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.
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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. 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. 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. 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. 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. Did you know one of the master brewers at Guinness was also the inventor of the Student’s T-test? Here’s the proof 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 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 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. Well the 1st quarter is over and had a few observations about life of an assistant professor.
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!
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. |
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