdoctoral position is available immediately in the laboratory of Paul Turner in the Department of Ecology and Evolutionary Biology at Yale University. We are seeking a highly motivated and creative individual to participate in ongoing experimental projects relating to eco-evolutionary theory.  These projects concern (i) role of environmental heterogeneity on adaptability of bacteriophages, (ii) role of niche construction in the evolutionary ecology of virus- cancer cell interactions, and (iii) effects of host density on virulence evolution in killer viruses of yeast. The successful candidate will engage in these projects in the first year, while increasingly developing and leading projects of their own design as the position continues. The experiments can utilize high-throughput, automated measures of evolving microorganisms via liquid-handling robotics. Experience with these technologies is preferred, but all strong candidates will be considered.
This postdoctoral position is in association with the Yale Institute for Biospheric Studies program in Eco-Evolutionary Dynamics, which is co-directed by David Vasseur, David Post, and Paul Turner. Through this program, the candidate will participate in regular working groups combining international leaders in experimental and theoretical approaches to eco-evolutionary dynamics. More information on the Department of Ecology and Evolutionary Biology is available atwww.yale.edu/eeb<http://www.yale.edu/eeb>. For information about postdoctoral appointments at Yale, seehttp://www.yale.edu/postdocs/.  Applications should be emailed to Paul Turner (paul.turner@yale.edu) and include a CV, short statement of research interests, and contact information for three references.  Applications will be considered beginning on May 1, 2014.