Category Archives: UCDavis

UC Davis MARS Symposium Wrap Up #globalfood #UCDavisMARS

Yesterday I went to a symposium at UC Davis that was the launching of a new partnership between UC Davis and the Mars Corporation. I note – I have been collaborating with some people at Mars on multiple microbiome related projects and generally have had great interactions with the people there. I am not directly involved in the planning for this new partnership between UC Davis and Mars and thus I was interested in hearing more about it at the symposium.

The symposium was at the Mondavi Center on UC Davis campus and I zipped in on my bike through the cold (for Davis) air and got there just before they opened the doors to the main theater. I saw a few folks I knew milling around in the lobby and said hello and then went inside with some people from my lab for the “show”.

 I will try to write more about this later but just one note – I found some of the big picture discussions about the importance of the nexus between food, agriculture and health to be pretty inspiring. For now – I hope the Storify I made and embedded below will give some idea as to the goings on of the symposium.

Talk for UC Davis Pre-Health Meeting (#UCDPHSA): Opening up to Diversity

Sunday I gave a talk at the “12th National UC Davis Pre-Health Student Alliance Pre-Medical and Pre-Health Professions Conference“.  I normally try to not give talks on weekends (to spend time with my family) but I made an exception here since this meeting has a strong commitment to issues relating to diversity in health and STEM fields.  This mission statement for the meeting reads:

The UC Davis Pre-Health Student Alliance’s objective is to introduce and support academic, admission, and preparatory opportunities for all students interested in health professions with a focus on those underrepresented in healthcare (with regard to gender, economic, social, educational, linguistic, cultural, racial, and ethnic background). We target universities, community colleges and high schools throughout the United States. The UC Davis Pre-Health Student Alliance aims to impact health education, increase diversity amongst the healthcare workforce, and inspire future leaders of healthcare through hosting the largest national pre-health professions conference.

It was that mission statement that got me to ditch my wife and kids Sunday AM (and also much of Saturday PM for a dinner and to work on my talk).  I went to a dinner Saturday for some of the speakers with the new Dean of the UC Davis School of Medicine Julie Freischlag.  The dinner had about 20 or so people and I met some quite interesting folks there working on various aspects of human and animal health.

And then Sunday AM I got up early, decided to use slides (was not sure) and finished off the slide set I had worked on the night before.  I decided that, in the spirit of the meeting, I would talk about two main things – diversity and access.  And I planned to tell three stories about my work in this area.  I wove in some personal stories since, at the dinner the night before Barbara Ross-Lee (who I sat next to) helped remind me of the importance of making talks personal.  So in the end I talked about myself, diabetes, diversity of microbes, antibiotics, diversity in STEM, and open science.  I came up with a title I was OK with: Opening up to Diversity.

My talk went well, I think.  I am pretty sure it was vbideotaped but not sure where that recording will end up. I did however post my slides to slideshare.  See below:

Opening up to Diversity talk by @phylogenomics at #UCDPHSA from Jonathan Eisen

And I also recorded the talk using Camtasia (basically, it allows recording of the screen, the video camera on my computer, and the audio).  I posted the recording (without the video feed which shows mostly my neck) to Youtube.  See below:

UPDATE 10/16 –

I have scanned in my notes that I made in planning this talk.  Figured, why not post them.

Update: 12/10/2014 – just discovered a video of the talk was posted to Youtube 

ASUCD (Associated Students, #UCDavis) Excellence in Education Awards

Very proud of this.  I was a finalist in the “Excellence in Education” awards given out by the UC Davis Undergraduate group ASUCD Associated Students, University of California, Davis. And David Coil, Project Scientist in my lba was another finalist. The award for my college (College of Biological Sciences) went to Jay Rosenheim, who is a great teacher, so no shame in losing to him.



 Anyway – here are some pics.

One of the ASUCD members doing introductions
Another ASUCD
David Coil getting is certificate
Hey, that’s me
Jay Rosenheim getting his certificate

#UCDavis Department of Evolution & Ecology Faculty Search for an "Ecologist"

ECOLOGIST, UNIVERSITY OF CALIFORNIA, DAVIS — The College of Biological Sciences, University of California, Davis invites applications and nominations for a tenure-track position in the Department of Evolution and Ecology at the ASSISTANT PROFESSOR level. Candidates must have a Ph.D. (or equivalent) in the biological sciences or related fields. We seek a terrestrial or freshwater ecologist with research interests that will complement and build upon existing faculty strengths to address important ecological questions. We welcome applicants who address important ecological questions at any spatial or temporal scale.   We seek a colleague who is committed to participating in the departmental community through collaborative teaching, research, service and graduate mentoring. Letters of recommendation should specifically address this aspect of the application. The successful candidate will be expected to teach in undergraduate and graduate programs, and should be committed to mentoring and fostering diversity. Applicants should submit materials online at
which contains additional information about the position. These should include: cover letter, curriculum vitae, description of current and projected research, summary of teaching interests and experience, and three publications. Applicants should also provide the information requested for three referees (fourth referee optional). Once entered, applicants will electronically request letters from referees who will then be prompted by email with upload instructions for their letters. Closing Date: Open until filled, but all application materials, including letters of recommendation, must be received by October 15th, 2013 to assure full consideration. Administrative contact: Carla Munoz ( Faculty contacts: Jay Stachowicz (, Sharon Strauss ( The University of California is an Equal Opportunity/Affirmative Action Employer with a strong institutional commitment to the development of a climate that supports equality of opportunity and respect for differences.

Thanks to Software Carpentry (@swcarpentry) for coming to #UCDavis

Quick post here.  Jenna Lang in my lab has a post at microBEnet about the recent workshop that the Software Carpentry folks ran at UC Davis: Software Carpentry comes to UC Davis! | microBEnet: The microbiology of the Built Environment network.  It was a major success.  For those who don’t know Software Carpentry’s mission is is to build basic computing skills among researchers.  From their web site:

Software Carpentry helps researchers be more productive by teaching them basic computing skills. We run boot camps at dozens of sites around the world, and also provide open access material online for self-paced instruction. The benefits are more reliable results and higher productivity: a day a week is common, and a ten-fold improvement isn’t rare.

A great idea and done really well.  Others out there should consider hosting or attending one of their Boot Camps and checking out their materials on their web site.  See for example their videos and their reading list and their lessons.  They really do great things …

Notes from talk by Stephen J. O’Brien at #UCDavis

Stephen O’ Brien talked at UC Davis a few days ago. I met with him in the afternoon before his talk. It was one of the more interesting discussions I have had in a long time. He has done some very interesting and important work (e.g., comparative genomics, HIV, feline evolution) though most of what we talked about was not work per se (e.g., we talked a lot about baseball and big cats since my kids are obsessed with big cats).

Anyway, below is a “Storification” of tweets from his talk. Best part – he signed a copy of his Tears of the Cheetah: The Genetic Secrets of Our Animal Ancestors book with a dedication to my kids.
//[View the story “Steven J. O’ Brien talk at #UCDavis on CCR5/HIV/AIDS” on Storify]

Steven J. O’ Brien talk at #UCDavis on CCR5/HIV/AIDS

Storified by Jonathan Eisen· Mon, Jan 07 2013 20:12:09

Today at #UCDavis Stephen O Brien on “Three Decades of Genomics and AIDS” Eisen
Can’t wait for talk at 4 PM today at #UCDavis Genome Ctr by Stephen O’Brien on “Three Decades of Genomics and AIDS” Eisen
@phylogenomics Wow! Interesting topic. Wish I was attending.Setor Amuzu
As an evolutionary biologist am jealous of name of Obrien’s “Theodosius Dobzhansky Center for Genome Bioinformatics” Eisen
@phylogenomics any podcasts available?Cuquis R
SJ Obrien – head of new Dobzhansky Inst – intro by Harris Lewin, discussing how Dobzhansky finished his career here at #UCDavis:Jonathan Eisen
Lewin point out that Steven O Brien has been called the Indiana Jones of Genomes (e.g.., ) #ucdavisJonathan Eisen
Lewin: Steven O’ Brien is also one of the coordinators of the genome 10K project #UCDavisJonathan Eisen
Steven O Brien launching into his talk at #ucdavis Eisen
O’Brien at #UCDavis: Giving props to T. Dobzhansky and his pioneering work on population geneticsJonathan Eisen
O’Brien at #UCDavis: discussing how population genetics help lead to many whole fields/areas incl. conservation genetics, DNA forensics, etcJonathan Eisen
Stephen J. O’Brien: is on Plagues and people Contagion Genomics & Beyond. 3 areas: Gene Discovery, Conservation Genetics, DNA forensicsDawei Lin
O’Brien at #UCDavis: began work on AIDS epidemic partly as model for way to connect human genetics and infectious diseaseJonathan Eisen
O’Brien at #UCDavis: close to 30 million people have died of AIDS and close to 30 million more are infected w/ HIV & disease still spreadingJonathan Eisen
@Curosik don’t think soJonathan Eisen
O’Brien at #UCDavis: heterogeneity in progression in HIV led him to try to use advances in human genetics to look for AIDS restrictive genesJonathan Eisen
SJO: Oct. 1996 AIDS quilt is a symbol of the pandemic disease with 40K Tabard Emblems on that day at the Capitol Hill.Dawei Lin
O’Brien at #UCDavis: early in AIDS epidemic got access to samples from different groups of people to test role of human genes in progressionJonathan Eisen
O’Brien at #UCDavis: looked for genetic variation in AIDS resistance, progression rate, outcomes, response to HAART therapyJonathan Eisen
O’Brien at #UCDavis: in 1996 5 groups discovered that CCR5 (a G coupled seven transmembrane receptor) was target of HIV for cell entryJonathan Eisen
O’Brien at #UCDavis: looked for CCR5 mutations in cohorts of patients w/ HIV & found that homozygous mutations were protectiveJonathan Eisen
SJO: CCR5 is the binding target for HIV. People with CCR5 delta with a 32 peptide deletions do not have HIV infections.Dawei Lin
O’Brien at #UCDavis: those people heterozygous for CCR5 deletions showed slower progression of HIV infectionJonathan Eisen
@phylogenomics would love to see the stats methods on thatLewis Lab
@Lewis_Lab seems to be relatively old data …Jonathan Eisen
Obrien at #UCDavis: many scientists occasionally like to do more than publish in a good journal, some would like to translate to bedsideJonathan Eisen
SJO: People study genes about infectious diseases should not stop at publishing on a good journal, should bring it to the bedside.Dawei Lin
Obrien at #UCDavis: re: delta32 mutation in CCR5 and modifies Dobzhansky “nothing in medicine makes sense except in light of evolution”Jonathan Eisen
Obrien at #UCDavis: discussing how frequency of CCR5 delta32 mutation has increased rapidly over time; suggest this is due to ++ selectionJonathan Eisen
@phylogenomics I’m not seeing any open access/open data reports.Lewis Lab
Obrien at #UCDavis: 20 mutations in CCR5 have been found outside of delta32 mutation; 18/20 are amino acid changing; suggests ++ selectionJonathan Eisen
SJO: 1/5 people now is CCR5 delta 32 carriers. There are 22 variants. 18 of them changes peptides.Dawei Lin
Obrien at #UCDavis: Suggests something influenced CCR5 mutations prior to AIDS epidemic (admits much of his theories on this controversial)Jonathan Eisen
OBrien at #UCDavis now reading from Tears of the Cheetah his book on genetics / genomicsJonathan Eisen
O’Brien at #UCDavis: suggests that bubonic plague may have influenced CCCR5 mutation frequencies over timeJonathan Eisen
O’Brien at #UCDavis: discussing plague epidemic in 1665 and 1666 (reading from his book)Jonathan Eisen
@phylogenomics that got me the statistical test I was looking for–thanks. I don’t find the article very intuitive, thoughLewis Lab
O’Brien at #UCDavis: discussing their estimates of the age of the CCR5 delta 32 mutations by looking at the size of the linkage groupJonathan Eisen
O’Brien at #UCDavis: estimates of the date of the origin of the spread of the CCR5 delta 32 mutation is correlated w/ plague epidemicJonathan Eisen
O’Brien at #UCDavis: many many waves of plague epidemics over time (though he notes many other possible epidemics also at same general time)Jonathan Eisen
@phylogenomics thanks. This is a good case study for the stats class.Lewis Lab
@phylogenomics O’Brien suggests that bubonic plague may have influenced CCCR5 mutation frequencies” No doubt a 1-2 insC mutation.Donald Atkinson
SJO: Conspiracy theories of black death cause CCR5 mutation hike, which mostly found in Caucasians.Dawei Lin
O’Brien at #UCDavis: refs a 2004 Nature study of mice w/ CCR5 delta 32 homozygous mutation; -/- have 90+% reduction in Y.pestis uptakeJonathan Eisen
O’Brien at #UCDavis: after 9/11 & anthrax attack collaborated w/ people to look at smallpox infection in CCR5 delta 32 mutant cellJonathan Eisen
“The O’Brien at #UCDavis” stream of tweets by @phylogenomics is fascinating. Must-read for biology folks.Rob Quarles
@phylogenomics What is his book? I show the PBS vid he was in few years ago to my molec epi class each year to discuss CCR5/plague/HIVTara C. Smith
O’Brien at #UCDavis: many other viruses have been screened for whether they make use of CCR5Jonathan Eisen
@phylogenomics thanks for tweets re O’Brien lecture. Say hi to Steve for me!Kathy Belov
Obrien at #UCDavis: delta 32 mutations in CCR5 may lead to higher risk to West Nile virus …Jonathan Eisen
SJO: people with homozygous CCR5 delta mutations are susceptible to West Nile virus, not HIV.Dawei Lin
Obrien at #UCDavis: looking back to 1996 b/c this is when HAART therapy for HIV was startedJonathan Eisen
Obrien at #UCDavis: showing slide from Tony Fauci of FDA Approved antiretroviral drugs; now many new drugs going after CCR5 interactionJonathan Eisen
@phylogenomics cool! I will order it.. Thanks for the link!Cuquis R
@phylogenomics thanks!Tara C. Smith
Obrien at #UCDavis: discussing “The Berlin Patient” (see; had AML; prognosis bad; bone marrow tplant from CCR5delta32Jonathan Eisen
OBrien at #UCDavis: 2008 Gero Hitter – the doctor for “The Berlin Patient” shows up at AIDS conference; news finally comes out in WSJ 2008Jonathan Eisen
Obrien at #UCDavis: here is the WSJ news story about The Berlin Patient Eisen
Obrien at #UCDavis: says the story of the Berlin patient is an anecdote; emphasizes it is one patient; need more information / data / casesJonathan Eisen
Obrien at #UCDavis: refs SciAm article where gene therapy for HIV patients reported; he’s skeptical about peer reviewJonathan Eisen
Obrien at #UCDavis: some researchers have been looking at how CCR5 might influence Graft Versus Host Disease (see Eisen
Obrien at #UCDavis refs new Nature paper showing CCR5 is a receptor for MRSA leukotoxin (see Eisen
@KathyBelov will do …Jonathan Eisen
SJO: Patients with bone marrow transplants with CCR5 negative genotypes remain HIV free without drug treatments. A potential breakthrough.Dawei Lin
Obrien at #UCDavis giving props to George W. Bush for PEPFAR program Eisen
Obrien at #UCDavis: OBrien ends his talk by thanking the patients who have provided samples cc: @rebeccasklootJonathan Eisen
Question at Obrien talk at #UCDavis: is CCR5 delta 32 the only restriction mutation? Obrien says yes but not yet translated to bedsideJonathan Eisen
Comment at talk by Obrien at #UCDavis: primate center at UCDavis played a major role in work on HIVJonathan Eisen
Comment at Obrien talk at #UCDavis: says to students in crowd that you have heard a talk about thinking which most people don’t do anymoreJonathan Eisen
@phylogenomics Nice. He definitely saw importance of donor appreciation/respect differently than most in the early days.Rebecca Skloot
@phylogenomics I wanna know what happened to his amazing frozen zoo at NCI! Hope he took it w/him; he worried re who would take care of itRebecca Skloot
@RebeccaSkloot he did not discuss this …Jonathan Eisen
Love @phylogenomics tweets on O’Brien’s talk at #UCDavis. Everything he said on CCR5/HIV/Berlin pt is right up my alley.Nathalia Holt
My kids are very happy w/ autographed copy of “Tears of the Cheetah” Steven O Brien gave me after his talk at #ucdavis Eisen
As follow up to post about “Tears of a cheetah” – my kids are a bit obsessed w/ big cats … Eisen
@phylogenomics How do the cats get along with all the microbes?Cindy Manson
@CynthiaManson1 extremely well Eisen

UC Davis Magazine … not just tooting the #UCDavis horn …

I have just joined an advisory group for the UC Davis Magazine and I am really happy with their new direction. They are trying to make the magazine a little less “UC Davis is awesome” and more “Here are some interesting things to think about, with a UC Davis angle”. The new Fall Issue is a good example of this. There is for example a nice article by Sasha Abramsky about student involvement (or the lack thereof it). Plus there is a little video interview to go with the article. Perhaps even more “interesting” is the article on the future of higher education by Clifton Parker. Not exactly a glory piece about UC or UC Davis. Anyway … just thought I would put this out there. Any opinions on the magazine please send them my way – the staff there seem great and really interested in feedback.

Dueling microbial diversity talks at #UCDavis on May 2 #symbioses #microbiology

Here is a storification of the dueling microbial diversity talks that happened at UC Davis on Wednesday May 2.[View the story “Dueling microbial diversity talks at #UCDavis” on Storify]

PLOTS ( is coming to #DavisCA

DIY Science & Citizen Science & Open Science all rolled into one -PLOTS is coming to Davis, CA & UC Davis.  See  Davis – for more information.

12 hours of me: Slideshows w/ audio from "BIS2C: Biodiversity & the Tree of Life" at #UCDavis

Well, it has taken a few months of processing but I have finally gotten my lectures from the introductory biology course I teach uploaded in some way to share.  The course is “BIS2C: Biodiversity and the Tree of Life” and it is the third quarter of a three quarter introductory biology series at UC Davis.  Each year some 2300 or so students take this series which means that we at UC Davis have to offer each of the courses (BIS2A, BIS2B, and BIS2C) each quarter.   Every fall I co-teach BIS2C.  Alas we do not have a lecture hall big enough for 700 students, so we do the course in two sections.  The way we teach it each of the faculty double up and teach their part of the course to each section.  The course also has a weekly lab.  It is a machine of sorts.

This fall I taught 13 lectures for the course.  I covered basically phylogenetic methods, the big picture of the tree of life, and microbial diversity.  I used the Apple presentation program Keynote for slides for my lectures and I used the “Record Slideshow” option to record audio in synch with the slides.  After a bit of pain, I managed to convert these recordings into video and then posted them to Youtube.  And today I am sharing them with you.  There are imperfections of course.  But I thought some might find them useful.  Plus I have made a YouTube playlist for all the lectures if you want to just sit down and enjoy 12 hours or so of me.  Now if only Youtube would allow me to change the thumbnail image for each lecture …  Plus I note – next year I will be doing much more interactive learning in class so this may be the last record of some of these lectures …

Lecture 1: Introduction to Course and the Tree of Life

Lecture 2: Trees, Taxa and Groups

Lecture 3: Characters

Lecture 4: Phylogenetic Inference

Lecture 5: Phylogenetic Inference

Lecture 6: The Tree of Life

Lecture 7: The Three Domains

Lecture 8: Three Domains and Microbial Diversity

Lecture 9: Microbial Diversity

Lecture 10: Endosymbioses and Lateral Gene Transfer

Lecture 11: Endosymbioses and Lateral Gene Transfer

Lecture 12: Extremophiles

Lecture 13: Human Associated Microbes