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March 2010
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Back from Ireland

I am back from a short trip to Ireland where I gave a seminar at National University of Ireland, Maynooth and spend some time with folks interested in evolution or fungi like David Fitzpatrick, James McInerney, Davide Pisani. I also learned about a new spinoff company from one of the faculty producing media that will help Bee immune systems. In my chats with some of the faculty I found out that I had lots in common with Sean Doyle on Aspergillus and some basidiomycete genomics questions and also much in common with Gary Jones working on prions in yeast.  After my trip to Maynooth, I spent a few days in Dublin afterwards to see the town which included a visit with some Dublin yeast researchers Ken Wolfe and Geraldine Butler who took me out to see Newgrange.

I learned that there is an abundance of yeast research in Ireland.  In addition to the researchers there is a whole shop devoted to Yeast.
The Irish Yeast Co
And my visit to the Guinness Brewery at St. James Gate taught me that that Yeast is a national treasure in Ireland.
Yeast!
Complete with an important safe for insuring there are backup strains. I have to assume there is a -80 freezer somewhere in the Guinness complex holding old strains as well.
P1000438-20100309

Did you know one of the master brewers at Guinness was also the inventor of the Student’s T-test? Here’s the proof
P1000436-20100309

So it was great to visit and look forward to going back at least in 2012 when SMBE will be held in Dublin.

PLoS Pathogens Pearl published

PLoS Pathogens has a short review format called Pearls.  We were invited to write a short summary on Batrachochytrium which was published in the January issue.

Rosenblum, E., Voyles, J., Poorten, T., & Stajich, J. (2010). The Deadly Chytrid Fungus: A Story of an Emerging Pathogen PLoS Pathogens, 6 (1) DOI: 10.1371/journal.ppat.1000550

Lab news for January

A quick January update.  Jason was appointed to a two year term as Councilor for Genetics/Molecular Biology for the Mycological Society of America, began a term on the editorial board of Eukaryotic Cell, and was also profiled in the GSA reporter. Finishing grants and working towards completing manuscripts from postdoc-land while we are computing results on from genome and RNA-Seq datasets. Working to getting our laboratory production up and running to generate more of our data.

Currently the lab is four strong with 3 graduate students. They are Divya Sain and Yi (Zoe) Zhou who have joined for the long haul of doing a PhD in the GGB program, and Yizhou Wang, a rotation student from Plant Biology.  Divya is working on a project that uses bioinformatics and phylogenetics to reconstruct history of the genes involved in the fungal cell wall across the fungi.  Zoe is using bioinformatics and phylogenetics to focus on duplicated gene evolution and is exploring other aspects of duplication in fungal genomes.  Yizhou will be getting going in the laboratory learning how to grow Neurospora and preparing some RNA extractions for some transcriptomics and RT-PCR validation.

In February John Abramyan will join us as a postdoctoral scholar to work on some molecular biology and genomics work on at least two fungi along with applying  bioinformatic analyses of these data.

I also setup the Gbrowse2 for Sordaria and Coprinopsis, worked on some new template themes for the blogs, and we setup a bioinformatics group website at UCR (which is still coming together). Hoping the rest of Jan and Feb will be clearing a few more to do things off the list and getting a chance to do a bit more research blogging on the Hyphal Tip.

Down to San Diego

Although I’m not going to be at PAG this year, I’ll be in San Diego for  the BioPerl and part of the GMOD meeting on Wed and Thursday.

Lessons from the 1st Quarter

Well the 1st quarter is over and had a few observations about life of an assistant professor.

  1. Remember to check that you don’t need to turn in grades! I thought I could safely ignore emails about sending in grades, since I wasn’t teaching this quarter, but meant I forgot to turn in grades for grad students working in the lab. Whoops! Lesson learned.
  2. Spending money isn’t that hard, but researching how to spend it on equipment is time consuming.  The optimization of trying to find the best deal, planning for current and future experiments, and establishing new technologies took more time than I expected.  Planning how to best spend money longer term is also taking some time, I don’t know if there is any good formula to rely on because it depends on what future grant support is awarded. But I think that I am getting better at making the equipment decisions – but I am my own sysadmin for macs in the lab and also the new separate (from the shared bioinformatics cluster) linux machines I have for our web and specialized compute needs and find that very time consuming.
  3. Travel is good, but takes up time that can be spent writing, instructing, and my own research. While I can do much of my research from my laptop and an internet connect, I am distracted when away from lab and doing a disservice to the meeting I am attending if I am always working while on the road.  Better to divide my time better and focus on the meeting at hand. Course this means I should always have the talks finished before I get to the meeting and that has been difficult to guarantee.
  4. People are important. I can’t do all the research myself. Getting students and postdocs into the lab who can be trained on techniques and the background of the research questions is the most important thing to get the lab moving forward.  I am excited about the teaching and learning process but it is a process that needs a vision and schedule that I establish.  I’m still fine tuning that schedule and the approaches while keeping us aimed toward a vision of the kind of research we will do in the next 3-5 years.
  5. Time flies – take stock of how you spent it! Stopping and reflecting on what was accomplished is good to remind me and remind trainees that we have done things even if it feels like there is a mountain of work ahead.  As the gets better at this I’ll probably be able to give better feedback about dead-ends and keeping people on track earlier in the game.  We are still getting our timing together to have regular lab meetings and journal clubs that I expect to be the heart of the learning that happens in the lab at this point. I’m teaching programming, bioinformatics, phylogenetics & molecular evolution, and mycology at the outset and so am working to make these subjects more approachable with the right kind of background reading materials.  Probably will have to turn this into a review or primer someday as I feel like this synthesis of different fields is not something I can point anyone to just one or two resources for.

I’m still getting aquatinted with who to ask for help and where to go for advice, but I’ve been lucky to have generous junior and senior colleagues who have provided encouragement and advice.  Here’s to hoping next quarter I learn a little more about how to do things, focus on the grant writing, and make some tangible progress on the research projects that need some new data before this summer. A lot of papers are queued up from collaborative work that were submitted this month and I hope that means more focus on the two main project foci of the lab.  New folks will be joining us next quarter and I’m excited about the progress we have made and will be able to make as everyone comes up to speed.

Happy New Year!

BioPerl on TWiT.tv

 

Chris Fields and I spoke about BioPerl past and present and tried to convince computer science types that biology is in fact interesting on TWiT.tv FLOSS. Check out the podcast for Episode 96.

Slides from Nov talks

A talk today in the CS department on open problems in bioinformatics and hope to entice some computer scientists to work on more of the problems here. Here are the slides in PDF and on SlideShare.

I also had a chance to present some work at UCLA in their Bioinformatics series and the PDF and SlideShare are available.

Back from EMBO mtg

Back from an excellent meeting in St Feliu du Guixols for the EMBO Comparative Genomics of Eukaryotic Microorganisms. Not a strictly fungi focused meeting, but lots of genome comparisons of yeasts and molds were presented.  It will be held again in 2 years so mark your calendars as it is a great scientific exchange and a beautiful location. Sophien posted the group photo.

IMG_6934-20091027Hotel Eden Roc

A primer on the Fungi

Our primer on the Fungi is available (currently free) on the Current Biology website.  A version with extra refs inserted is available in pre-print format here. In this primer we provide a broad overview of the major evolutionary defined groups within Fungal kingdom. Our intention is make the kingdom a little less mysterious for non-mycologists and introduce some open areas of research that require integrating evolutionary, morphological, and molecular research. This was joint work with Mary BerbeeMeredith BlackwellDavid HibbettTim JamesJoey Spatafora, & John Taylor.

Also thanks to several people for access to images: Jeffrey RollinsSabine HuhndorfDavid McLaughlin & lab, George L BarronGreg Jedd and Michelle Momany.

 

Abstracts wordle

Making some signs for the doors to offices.  Here’s a Wordle plot from abstracts of last 7 years of papers. Tip the hat to M. Dunham for the idea to make it part of the lab signs.

 

Wordle for StajichLab (2009)

Wordle for StajichLab (2009)