Category Archives: news

WRIFO: Women Researchers in Fungi & Oomycetes

In an effort to promote the diversity of women in fungal and oomycete biology research we started a list of Women Researchers in Fungi & Oomycetes (#WRIFO) in our fields. We hope this will make it easier for conference, seminar and award committees to consider a broad pool of candidates when inviting speakers or nominating individuals.

We seeded the WRIFO list with 150 women whose research we know or who were suggested by colleagues, but it is by no means complete. Please add names and add missing details to those already on the list. The WRIFO list is available as a google spreadsheet here (shortlink: http://s.fungidb.org/1SU45hk ). As an experiment in community dynamics WRIFO is an open sheet for editing. We will change this to “make comment-only” after a time to try to avoid getting overrun with spam. If you cannot add to the WRIFO list directly, comments on this post are accepted. However direct adding is preferred to avoid losing track of any suggestions.

As a test for how many will read directions:

  1. Please add new entries at the end of the sheet rather than trying to insert alphabetically.  You can always re-sort the sheet by last name after entries are made
  2. List institution, include 2 letter country code in parentheses.
  3. Select region from the available options.
  4. Pick up to two general research areas from the drop down lists.
  5. Add specific Keywords for research.  Make these as general as possible–a meeting organizer is much more likely to search “cytoskeleton”, than “tyrosinylated microtubules.”
  6. Include a laboratory website link. Use publicly available websites that do not require memberships to view
  7. Select the classification of career stage. Mapping this to job titles in the US
    • Junior: Assistant Professor, Assistant Research Scientist, or equivalent
    • Intermediate: Associate Professor, Associate Research Scientist,  or equivalent
    • Senior: Full Professor, Research Scientist or equivalent
    • Emeritus

–Michelle Momany (@mcmomany) & Jason Stajich (@hyphaltip)

Update 1: A landing page was made for info on WRIFO and where archive and Excel versions of the spreadsheet will be made available.

Remembering fungal genetics legends

The passing of two members of the fungal genetics community has saddened many of us but also brought smiles in remembering all the wonderful things they brought to the community. So sending this out to ask you to take some time to remember Rowland Davis  and Hans Van Etten who have passed away in the past month.

Rowland Davis, an eminent figure in the fungal genetics community, died on 18 July at his home in California. Rowland was 81 years old. He made many contributions to the community as a researcher, as an editor and reviewer, as a mentor, and as a valuable source of wise counsel, always delivered with intellect and humor. As a graduate student at Harvard University he developed an interest in microbial genetics and began to work with Neurospora. As a postdoc at Caltech with Herschel Mitchell he started his lifelong involvement in biochemical genetics. His early years as a Professor were at the University of Michigan (1960-1975). He subsequently moved to the Department of Molecular Biology and Biochemistry at the University of California, Irvine and became Emeritus in 2005. Rowland’s graduate research focused on heterokaryosis. As a young assistant professor he began to investigate the pyrimidine biosynthetic pathway, discovering that the pyr-3 gene encoded two catalytic activities – one of the first examples of “one gene, two enzymes.” He then went on to show that carbamyl phosphate, required for two different metabolic pathways, was synthesized by the enzyme products two different genes, each in a different organelle. This was a foundational discovery in understanding the role of compartmentation in the regulation of metabolism. He pursued this with seminal studies of arginine metabolism, showing that 99% of cellular arginine is sequestered in vacuoles, thereby avoiding wasteful catabolism by enzymes in the cytosol. In the latter half of Rowland’s career, he investigated the enzymes responsible for synthesizing polyamines. His lab group identified the genes that encoded these enzymes, discovered novel mechanisms by which polyamine levels are controlled, and described the systems by which polyamines were transported across the cell membrane. Rowland was a key player in the decision to open the Neurospora Information Conference to the larger Fungal Genetics Community. He served this community in many ways. He was a supportive presence on NSF and NIH review panels and a long-term Editor for Genetics. He wrote the definitive “methods guide” for Neurospora (Davis and De Serres, Methods in Enzymology, 1970). The breadth of his knowledge is illustrated by his book, Neurospora, Contributions of a Model Organism (Oxford, 2000). In his retirement Rowland pursued his life-long interest in writing by publishing two novels (co-authored with his wife Margot [Norris] Davis) and a collection of short stories. Rowland was always available to help people. Young and not-so-young investigators went to him to discuss research ideas, grant proposals, and manuscripts. He was a superb teacher at all levels, delivering flawless lectures to huge undergraduate classes and providing hands-on instruction to graduate students. He will be greatly missed. — Barry Bowman, Neurospora Policy Committee

Hans Van Etten finished his career at University of Arizona and trained so many scientists and students. I have heard some great stories from student who took his classes, or where he sat on their committee, those who trained in his lab, or collaborated with him on research all remark on what a positive and enthusiastic person for the science and for the people he worked with.  A longer remembrance from those who can tell even better stories will be circulated soon I am sure but I wanted to just post something now to note his passing.

 

 

 

An open letter to the fungal research community regarding genome database resources

An open letter to the fungal research community regarding genome database resources (from the Broad Institute & FungiDB/EuPathDB):

As many of you are already aware, fungal genome websites at the Broad Institute are undergoing a major transition. These resources were originally developed in support of sequencing projects, many of which have long-since been completed. While we have tried to keep such sites operational for as long as possible without funding, infrastructure changes now underway will make these websites nonfunctional over the coming weeks. We are therefore replacing formerly interactive websites with a static page providing information on fungal projects, along with links to the Broad FTP site where datasets can still be downloaded, and links to NCBI – the primary repository for all genomic data, where all genomes and annotation have been deposited and can be accessed, queried, and downloaded. We are also working to incorporate genomic data into other sites that support comparative analysis of fungal genomes, including FungiDB and MycoCosm.

The EuPathDB family of databases (funded by NIAID/NIH and the Wellcome Trust) supports a wide range of microbial eukaryotes; FungiDB includes many fungal (and oomycete) species, including non-pathogens. This resource has been designed to provide sustainable, cost-effective automated analysis of multiple genomes, integrating curated information (when available), with comments and supporting evidence from the user community (PubMed IDs, phenotypic information, images, datasets, etc). In addition to gene records, browser views, and data downloads, FungiDB offers sophisticated tools for integrating and mining diverse Omics datasets that fungal biologists will find quite useful. See the sidebar on the FungiDB web site for access to tutorials, videos, and exercises.

MycoCosm (supported by JGI/DOE) offers the largest available collection of fungal genomes, for comparative genomics across phylo- and eco-groups, along with interactive web-based tools for genome downloading, searching and browsing, and a form for nominating new species for sequencing to fill gaps in the Fungal Tree of Life.

For many years the Broad has been pleased to work closely with various fungal research communities, and we will continue to work with EuPathDB and MycoCosm to transition data valued by the community. Please direct any inquires or requests for help to help@FungiDB.org

Apply for EuPathDB workshop

Dear Colleague,

We are pleased to announce the 10th annual EuPathDB workshop to be held in Athens, Georgia, USA from May 31 – June 3rd, 2015.

Learn how to effectively use EuPathDB resources and mine available data to help guide your research.

For more information and to apply, please visit: http://workshop.eupathdb.org/current/

*********************

Databases covered: EuPathDBAmoebaDB, CryptoDB, FungiDB, GiardiaDB, HostDB, MicrosporidiaDB, OrthoMCL, PiroplasmaDB, PlasmoDB, ToxoDB, TrichDB, TriTrypDB

Costs and Fees: The course is free. Housing, all training materials and lunches are covered. Attendees are expected to provide their own transportation to the course and pay for a few of their meals. Letters of acceptance will be mailed early to facilitate the solicitation of outside travel funds.

When: 6:30pm on Sunday, May 31 to 5:00pm on Wednesday, June 3, 2015

Where: University of Georgia, Athens, GA, USA
Davison Life Sciences Building, room C128.

Application deadline: February 1, 2015. Click here to apply. NOTE: Deadline extended apply before Feb 20!

If you have any questions or concerns please email help@eupathdb.org

Mary Berbee’s MSA outgoing presidential note

Mary Berbee has a lovely tribute to the spirit of the Fungal Genetics community in her last President’s column for the MSA newsletter Inoculum. She mentions the great joy she got in the insight from people like Bob Metzenberg and their engagement with the community. I would also equally mention David Perkins as someone who saw the success of the community as being the same as his own success and worked hard to help others use Neurospora in their own work.

I quote her parting thanks which I think speak well for what we can all aspire for in being participants in the scientific endeavor. So remember – ask questions ! – curious and insightful thoughts benefit us all.

Thanks to everyone who:
Asks questions in meetings, especially if the questions help make us all participants in shared and exciting scientific discovery.

Puts their sequences in GenBank, their strains in
culture collections and sends all of the above to
colleagues on demand whenever possible; and
writeslettersin support of these and other kinds of
science infrastructure. Once lost, the damage to
these resources cannot be undone.

Submits a timely, kind and incisive review of a
paper or grant that highlights the importance in the
work and encourages more and better of the same.

Helps a student or colleague do the best research of
their lives, by sharing ideas and encouraging creativity.
Makes our discipline an exciting home by writing
important papers for a broad audience.

Applies care, thought and enthusiasm in the many
volunteer roles that make our journal, our meetings
and our society work as well as they do.

I hope we continue to honor those who are working hard for the good of their respective scientific communities, even before they reach retirement and beyond. So thanks to Mary and the MSA leadership as well those of other societies which keep the field moving forward. I know I don’t take it for granted the work that these volunteers do.

FungiDB 2.3 released with 52 genomes

The latest release of FungiDB (2.3) is now live and includes 52 genomes, 11 of which are new for this release. This was a longer than expected release cycle due to reintegration with the EuPathDB software team. Programmers Raghu Ramamurthy and Edward Liaw at UC Riverside did nearly all the Fungal specific work, collaborating closely with the EuPathDB team who provided many site-specific corrections and assistance in running the workflow. This is a joint collaborative project between the UCR,Oregon State (FungiDB) and U Penn, Univ of Georgia (EuPathDB) and the work in this release was funded through grants from the Burroughs Welcome Fund, the Alfred P. Sloan Foundation, and the USDA-NIFA.

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.

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