An announcement for FungiDB 2.3 is here and included below.

New genomes included in this release include

Botrytis cinerea
Sclerotinia sclerotiorum
Aspergillus carbonarius
Neosartorya fischeri
Trichoderma reesei
Schizosaccharomyces japonicus
Schizosaccharomyces octosporus
Phanerochaete chrysosporium
Sporisorium reilianum
Malassezia globosum
Mucor circinelloides f. lusitanicus
Mitochondrial genomes were added for the following organisms

Aspergillus fumigatus
Neurospora crassa
Saccharomyces cerevisiae
Schizosaccharomyces japonicus
Schizosaccharomyces octosporus
New genomics data available in this release include additional RNA-Seq experiments for Coprinopsis cinerea. High Throughput SNP (HTS) discovery module have been addded for Aspergillus fumigatus and a population of 23 strains from JCVI.

Data fixes and update

Updated in this release include new versions of annotation for

Aspergillus fumigatus – s03-m02-r18 from AspGD
Aspergillus nidulans – s09-m05-r03 from AspGD
Fusarium oxysporum f. sp. lycopersici – correcting some annotation problems in Broad v2
Neurospora discreta – correcting some annotation problems from JGI
Saccharomyces cerevisiae version from 2012-11-20
The current annotation for N. crassa is still v10 release and does not reflect the V12 release made March 2013. The updated version will be available in the 3.0 release of FungiDB.

Corrections

The Coccidioides RNA-Seq data in the previous release had flipped the labels of the spherule and mycelium results, this has been corrected.

Errors in previous loading of gene product information for P. sojae had left many genes without sufficient product information and description. This has been corrected.

Synteny results between several species were not properly loaded in the previous release. This has been corrected.

Data summary tables of genomes and gene metrics have been updated to reflect the current state of the database.

Known errors

Alternative splicing and starting/ending non-coding exons may not be properly represented in GBrowse and in the GFF files available for download.

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.

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.

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).

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)

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.

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 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.

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

Research Molecular Biologist in Fusarium

The incumbent serves as a Research Molecular Biologist in the Bacterial Foodborne Pathogens and Mycology (BFP) Research Unit, National Center for Agricultural Utilization Research (NCAUR), Peoria, Illinois.  BFP scientists conduct research in genetics, microbiology, chemistry, and plant biology to produce information and technologies needed to enhance food safety and crop production in the U.S. and around the world.  The incumbent will conduct research on the molecular biology and biochemistry of production and detoxification of Fusarium mycotoxins, and elucidate the role of mycotoxins and other secondary metabolites in plant-pathogen interactions.

Post-Doctoral Research Position, Colletotrichum genomics

We are seeking applications for a Post-Doctoral Researcher to study transcriptome and genome evolution of five closely related species of Colletotrichum fungi impacting the health and productivity of grasses used for bioenergy, food, and turfgrass.  The incumbent will: (1) Develop and test hypotheses related to infection and cellulolytic degradation of host tissue by diverse Colletotrichum strains, (2) Take the lead on performing inoculations of grasses with these pathogens for RNA-Seq analysis from the host/pathogen interaction, and (3) Contribute to a larger collaborative Colletotrichum genome sequencing initiative.

Using genomic and transcriptomic (RNA-Seq) resources provided through a grant from the DOE/Joint Genome Institute (JGI), we seek to understand the molecular basis of host specialization, pathogenicity, cellulosic biomass degradation and other traits that characterize this diverse, yet closely related group of grass pathogens.  Fully assembled genomic datasets will soon be available for 20 Colletotrichum isolates and mapped transcriptomes for 14 of these isolates.  Data analysis will be facilitated through inclusion in the JGI MycoCosm Fungal Genome pipeline.

The incumbent will work under the joint direction of Dr. Bruce Clarke, Rutgers University, Dept. of Plant Biology & Pathology, and Dr. Jo Anne Crouch, USDA-ARS.  The position will be physically located at the Rutgers University’s Cook Campus in New Brunswick, NJ.

Qualifications

A Ph.D. in plant pathology, microbiology, mycology or a closely related field is required.  Candidates should be proficient in working with large datasets, and must have strong analytical, statistical and writing skills.  Candidates with experience working with fungi and/or plant pathogenic microorganisms, or any of the following areas are especially encouraged to apply: next-generation sequencing datasets; comparative genomics using Galaxy tools; experience analyzing RNA-Seq data; population and evolutionary genetics; phylogenetics.  Skills in bioinformatics (python, perl, R, etc) are desirable.

Terms of Appointment

Starting salary is $37,000 – $45,000 depending on experience, plus Rutgers University benefits.  Funds are guaranteed for one year, and renewable for a second year pending satisfactory research progress and availability of funds.

Review of applications will begin January 23, 2013, and continue until a suitable candidate is found.

Applications should be sent to:

Bruce Clarke (clarke@aesop.rutgers.edu) and Jo Anne Crouch (joanne.crouch@ars.usda.gov) and must include: (1) a cover letter containing a brief description of research interests and career goals, (2) curriculum vitae, (3) PDFs of two publications, and (4) contact information for three references.

Rutgers University is an equal opportunity, affirmative action educator and employer. Applications from women and minorities are encouraged.

There might even be a way to use these projects to support mycology or genomics classes. For example one part of a class could work on isolation and growth of the fungi, obtaining RNA and DNA and sending this off to to the sequencing center. The rest of the class would be spent analyzing existing fungal genomes. In the subsequent year the nominated genome would likely be completed and the next year’s class could work on processing it.

I made a NCBI PubMed Collection of these here Fungal Genomes 2012

Some notable fungal genome publications include

• the button mushroom Agaricus bisporus (your pizzas would never be the same without it)
• plant pathogens Colletotrichum
• comparative analyses of 18 genomes from plant associated Dothideomycetes
• new microsporidian genomes including two new Encephalitozoon and C. elegans parasites helping resolve some phylogenetic position of these fungi also explored in another paper.
• multiple genomes of the wine spoilage yeast Dekkera
• the Chinese medicinal mushroom Ganoderma
• the barley pathogen Ustilago hordei and comparison with maize pathogens U. maydis and Sporisorium reilianum
• human pathogen Candida orthopsilosis and comparison with its close relative C. parapsilosis.
• the basal basidiomycete and xerotolerant Wallemia sebi
• The transcriptome of Glomus intraradices

There were also several new insights into the evolution of wood decay fungi derived from new genomes of basidiomycete fungi. This includes

• the tree pathogen Heterobasidion annosum
• the white rot fungus Ceriporiopsis subvermispora
• a draft of the brown rotter Fibroporia radiculosa
• a magnum opus reconstructing the evolution history of lignin degradation in basidiomycete fungi in “The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes“.

(Now I might have missed a few in my attempt to get this done before holidays overtake me – if so, please post comments or tweets and I’ll be sure to amend the list on pubmed and here.)

A new trend for fungal genome papers can be seen now in the Genome Announcements of Eukaryotic Cell which aim to get the genome data out quickly with a citateable reference. These are short descriptions which I expect will become more popular ways to insure data made public can also be cited. I only counted about 5 published in 2012 but I expect to see a lot more of these in the 2013 either at EC or other journals. I’m sure there will still be some tension between providers making data public as soon as possible and the sponsoring authors’ desire to have first crack at analyzing and publish interpretations and comparison of the genome(s). The bacterial community has been doing this for Genome Reports in the SIGS journal and the Journal of Bacteriology so will see what happens as these small eukaryotic genomes become even easier to produce.

I look forward to exciting year with more of the 1000 Fungal genomes and other JGI  projects start to roll out more genomes.  I also predict there will be many more resequencing datasets published as functional and population genomics. It will also probably be a countdown for what are the last Sanger sequenced genomes and how the many flavors of next generation sequencing will be optimized for generation.  I am hopeful work on automation of annotation and comparisons will be even easier for more people to use and that we start to provide a shared repository of gene predictions.  I’ve just launched the latter and look forward to engaging more people to contribute to this.

Dec 12 is also the deadline for satellite meetings including organism specific focus meetings. The 10th Aspergillus meeting, 6th Ustilago meeting, and the Fusarium workshop will take place on the days before the FGC meeting. There are opportunities to present talks and posters at this meeting and many openings for more abstract submissions, so if you’d like the chance to give a talk on your work in one of these species, this is a great opportunity.  You need to register separately for the satellite meetings – go here to register and submit abstracts.

The Oomycete Molecular Genetics Annual meeting will also take place in the days before FGC (March 10-12) but the registration deadline isn’t until end of January.

Institute of Molecular Biosciences invites applications for the following position: JUnior Professorship (W1) for Biochemistry and Biotechnology of Fungi 

We are seeking a scientist with research activities complementary to the activities in the LOEWE priority program “Integrated Fungal Research”. The newly established priority program brings together scientists from four hessian universities and a Leibnitz Institute, all working in different areas of mycology ranging from fungal biodiversity, molecular biology and genomics to applied aspects of fungal biotechnology and biochemistry.  Possible areas of research could be biochemistry and biotechnology of ribosomal peptides, alkaloids, unusual amino acids, or sugars in fungi, the production of biotechnologically relevant products in fungal model organisms (like Aspergillus, Penicillium, Yarrowia or Rhodotorula), or fungal cultivation technologies.  Candidates must have an excellent publication track record. The successful applicant is expected to engage in crossdisciplinary research activities, as well as to compete for research funding actively. Willingness to participate in the LOEWE priority program “Integrated Fungal Research” is expected.

The position comes with adequate administrative and teaching obligations within the Institute of Molecular Biosciences.  The junior professor will be hired for a period of three years.  An extension for another three years can be granted subject to a successful evaluation. The designated salary for the position is based on “W1” on the German university scale. For further information regarding the general conditions for professorship appointments, please see: http://www.uni-frankfurt.de/aktuelles/ausschreibung/professuren/index.html.  Qualified scientists are invited to submit their applications accompanied by the usual information, such as CV, degrees and certificates, list of publications, details about teaching and international experience, information on grant applications and a concept for future research and teaching within three weeks of publication of this announcement. Please send applications preferentially by E-Mail in a single PDF file to the Dean of the Faculty of Biosciences,

Prof. Dr. Anna Starzinski-Powitz, Johann Wolfgang Goethe-University Frankfurt, Maxvon- Laue-Straße 9, 60438 Frankfurt/M. Germany, E-Mail dekanat1[AT]@bio.uni-frankfurt.de.

Details regarding the LOEWE priority program “Integrative Fungal Research” can be obtained from Prof. Dr. Helge B. Bode (h.bode[AT]bio.uni-frankfurt.de) or Prof. Dr. Marco Thines (thines[AT]bio.uni-frankfurt.de).

The incumbent will generate strains of fluorescent protein-labeled C. pseudonaviculata and inoculate susceptible and non-susceptible boxwood plants to evaluate the infection process and fungal development in planta. Available bio-imaging platforms will include digital light microscopy, fluorescence microscopy, confocal laser scanning microscopy, variable pressure and low temperature scanning electron microscopy (SEM), and the Oxford X-ray Diffraction System for qualitative and quantitative identification of chemical elements. The incumbent will simultaneously generate RNA-Seq data from the host/pathogen interaction to develop hypotheses related to the colonization of hosts by this pathogen.

The position is based on the campus of the USDA-ARS Henry A. Wallace Beltsville Agricultural Research Complex in Beltsville, MD, the world’s largest and most diverse agricultural research center, located just 16 miles north of the U.S. capitol city of Washington, D.C. The incumbent will work under the guidance of Dr. Jo Anne Crouch at the Systematic Mycology & Microbiology Laboratories and in collaboration with Dr. Gary Bauchan at the on-site core Electron & Confocal Microscopy Unit. The Crouch lab is part of a multidisciplinary, multi-state collaboration between the USDA-ARS, the U.S. National Arboretum, the IR-4 Project, and eleven university and experiment station research groups, working in cooperation with the nursery industry in an integrated, coordinated effort toward the common goal of understanding and mitigating boxwood blight disease.
* Qualifications *
This position requires a recent (within 4 years) Ph.D. in plant pathology, microbiology, mycology, molecular biology or a closely related field that has equipped the applicant with the necessary knowledge, skills and abilities to perform the duties and responsibilities of the position. Knowledge of fungal transformation, advanced microscopy techniques, biostatistics and transcriptome analysis are desirable. Demonstrated ability to conduct experiments independently, produce quality research output and a strong publication record are required.

* Terms of Appointment and Application Instructions *
This is a two-year appointment, at the GS-11 level (starting salary $62,467).

Citizenship restrictions apply. Eligible Foreign Nationals must meet both Appropriations Law and Immigration Law requirements found under “Foreign Nationals Eligible for Federal Employment” at http://www.afm.ars.usda.gov/hrd/EmployForeignNationals/index.htm.

Visit the following website for instructions on how to apply for the position: https://www.usajobs.gov/GetJob/ViewDetails/331850000.

Informal inquiries are welcome: Dr. Jo Anne Crouch, joanne.crouch[AT]ars.usda.gov
ARS is an equal opportunity provider and employer. Women and minorities are encouraged to apply.

Review of applications will begin immediately, and continue until a suitable candidate is found.

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)

An alpha version of the ITS reference database for use with QIIME was released this week as part of the QIIME team development. There are more details on the release and how to obtain it from the project’s post here.

Please note that this is an Alpha release and may not be completely consistent, but the team wants to make something available now to give people a starting DB for use of QIIME and ITS data.  Parameters will need to be modified from the defaults, so watch the QIIME space, and we are working on a best practices document in the lab here to help ease the training in this.

All the data are also in a github repository and this is built starting from the database provided and curated by the UNITE team. I love that the data are getting version controlled here so it is easy to look at versions and revisions.