Basidiobolus! – genus of the month at ATCC

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ATCC sent out this email with the Genus of the month as Basidiobolus. It is worth noting they call out B. ranarum as inhabitant of bat and rodent guts but it is mainly known (and named) for being associated with frogs (hence the ‘rana’). It has some quite cool biology, it grows dimorphically as a yeast or hyphae, and is reported to have a large genome (Henk and Fisher PLoS One 2012).
Note that the genome and transcriptome of B. meristosporus is being sequenced as part of the 1000 Fungal genomes project from samples Andrii Gryganski prepared. Don’t forget that YOU can propose genomes to this project by logging in here and submitting a proposed species in a family that is not sufficiently sampled (2 per Family).

The info below is from ATCC®. I couldn’t find a link to the on their site so I am copying the email text in.

There is nothing more fascinating than when a microbial species begins popping up in the literature as a true pathogen. Basidiobolus ranarum, which typically inhabits the guts of bats and small rodents, has been recently tagged as an emerging human pathogen that may have previously been unrecognized.1

       B. ranarum was first added to the CDC’s Morbidity and Mortality Weekly Report (MMWR)1 in 1999 after 6 immunocompetent individuals tested positive for gastrointestinal basidiobolomycosis over a 5-year period. The most interesting aspect of this study, however, was the fact that each patient was originally misdiagnosed with some other intestinal ailment, ranging from diverticulitis to cancer.

While many of the Zygomycetes, including Basidiobolus, have been implicated in subcutaneous human diseases, it is still relatively uncommon for Basidiobolus to colonize the human intestine. This new development piqued the interest of several researchers at the Mayo Clinic in Scottsdale, Arizona, a region of the U.S. where the majority of such cases have been reported.  Following an in-depth analysis of all known case records, they discovered a total of 44 cases of gastrointestinal basidiobolomycosis worldwide; 19 of which occurred in the southwestern U.S., 11 in Saudi Arabia, and 14 in other arid regions of the globe.2

Symptoms displayed in each case were similar, with complaints ranging from abdominal distention and pain to a palpable abdominal mass. Of particular interest was a patient originally treated for Clostridium difficile colitis. This patient underwent several surgeries and treatment with oral vancomycin before a stool fungal culture revealed the presence of B. ranarum. While this patient was successfully treated with a 3-month course of voriconazole, repeated at 1-year follow-up, the investigators cautioned that antifungal resistance may pose a problem in the future. Earlier work performed by the same group revealed uniform resistance to amphotericin B and flucytosine in four  B. ranarum isolates, as well as mixed resistance to several other azoles.2

The source of B. ranarum infection leading to gastrointestinal disease is still not understood, but the fecal-oral route has been suggested. Pathologists and clinicians should be aware of this potential new threat, and additional work to understand the pathogenesis and antifungal susceptibility/resistance of B. ranarum should be an on-going effort among the research and medical communities.

ATCC® Basidiobolus Strains
Want to learn more about ATCC Basidiobolus strains available from ATCC? View a list of Basidiobolus spp. online.

References

1. Centers for Disease Control and Prevention (CDC). MMWR: Gastrointestinal Basidiobolomycosis – Arizona, 1994-1999. August 20, 1999.

2. Vikram, et al. Emergence of Gastrointestinal Basidiobolomycosis in the United States, with a Review of Worldwide Cases. Clinical Infectious Diseases Advance Access published on March 22, 2012.

Fungal Genetics memorable parts?

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Well we’re back from a great meeting. We have pictures to upload, notes to review, and backlog of emails to try and read. If you have any memorable points from the meeting you want to share, please feel free to use the comments system or tweet about it referring to this post and it will link in or use the #fungal2013 hashtag. If you have any pictures to share, please feel to also post links to them. A few years ago we used Flickr to make a pool for these, may try again if there is any interest.

I didn’t do a good job finding my favorite data viz posters as it seemed like it was always such a packed poster session and hard to focus after the long days.

Fungal Genome Tools session at Asilomar

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On Wednesday of the Fungal Genetics meeting in the Chapel from 12:15 – 1:30 there will be a fungal genome tools session. Box lunches will be available at the Chapel so you can have a chance to eat during the session.

12:15 – 12:30 AspGD / CGD / SGD – Martha Arnaud (Stanford)
12:35 – 12:50 CFGGP 2.0 – Jaeyoung Choi (Seoul National University)
12:55 – 1:10 Ensembl Genomes – Uma Maheswari (European Bioinformatics Institute)
1:10 – 1:25 FungiDB – Jason Stajich (UC Riverside)

This will be followed by a One Fungus = One Name session from 1:30 – 1:50. See this paper for more information.

Talks will also be posted at tools.fungalgenomes.org and you can see the talks from the previous conference.

On Thursday March 14 there will be a lunch workshop on JGI’s Mycocosm and the 1000 Fungal genomes (Igor Grigoriev) project in Merrill Hall.

On Friday March 15, there will be a lunch workshop on FungiDB (Omar Harb).

2013 FASEB Summer Research Conference “Microbial Pathogenesis: Mechanisms of Infectious Disease”

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Snowmass Village, CO

Registration is now open for the 2013 FASEB Summer Research Conference “Microbial Pathogenesis: Mechanisms of Infectious Disease” that will be held in Snowmass, Colorado July 21-26, 2013. The current schedule of invited speakers is attached here. An important feature is that 16 short talks remain to be chosen from submitted abstracts, so there is ample room to be included on the program.

See the program here: 2013 FASEB PROGRAM AGENDA-July 21-26 2013 Snowmass CO and the FASEB SRC site

The history of this unique meeting is that it strives to be truly cross-disciplinary. It is attended by ~ 100+ bacteriologists, virologists, mycologists, parasitologists, prionologist, and immunologists, and the conference seeks to create an interactive environment for a diverse audience of senior and junior scientists who approach similar questions from a variety of angles and model systems. The meeting will begin with the Bernie Fields keynote address on Sunday evening by Jeremy Luban followed by four days of morning and evening talks and late afternoon poster sessions. Like the Gordon and Keystone meeting format, participants gather for all meals and talks, making it easy to get to know many new colleagues during the course of the meeting. The accommodations and site are exemplary, with ample hiking, biking, river rafting and other outdoor activities available during the unscheduled afternoons.

A central goal for the conference is to develop the next generation of colleagues in the microbial pathogenesis field. At this past summer’s meeting, Peggy Cotter continued the “meet the speaker” and “meet the scientist” breakfasts and lunches to encourage greater interaction between students, post-docs and faculty. There was also a career development session the closing morning titled “Grant, manuscript and tenure review” that was led by Peggy Cotter and Eduardo Montalvo and Joe Heitman and this was well received. These will be features of the 2013 meeting, as well as a series of poster and young speaker awards. We are working to invite journal editors to the meeting, and also representatives from the NIH/NIAID (Eduardo Montalvo has attended the meeting previously several times) and possibly also from the Burroughs Wellcome Fund.

A series of short talks will be selected from Abstracts submitted by graduate students, post-doctoral fellows, and faculty.
In the past, this has been a particularly attractive feature of the meeting that has contributed to its popularity and success. 16 short talks will be chosen from the submitted abstracts for inclusion on the program.

The 2013 meeting will be the 10th in this series of highly successful interdisciplinary meetings, and all have been held at the Snowmass site. Thus, there is a rich history and tradition, and many if not all of the previous chairs and co-chairs will be attending the meeting, and which further contributes to the success that the meeting enjoys.

We look forward to hearing from you if you have any questions.

Sincerely,

Joe Heitman
Chair, 2013 FASEB Summer Research Conference

John Leong
Vice-Chair, 2013 FASEB Summer Research Conference (Chair 2015 conference)

Posters for Fungal Genetics Conference

Link

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To those making their posters for Fungal Genetics meeting, we salute you. Get those 3’10″ x 3’10″ works of art printed & ready to impress the 900 colleagues who will be at the conference.  I’ll try and count the distribution of fabric posters vs the big prints vs the hand-made 8×11 sheets. I think I’ll also be giving unofficial awards for best non-boring Venn Diagram (think outside the banana) or other memorable data viz. The abstract book should be released soon and I hope to get a Wordle up like from years past. I’m curious to see what topics are trending and if it belies how the fields are changing to address areas in biofuels, use of next gen sequencing, or other areas.

Consider submitting your posters to F1000 or other repositories if you want to share you work outside the meeting. I’m even seeing on public on twitter already from @BenoitCalmes.

The twitter hashtag is #FUNGAL2013 so get your clients ready.

Posters for Fungal Genetics Conference

Postdoc: Life strategies in the Archaeorhizomycetes soil fungi

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Post doc, Life strategies in the Archaeorhizomycetes at Uppsala University

The Archaeorhizomycetes is an ancient class of ubiquitous soil fungi. Sequences representing the class have been identified from vegetated terrestrial habitats across the globe. Estimates indicate that there are hundreds of species within the class and strong patterns of habitat specificity has been documented among species. Yet the ecological role of the Archaeorhizomycetes remain unknown.

Deadline for application is March 15, 2013.

For more information contact Anna Rosling (anna.rosling@ebc.uu.se) and visit the Rosling Lab website

Job: Asst Prof Microbiology – Western Illinois University

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Assistant Professor – Microbiology – 140005-E 

Job Description:

APPOINTMENT: Tenure track position starting in August of 2013

RESPONSIBILITIES: Teaching responsibilities may include introductory microbiology, virology, immunology, pathogenic bacteriology, and other upper division/graduate courses in the candidates\’ area of expertise. The successful candidate is expected to develop an active research program involving graduate and undergraduate students. Service on committees at the Department, College and University level, and with the general public is also expected.

RANK & SALARY: Assistant Professor rank. Salary commensurate with background and experience. Western Illinois University offers a competitive benefits package that includes domestic partner benefits. For full benefit information visit: http://www.wiu.edu/vpas/human_resources/benefits/.

Requirements:

REQUIRED QUALIFICATIONS: Ph.D. is required. Seeking a broadly trained microbiologist with expertise in genetics, genomics, and /or microbial bioinformatics. The chosen candidate will be expected to develop an active research program involving masters’ level and undergraduate students. Candidates must be able to demonstrate oral English proficiency requirements evaluated through presentation during the interview and must have teaching experience at least at the graduate assistant level.

PREFERRED QUALIFICATIONS: Candidates with postdoctoral experience, collegiate teaching experience, and peer reviewed publication(s) and grants obtained from competitive granting programs are strongly preferred.

About Western Illinois University:

Western Illinois University, accredited by the Higher Learning Commission and a member of the North Central Association of Colleges and Schools, serves more than 12,000 students at its traditional, residential four-year campus in Macomb, IL and its metropolitan, non-residential campus in Moline, IL. Compliance to state and federal hiring standards is coordinated through WIU’s Office of Equal Opportunity & Access.

Western Illinois University is an Affirmative Action and Equal Opportunity employer with a strong commitment to diversity. In that spirit, we are particularly interested in receiving applications from a broad spectrum of people, including, but not limited to, minorities, women and individuals with disabilities. WIU has a non-discrimination policy that includes sex, race, color, sexual orientation, gender identity and gender expression, religion, age, marital status, national origin, disability, and veteran status.

Additional Information:

THE DEPARTMENT: The Department of Biological Sciences offers majors in Biology (with options in Botany, Medical Sciences, Microbiology, Teacher Certification, and Zoology) leading to a Bachelor of Science degree. There are approximately 471 undergraduate majors. Minors are also offered in Zoology, Botany, Microbiology, and Environmental Science. The Department offers a Master of Science in Biology degree and currently has 104 graduate students; also available are Post Baccalaureate Certificates in Zoo and Aquarium Studies, and Environmental GIS. There are 22 full time faculty members and a full time academic advisor. The Department has the Alice L. Kibbe Life Science Station (www.wiu.edu/kibbe) located 45 miles west of campus on the Mississippi River as well as the Rodney and Bertha Fink Environmental Studies Field Laboratory and Conservancy located 2 miles from campus. The Department’s mammal collection contains over 2000 specimens. The Biological Sciences Department also houses modern analytical and molecular biology equipment such a high-pressure liquid chromatography system, microarray scanner, DNA sequencer, quantitative real-time PCR system, bioanalyzer, etc. For more information about the University and our Department, visit our website at http://www.wiu.edu/biology.

THE UNIVERSITY: Recognized as a “Best Midwestern College” by the Princeton Review and one of 37 public universities ranked a top tier “Best Regional University” by U.S.News&World Report, Western Illinois University (WIU) serves nearly 13,000 students in the heart of the Midwest through its traditional residential campus in Macomb and its metropolitan, non-residential location in Moline, Illinois.

The WIU-Macomb and -Quad Cities campuses are comprised of accomplished faculty, state-of-the-art technology and facilities, and a wide range of academic and extracurricular opportunities. Western is a comprehensive university offering 66 undergraduate and 38 graduate degree programs, including a doctorate in education. With a student-to-faculty ratio of 16:1, the University’s 666 full-time faculty members teach 94 percent of all undergraduate and graduate courses, in addition to 10 pre-professional degree programs and 17 certificate programs.

Western offers a broad-based athletics program, sponsoring 20 NCAA Division I intercollegiate varsity sports. Football competes in the NCAA Division I Football Championship Subdivision through the Missouri Valley Football Conference; all other varsity sports compete at the Division I level through The Summit League. WIU is the cultural center of the region. University Libraries house an extensive collection and offer online database access to thousands of academic periodic journals and publications.

WIU-Macomb, IL (Student Population: 10,423): A traditional, residential four-year campus with select graduate programs, WIU-Macomb is located in the heart of west central Illinois in Macomb (population 20,000). Macomb is an Amtrak city with twice-daily service to Chicago. Macomb is located approximately 75 miles from the Quad Cities International Airport (Moline, IL) and 70 miles from the Greater Peoria Regional Airport (Peoria, IL).

WIU-Quad Cities (Student Population: 1,235): The only public university in the Quad Cities area, WIU-QC offers select undergraduate and graduate programs, including a doctorate in education, at its metropolitan, non-residential campuses in Moline, IL (population 44,000). The Quad Cities (population 376,000) rests on the banks of the Mississippi River and is comprised of Moline and Rock Island in western Illinois and Davenport and Bettendorf in eastern Iowa. The Quad Cities is home to the Quad Cities International Airport.

Western Illinois University is accredited by The Higher Learning Commission and is a member of the North Central Association of Colleges and Schools. Information about the Commission may be obtained by visiting www.ncahigherlearningcommission.org.

Application Instructions:

APPLICATION: A completed application will include: 1. A letter of application, 2. Curriculum vitae, 3. Copies of transcripts, 4. A maximum of three reprints, 5. Statements of teaching philosophy and research interests, and 6. Please provide a list of references who will be requested to submit reference letters at a later time.

Please upload the requested documents by clicking APPLY NOW or by navigating to the WIU Employment page at the following URL http://www.wiu.edu/employment/

Screening will begin on February 25, 2013 and continue until the position is filled.

Questions regarding the search may be directed to: Dr. Charles Lydeard at AR-Brown4@wiu.edu.

For assistance with the online application system, please contact the Office of Equal Opportunity and Access at (309)298-1977.

postdoc and PhD positions in Fungal evolution at Uppsala University

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Two positions at Uppsala University in Hanna Johannesson’s lab at Uppsala University in Sweden are available. One is a PhD student position and one for a Postdoc working on experimental biology and using next generation sequencing techniques to address evolutionary questions.  Please see the ads linked for more information on applying for these positions.

Job: Junior Group Leader Functional Genetics and Genomics of Fungi

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Job Advertisement Junior Group Leader – Ref. #01-13001

The Senckenberg Society has an international reputation in all fields of Natural History research. It runs six research institutes and two museums in Germany and is also custodian of the UNESCO World Heritage Site at Messel.

From 1st of April 2013 we are looking for a

Junior Research Group Leader in Functional Genetics and Genomics of Fungi in the framework of a government funded LOEWE excellence cluster in “Integrative Fungal Research (IPF)” in Frankfurt am Main.

We are looking for an individual whose research will be adding significantly to the research aims of the LOEWE excellence cluster “Integrative Fungal Research”. The cluster includes researchers in mycology from Goethe-University Frankfurt a.M., Justus-Liebig-University Gießen, Philipps-University Marburg, University Kassel and the Senckenberg Society. The aim of the LOEWE excellence cluster will be to synergistically tie together the basic research areas of biodiversity research, molecular genetics, and genomics with translational research in biochemistry and biotechnology. Thus, the research cluster offers an ideal environment for scientific development and profiling.

Salary and benefits are according to a public service position in Germany (TV-H E14). The position is limited to three years, with the possibility of extension for two years in case of positive evaluation. Senckenberg advocates gender equality. Women and other underrepresented groups are therefore strongly encouraged to apply. The possibility of academic development (Habilitation, equivalent to assistant/associate professor) will be given.

Apart from the salary of the group leader, a competitive core funding for instrumentation, running costs and personnel will be provided.

Research expertise in the areas of comparative genomics and transcriptomics, annotation of metabolic pathways and regulatory networks, or systems biology of fungi or oomycetes are particularly welcome. Applicants should have an international track record and have demonstrated their ability to develop innovative ideas in their field of research. Previous experience with independent research is a plus but not mandatory. A record in third party funding acquisition is an advantage; willingness to acquire funding through research proposals is required.

Applicants are encouraged to submit their applications including a cover letter, CV, statement of research achievements, future research proposal (only one page, each), certificates (PhD, MSc, BSc, or similar) and the names of three scientists who could provide references. Applications should be submitted in a single PDF file by E-Mail to recruiting@senckenberg.de. Closing date for application is: January, 31th 2013

Enquiries about the LOEWE excellence cluster Integrative Fungal Research and regarding the position please contact directly Prof. Dr. Marco Thines (thines@bio.uni-frankfurt.de).

Flier