Category Archives: opinion

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.

Vote for your favorite plant pathogenic fungus

Molecular Plant Pathology (twitter: MPPjournal) is engaging the community to vote for their favorite plant pathogenic fungus. Below is info requesting your vote.

As a member of the MPP community we would like you to take part in a fun but informative vote.

We aim to publish a Review detailing the top 10 plant pathogenic fungi worldwide, and we need your help.

Please could you list 3 fungi you feel should be in the top 10.
There is no need to rank them. Please state after the name whether it is for
scientific impact (SI) or economic impact (EI).

An example might be…

Magnaporthe grisea (SI/EI)
Melampsora lini (SI)
Botrytis cinerea (EI)

We will rank all the entries to compile a list. We will then find authors to write a short piece (1/2 page or so) on each one, introducing the pathogen and explaining its importance. This Review will be published in MPP for people to use, comment upon and discuss.

We hope you will take part, it will only take a few seconds of your time.

Please send your vote to diane.hird[AT]bristol.ac.uk by 11th February at the latest.

Feel free to pass on this email to any colleagues or co-workers as the more votes we get the better. Many thanks

Best wishes
Diane

-------------------------------
Dr Diane Hird
Journal Administrator
Molecular Plant Pathology
School of Biological Sciences
University of Bristol
Woodland Road
Bristol, BS8 1UG, UK

Tel/Fax: +44 (0)117 331 7021
Email: diane.hird[AT]bristol.ac.uk

In bookstores now

I am excited to dig into the newly published Cellular and Molecular Biology of Filamentous Fungi edited by my next door neighbor Katherine Borkovich and Daniel Ebbole from Texas A&M which was recently published by ASM Press.  The book is a comprehensive look at biology of filamentous fungi including ascomycetes and basidiomycetes and covers cellular biology and structure, metabolism, growth, organelles, photobiology, sexual and asexual development, and mutualistic and pathogenic interactions with plants & animals.  I’ve yet to get my own yet but I’ve leafed through a copy and this looks to be an excellent reference for those wanting a review of current knowledge on many aspects of fungal biology and I anticipate important reading for new students and postdocs in the field.

A word about databases

Logo for fungal GenomesReport concludes that a fungal genome database is of “the highest priority”.

This is the title as listed in PubMed for this article from Future Medicine about the AAM report on charting future needs and avenues of research on the fungal kingdom.

The need for a comprehensive database for information about fungi, starting at least with systematic collections of genomic and transcript data, is highlighted as a major need.  Really and sort of new database effort should strive to be more comprehensive and include genetic and population data (alleles, strains) and information like protein-protein, protein-nucleic acid interactions (as Pedro mentioned). But on top of that it, it needs to be comparative so that information from systems that serve as great models can be transferred to other fungal systems that are being studied for their role as pathogens or interacting in the environmental.

Affordable next-gen sequencing will allow us to obtain genome and transcript sequence for basically all species or strains of interest.  Researchers with no bioinformatics support in their lab will likely be able to outsource this to a company or campus core facility.  But how can they easily map in the collective information about genes, proteins, and pathways onto this new data?  And have it be a dynamic system that can update as new information is published and curated in other systems.

I think this has to be the future beyond setting up a SGD, CGD, etc for every system.  The individual databases are useful for a large enough community where there are curators (and funding), but we will have to move to a more modular system in the future (aspects of which are in GMOD) that can have both an individual focus on a specific species/clade and a more comprehensive view of the that is comparable across the kingdom.  There are 100+ fungal genomes, but the community size for some of them are in the dozens of labs or less. How can they take advantage of the new resources without an existing infrastructure of curators?  Their systems serve an important need in a research aim, but how can discoveries there make its way back into the datastream of othe systems?

I see it as there are several ways one would interact with a system that provided single-genome tools as well as a framework for comparative information.  At a gene level, one might be looking for all information about a specific gene, based on sequence similarity searches, or starting with a cloned gene in one species. Something akin to Phylofacts or precomputed Orthogroups for defining a Gene but with more linking information about function by linking in information from all sources.  So a comparative resource, but also tapping into curated andliterature mined data.

At a genome level, one might want to do whole genome comparisons of gene content from evolutionarily defined families genes (gene family size change) or at a functional level.  To start out with, each gene/protein would already need a systematic functional mapping.  This could be as simple as running InterProScan on every protein, expanded to find Orthogroups (or OrthoMCL orthologs) and transfer function from model systems, and finally even more advanced, do further classified better with tools like SIFTER.

Interlinked with these orthologous and paralogous gene sets would be anchors for analyses of chromosomal synteny and even comparative assembly including tools like Mercator.  Certainly things like all of this exist but making it more pluggable for different sets of species would be an important additional component.

At a utility level, the gene annotation and functional mapping of all this information should be possible. I would imagine a researcher could upload the sequence assembly they received from the core facility and the system can generate multiple gene predictions, annotate the genes, and link these genes within the known orthogroups of the system (preserving their privacy for these genes if desired).  Presumably this sort of thing would be easier as a standalone in-house for the researcher, but web services could also be the place for this.

For fungal-sized genomes this amount of data is not too extereme.  Things like Genome Browser, BLAST, etc should all be rolled out of the box based on the basic builds.

On the DIY and community annotation front, there would also need to be a layer of community derived annotation that could be layered on all these systems.  I would imagine this both to be for gene structure annotation (genome annotation) and functional annotation (protein X does Y based on experiment Z, here is the journal reference).  I think aspects of this would be visible, auditable (tracked), but maybe not blessed as official until a curator could oversee these inputs. In my mind, whether or not this is in a Wiki per se or just new system that allows community input is less important to me than having it be a) structured (not a bunch of free text) b) tracked and versionable c) easy for researchers to input so that the knowledge is captured, even if it has to be reorganized later on.

Seems like a lot of work to be done, but really many of these things already exist through what  the GMOD project has built.  Many loose ends and software that doesn’t fully meet up to these needs, but I think the important concept is these are all general solutions that will be of benefit to most communities, not just the fungal ones.  One lingering question I always have when approaching genomic datas

that will be dynamic, what if any of this makes its way into GenBank?  How is this sort of thing banked so that it can be captured, and does the improved functional or gene structure annotation ever make its way into the repository databases to correct and improve what has already been submitted there?