Congratulations Dr Yizhou Wang

The end of the quarter was a blur but I wanted to properly congratulate Yizhou Wang. Dr Wang successfully defended his PhD in December and submitted his dissertation “Discovery and Properties of Small RNAs from Meiotic Silencing by Unpaired DNA in Neurospora crassa”  in the Plant Biology graduate program. He is our newest graduate from the lab and we couldn’t be happier and proud for him. He was able to complete a concentration MS in Statistics at the same time and was able to master bioinformatics and data analysis of next generation sequencing and comparative genomics along with small RNA Northerns, Southern Blots, and Neurospora culturing and care. He has been a great asset to the lab and I am delighted that he has finished this part of his education and training and excited for his next steps.

Yizhou_Asilomar_1He is serious about his cooking, treating us to some great meals from BBQ to a Chinese seafood extravaganza.
Yizhou_cooking

New Zygomycete evolution project in lab

A new NSF funded project on Zygomycete fungi was recently funded. The press release from UCR and NSF provide some more information on the scope of the project and the goals of the new Genealogy of Life initiative at the NSF.

We’ll be sharing news, data and protocols, and progress on the project website ZyGoLife.org and @zygolife  and looking to recruit one graduate student and some undergraduates to work on the projects in our lab focused on genomics and phylogenomic studies of these diverse lineages.

IMC10 – Bangkok, Thailand

I had the great opportunity to attend the International Mycological Congress 10 in Bangkok, Thailand during this summer. It was filled with talks from mycologists studying cell biology, genetics, evolution, symbioses, ecology, production of secondary metabolites, and many other aspects of mycology from across the world. It was a great chance to hear about new work in many different experimental systems.  I chaired a session on Population Genomics and GWAS in Fungi and got to hear some great perspectives and approaches on model and non-model systems. I presented my talk on data analysis tools in metagenomics. I got to catch up with many friends/collaborators/colleagues and meet some new folks.

I’m jealous of the folks who got to take some of the post-conference excursions through Thailand or ventured even further to Laos and Cambodia. Hopefully next trip to this area I’ll have the chance to explore more.

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Fig1_Mucormycotinacellwall

Mucormycotina cell wall paper published

Congrats to Divya and Jason as our paper with collaborators Hugo Melida and Vincent BuloneDeciphering the uniqueness of Mucoromycotina cell walls by combining biochemical and phylogenomic approaches is now available at Environmental Microbiology. We discovered in this work that two Mucormycotina species have novel fucose sugar composition in their cell walls which is not found in other Fungi. We also identify expansions and unique subfamilies of Chitin synthase genes.

Fig1_Mucormycotinacellwall

MSA 2014 fungi-fun

Steven and Jason attended the Mycological Society of America’s 2014 conference in East Lansing, MI. This included  coming in a day early enough for some of us to go on the foray on Sunday after we attended the Microbiology of the Built Environment conference in Boulder, CO.

MSA2104 was a great chance to catch up with friends and colleagues and hear some excellent talks on the current state of research in the fields of systematics & taxonomy; ecology & pathology; genetics & molecular biology. Genomics pervades a lot of the research where it was not quite part of the picture when I first started attending so it was great to see how many people taking advantage of the amazing resources produced by the JGI sequencing programs.  I also really enjoyed the Karling lecture from Bruce McDonald on domestication in fungi and plants and the “dark side” of this domestication (meaning mostly that there are unintended consequences).

There was some tweeting going on at the meeting – I tried to capture some with a storify available here.

Jason presented research on the evolution of the fungal cell wall examining early diverging lineages of fungi which is the work of former graduate student Divya Sain.

Steven presented his poster on the inhibitory properties of a Chytridiomycota fungus we work on that affects growth of some filamentous fungi and won the award for best graduate student poster!

Jason was also honored with the 2014 Alexopoulos Prize to honor a young Mycologist. The prize is in memory of C. J. Alexopoulos who among other things authored the great Introductory Mycology textbook. I have not yet decided how I will spend the prize money but I intend to support a project in the lab or to support travel for collecting more strains tied to chytrid work.

A photo of Steven and Jason at the banquet.IMG_1645

 

Cryptococcus literature curation paper

We published a paper on the manual curation of the literature for the Cryptococcus complex of species (C. neoformans var neoformans, C. neoformans var grubii, and  C. gattii) this includes associated gene names with systematic locus names, something that was not easy to lookup without reading the published literature. In all more than 600 loci had gene names associated with them and include updated Gene Ontology associations, gene product names and descriptions and a table of orthology relationships between the genes in the different species genomes.

The early access to the paper is available was released at  Eukaryotic Cell in May and includes guidelines of how the community can go forward naming genes in these species. In addition we make available a table of these names available at FungiDB at this link. And future updates are being posted through GitHub so that community contributions can happen directly through edits to the file or through the comments section at FungiDB where comments can be added by any user indicating a gene name and these will be evaluated and curated by a Scientific Curator.

This work was done my a lot of hard work from Diane Inglis and Marek Skrzypek who are scientific curators at (Stanford University)  under the direction of Gavin Sherlock and the gene names and descriptions are loaded and available in FungiDB through the work of Ed Liaw and Venky Moktali at UC Riverside. We were able to do this work through an NIH R03 grant and look forward to finishing the complete literature curation by the end of this year.