MSA 2016

August 15, 2016fieldwork, outings, travelberkeley, fungi, msa, msa2016, pinnacles, zygomycetesJason Stajich

Some us from the lab took a trip up to Berkeley, CA for the MSA 2016 meeting. We road tripped by car from Riverside through the central valley up to Berkeley.

At the conference we had a great chance to meet with other mycologists, ecologists, and fungal enthusiasts. The meeting was fantastic from the Clark Kerr campus at UC Berkeley we had dorm life living so everyone was close by and could eat meals together. The talks and posters were really outstanding and such fun to talk about interesting research in fungi. Clearly genomics, next generation sequencing are at the forefront of tools used by the community but new approaches to visualizing communities and exploring the interactions between fungi and partners like bacteria and plants were very well explored in the meeting. Some great work on microbiomes and mycobiomes of insects and amphibians also made for some fascinating new results. There was a MSA session dedicated to some results from the ZyGoLife project and our team also had a one day meeting earlier in the week at the Joint Genome Institute to catch up on all the different team projects (a long post on this will appear on the zygolife project page soon). It was also fun to catch up with former lab member Steven Ahrendt who now works at JGI on early diverging fungi genome projects.

The meeting also featured Arturo Casadevall as the Karling lecture – an honor to bring in a scientist who is likely an outside member of the MSA community to speak about fungi. Dr Casadevall gave a lecture that covered the importance of collaboration, the impact of the pressure to publish in ‘one word journals’, and reviewed his provocative hypothesis about the link in the success of fungi, dinofall of dinosaurs, and rise of mammals. He also paid tribute to Thomas Taylor, a Zygolife collaborator who sadly passed away this Spring but who would have been the Karling lecturer this year.

Jason spoke on new population genomics work on Candida and Fusarium, while Sawyer presented a poster on Rhizopus stolonifer resequencing and population genomics; Derreck presented a poster on Bacteria-Fungi interactions on Serratia and zygomycete fungi; Nat presented his poster on data from first environmental sequencing of desert biological soil crusts from Joshua Tree National Park. On the way back we stopped for an overnight in Pinnacles National Park. Much fun, science, and discussions were had throughout the week.

We also stopped to take our first lab album cover photo while in Pinnacles. More to come!

Desert Crust collecting, Summer edition

August 6, 2016fieldwork, outings, people, researchbiological crusts, environmental sequencing, field trip, joshua tree, JTNP, samplingJason Stajich

On August 4th, 2016, Nat, Derreck, Sawyer, and Jericho went to Joshua Tree National Park to collect more Biological Soil Crusts samples. They were lucky to find some Lichen crusts which we could not find in our last sampling trip. Here are some pictures of our sampling team.

Stajich lab sampling team: Derreck, Nat, Sawyer, and Jericho

LightLichenCrust_JTNP — Our first collection of Lichen crust from Joshua Tree National Park

SurfaceTemp_DerreckJericho — Derreck measured crust surface temperature, while Jericho was getting ready for sampling

New funding, new papers, new data

August 5, 2016newsJason Stajich

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.

French connection

April 19, 2016travelconference, ecfg, fungi, parisJason Stajich

Jason was at the European Conference on Fungal Genetics in Paris this April and had a chance to deliver a lecture. It was a great meeting of science and there was a lot of social media coverage by participants.

Jason and Ousmane also attended the 1st conference on multicellular development in fungi where Ousmane presented his work on the Neolecta genome and comparative biology of the Taphrinomycotina fungi.

It was a bit imposing to be on stage with bright colored backdrop

Mural at a school with a mushroom little red riding hood and mushrooms in the forest

A desert foray

We started some explorations on fungi in desert crusts this week with a project in Joshua Tree National Park. Nuttapom received a Robert Lee Graduate Student research grant to explore impacts of visitor disturbance on biodiversity of desert crusts in JTNP. Nat with the help of Claudia, Derreck, and Prof Mike Allen did a first exploration of a few sites. We are happy to see some rain falling this week so there should be some changes to the crusts in some subsequent visits this week and weekend and coinciding with a workshop on desert crusts in the park this weekend. Here’s a few pictures of the team out in the field last week.

Mike leads the team — Mike and Derreck ahead in Hidden Valley

Nat Sampling — Nat, getting his first taste of sampling in the desert.

Claudia looking for sandtsone associated fungi — Dereck and Claudia helping to look for crusts. Claudia is researching sandstone associated fungi from a variety of habitats.

Cyano Crust — Cyanobacteria dominated crust

Migrating fungal biologists

February 4, 2016news, peoplepeople, travelJason Stajich

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.

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.
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.

2014-15 lab publication wordle

December 10, 2015newsJason Stajich

Recent lab news

December 9, 2015news, outings, peoplefarewell, newsJason Stajich

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.

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.

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.

Undergraduates Dillon and Jericho joined us for lunch as well. They have both worked closely with Peng this Summer and Fall.

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

Happy trails!

September 11, 2015newsJason Stajich

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.

Congratulations Steven

June 6, 2015news, peopleJason Stajich

Congrats to Steven Ahrendt who successfully defended his PhD Dissertation this week. Graduation ceremony (and pictures) to follow next weekend before he moves on to his postdoc position at UC Berkeley/LBNL/JGI at the end of the month.

Fungal Evolutionary Genomics

Stajich laboratory @ UC Riverside