Category Archives: news

2016 Round Up – by the numbers

Quick post to sum up some of the news from 2016 and head into 2017.

  • Six manuscripts were published and an additional two were accepted and three more were submitted or being revised in 2016
  • Three graduate students survived another year in the lab: Sawyer, Nat, Derreck
  • Joined by one Microbiology graduate student Jesus Pena joined in Fall 2016.
  • Nine undergraduates worked in the lab Deane, Josh, Jericho, Dillon, Na, Justin, Serena, Leandra, George and Travis has been part of bioinformatics projects
  • One postdoc, Jinfeng has been the bioinformatics and genomics guru from genome assembly to transposon bioinformatics
  • One new assembly of a Citrus genome
  • At least 15 new genomes from our work with Zygolife and 1000 Fungal Genomes project were released or material processed. More than 100 cultures of some fungi are being examined in the lab.
  • One NSF grant started on systematics of anaerobic chytrid fungi and one new grant awarded as part of the UC MRPI http://ucop.edu/research-initiatives/programs/mrpi/2017-Awards.html program on the “UC Valley Fever Research Initiative” lead by UCSF and including several other UC campus.
  • Jason is on sabbatical in 2017 at Oregon State University.

New funding, new papers, new data

We celebrated a few events in April and May.

  • A new NSF grant was funded and started in April on rumen fungi “Phylogenomics and evolutionary history of the anaerobic fungal group, Neocallimastigomycota“. This is a collaboration with Noha Youssef and Mostafa Elshahed at Oklahoma State University and will give the opportunity to work on systematics of these anaerobic gut fungi.
  • Raúl Castanera who came to the lab for a short stay last year, authored a paper that was accepted this week on transposable elements in the Pleurotus (oyster mushroom) genome and comparisons in proliferation rates and impact on gene expression. Castanera R et al. PLoS Gen doi: 10.1371/journal.pgen.1006108
  • We just started to get our first microbial diversity (16S and ITS) results for rock and soil communities from California desert environments and Antarctica as part of project by visiting student Claudia Coleine and Nat Pombubpa. Claudia is a PhD student with Laura Selbmann of Tuscia University and visited for nine months, but we processed isolates the lab collected from Antartica expeditions. We are also sequencing genomes of a handful of cultured fungal species from Antarctic locations and the first assemblies look pretty good (200-400 contigs for these 25-40Mb genomes) for a MiSeq only assembly.
  • Nat is collecting samples from Joshua Tree National Park and in collaboration with other desert crust researchers Paul De Ley and Nicole Pietrasiak examining fungal and bacterial distribution.

Migrating fungal biologists

  • We said bye to Marco Marconi, visiting student from the Wilkinson Lab in Madrid, in December. He worked on some data mining from the 1KFG project and brought some new R tools for looking for enrichment across the CAZY, Interpro, and Pfam differences in species.

Marco

  • We welcome Plant Pathology graduate student Derreck Carter-House to the lab in January – after spending time working on molecular biology projects in plants and plant-microbe interactions in another lab. carterhouseweb
  • Jason went across to England to serve on Ensembl Genomes  SAB and give seminar at University of Exeter – he came back with more appreciation for sunny California winters.
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Recent lab news

The past few months have passed quickly but wanted to share a few updates.

Jason presented at the EMBO Eukaryotes meeting in Spain, Mexican Mycology Congress, Univ of Arizona, attended the Kavli Frontiers meeting, co-organized the Southern California Eukaryotic Pathogens meeting held again at UCR and taught graduate course on Programming and Data analyses.

The past few months we hosted Yinka Odebode from University of Lagos from August to November. He was supported by the West African Research Association. Yinka learned about ITS sequencing of fungi to identify his isolates in his work in Africa. He also explored properties of dust associated fungi in Nigeria before he returned home in November.

yinka1 yinka3

We also welcomed Marco Marconi from Madrid for a few months and is working on comparative genomics of fungi using the 1KFG datasets.

Starting in  September we welcomed new graduate student in Plant Pathology, Nuttapon Pombubpa (right). Here he is (right) enjoying lunch along with visiting student Claudia Coleine and graduate student Sawyer.

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We gathered to say goodbye to project scientist Peng Liu who returned to China in December. Here she is with postdoc Jinfeng and visiting student Zhinquan.
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Undergraduates Dillon and Jericho joined us for lunch as well. They have both worked closely with Peng this Summer and Fall.lablunch4

Most of the lab together for a farewell lunch for Peng including Deane on the far right.lablunch5

Happy trails!

A quick note to say congrats and good luck to postdocs and students who finished up the summer.

Graduate student Steven Ahrendt who graduated from the GGB program and is now a postdoc at the JGI / UC Berkeley.

Postdoc Ousmane Cissé finished his fellowship from the Swiss National Science Foundation and moved on to the NIH on a fellowship to work on Pneumocystis.

Postdoc Rod Olarte moved to the University of Minnesota on a NSF postdoctoral fellowship.

Undergraduates Dillon McDonald and Christina Uriarte also finished their summer projects in the HSI-STEM and MARCU programs.

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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.