Lab Tweets

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July 2010
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Our work on the cover

Our work on the mushroom genome of Coprinopsis cinerea is featured on the cover of this week’s PNAS.  Check out the blog post and the article.

A sendoff for the lab visitor

We bid farewell last weekend to our lab visitor, Nastassa Gioti, who is headed back to Sweden after 6 fun weeks in Riverside.  We learned from her, and she got to dig into her genome datasets for Neurospora in the context of the comparative and genome annotation tools we have, so it was fun all around!

This also marked the second get together (but the first where we remembered to bring a camera). Since we gathered at a local mexican restaurant with whimsical and amazing sculptures and art from recycled material, it was fitting we document it with pictures.

Everyone together for a meal

P1010092_0526

Concrete mushrooms
The air band...

A whirlwind spring

Spring is flying along. We’ve been presenting some of our work at conferences and getting ready for a full summer of meetings and Divya preparing for her qualifying exam.

A few papers have come out or are now accepted. One I’ll highlight here is the publication of the Sordaria macrospora genome.  This was a fun collaboration with groups in Germany, France, Oregon State, and Edinburgh where we sequenced Sordaria with 454 and Illumina sequence and assembled the genome using de novo assembler and comparative scaffolding to the available Neurospora genomes.  Sordaria is an important model system for sexual development and provides a great evolutionary not-too-distant outgroup to the Neurospora clade for evolutionary genomic analyses we are trying to finish off.

Also have had a chance to interact with colleagues at the JGI User meeting, the Neurospora conference, and a special treat of speaking at the PBoFF symposium at Texas A&M.

Everyone is getting their projects underway in the lab and we’ve had two visitors come to work on Neurospora and Chytrid genome project analyses so a busy but exciting time for us.

Several more weeks left in the quarter where I’m teaching introductory biology and  then the Gordon Conference, MSA, and IMC9 will be conferences to finish preparing for.  The lab will also be represented at Evolution meetings in Portland as John attending.

Fusarium mobile chromosomes

Congrats to graduate student Divya Sain a co-author on a paper published in Nature on mobile chromosomes in Fusarium, stemming from her work her work during a rotation in the Borkovich laboratory.

The work highlights the important aspect of how pathogenicity factors can be exchanged via mobile chromosomes and can be an important pathway for adaptive evolution and acquisition of new function through whole chromosome exchange between strains.

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.