Category Archives: news

Welcome new graduate students Tania and Julia

Welcome to first year graduate students Julia Adams (Plant  Biology) and Tania Kurbessoian (Microbiology). Tania joins us after completing a MS in Microbiology at Cal State-Northridge. She will starting out work on projects relating to genomics and physiology of extremophilic fungi,  black yeasts and efforts to culture and describe diversity of desert fungi. Julia completed a BS at Wellesley and has worked on a variety of projects related to lichen fungi. She will focus on lichen fungi from desert regions and will use genomic and potentially metabolomic tools to study evolution and unique properties of some lichenized fungi endemic to Joshua Tree National Park and the Mojave desert.

Congrats Nat on passing qualifying exam

Congrats to Nuttapon (Nat) who passed his qualifying exam this week and is now a PhD Candidate. Along with Derreck he is the second Plant Pathology graduate student in the lab and is working towards his PhD on microbial diversity of cryptogamic or biological soil crusts found in the desert. His primary research area is Joshua Tree National Park and desert areas in the UC Reserve System. Nat and Jason have benefited greatly from collaboration with New Mexico State Univ Professor Nicole Pietrasiak who is an expert in crusts, desert algae, and did her PhD work in Joshua Tree which harbors tremendous diversity of biological soil crust types.

Biological Crust
Cross section of crust. Image by N. Pietrasiak

 

Chytrid Opsin structure paper published

Great work by former graduate student Steven Ahrendt (@sahrendt0), visiting student and current Duke graduate student Edgar Medina (@WhippingFungi) on the publication of a manuscript describing a Type II Opsin found in the zoosporic fungi.  “Exploring the binding properties and structural stability of an opsin in the chytrid Spizellomyces punctatus using comparative and molecular modeling” in PeerJ! Thanks also to co-author and collaborator Chia-en Chang in Chemistry Dept at UCR who helped mentor Steven on homology modeling and docking analyses. I also learned a lot through this project and was excited to be able to merge evolutionary and computational approaches. The project lead to the surprising findings of a gene important for light sensing that is shared among just the zoosporic (fungi with a flagellate life stage) and animals.

This project has been going for a while … Edgar and I discovered this protein in ~2008 when we started independently analyzing the Batrachochytrium genome, the first chytrid fungus sequenced. Based on sequence similarity we realized it looked like an animal rhodopsin, a 7 transmembrane G-protein coupled receptor (GPCR). These rhodopsins are called type II opsins and typically respond to green light.  We went looking for this in the first place because of work published in 1997 from Ken Foster’s lab which showed that zoosporic chytrid fungi respond to green light and that likely this behavior is due to a rhodopsin or rhodopsin-like GPCR  We found longer intact copy in the genome of the chytrid S. punctatus, so decided to focus on that copy – though we later discovered additional modifications of the predicted gene structure appeared necessary. We decided to do some homology modeling with the solved structure of a squid rhodopsin as shown in Figure 1. This confirmed that the sequence was compatible with the Type II Opsin structure. The paper documents several other computational simulations to test for the likely binding chromophore and hypothesis testing about the stability of the protein structure. Overall this work provides confidence that the sequence encoded in the genome of the zoosporic fungus can fold into a structure compatible with an opsin.

fig-1A
Figure 1A: Structural alignment of S. punctatus homology model (grey) with T. pacificus crystal structure (light purple)

It still remains to be tested if this opsin-like gene can biochemically function in this way. We hope to explore more of that with some additional work in the future. We have also nearly completed our manuscript analyzing the evolutionary history of this protein in fungi and related species to give a better picture of the timing of the emergence of this receptor-like protein. This project has helped advance some ideas about how zoosporic fungi interact with their environment based on genomic and computational analyses. This gene is a good candidate for future investigations into environmental sensing and signaling in zoosporic fungi.

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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