Trying to sort out all the STEM and STEM related departments, graduate programs , at #UCDavis

Well, I was in a meeting yesterday for the UC Davis ADVANCE program. This program is an NSF funded project to improve presence of women and underrepresented minorities on the faculty in Science, Technology, Engineering and Math (STEM). So I decided to see – how many departments at UC Davis might participate in such an initiative. And, well, wow. I knew there were a lot of STEM or STEM-related departments at UC Davis but I did not know there were this many.

Here is a list I compiled of UC Davis STEM or STEM-related Departments. I included medical departments here since many people in such departments do medical/science research. But clearly this is a broad definition of STEM. But nevertheless, this gives some picture of the scope of science and medicine and related departments at UC Davis.

Vet School departments in Yellow
Med School departments in Red
College of Biological Sciences Departments are In Green
College of Agricultural and Environmental Sciences in Orange
College of Letters and Science in Light Blue
College of Engineering in Grey

And then of course UC Davis has a TON of graduate groups and almost all of these are separate from departments. They do not hire faculty but they are a key part of the atmosphere and academics at UC Davis. And there are an enormous number of these in STEM or STEM-related fields. See below

Graduate Groups

Agricultural and Environmental Sciences Graduate Programs

Biological and Life Sciences Graduate Programs

Engineering Graduate Programs

Health Sciences Graduate Programs

Physical Sciences and Mathematics Graduate Programs

Social Sciences Graduate Programs

And then there are the Undergraduate Majors of which many are in STEM or STEM-related fields

So – lots and lots of STEM stuff at Davis and lots of chances / opportunities to improve the presence / treatment / life of women and underrepresented minorities.

UC Davis’ 2nd Annual BioBlitz will be sampling MICROBES!

The first-ever MicroBioBlitz will be held tomorrow, April 27th, from 9am-2pm! Join the Eisen Lab and the UC Davis chapter of SEEDS (the Ecological Society of America’s Undergraduate Ecology Club) at the Putah Creek Riparian Reserve for their second annual BioBlitz. The event is open to the public, and SEEDS just finished putting out some traps, so there could be lots of fun critters to see tomorrow!

I just chatted with the BioBlitz organizers, and they are super-excited to have us there to recruit the BioBlitz participants. As they catch frogs and butterflies, and identify flowers and trees, they will all be armed with a microbial sampling kit! Microbial samples will be sent to Jack Gilbert for sequencing as part of the Earth Microbiome Project!

Bring friends, family, co workers, or anyone else you might know!

Here is the link to iNaturalist, which is the site they will be using to upload all of their species accounts. Come out and help the UCD SEEDS chapter win the BIOBLITZ contest this year!!

Hmmm… wonder if our microbial species will count for the contest???

Here’s the official BIOBLITZ FLYER

and a BioBlitz Map

Crosspost: New papers from our undergraduate “microbiology of the built environment” genome sequencing project

Crossposting from microBEnet.

We have two new papers out from our lab as part of our microBEnet supported undergraduate genome sequencing project:

Lo JR, Lang JM, Darling AE, Eisen JA, Coil DA. 2013. Draft Genome Sequence of an Actinobacterium, Brachybacterium muris Strain UCD-AY4. Genome Announc. 1(2):e00086-13. doi:10.1128/genomeA.00086-13.
Bendiks ZA, Lang JM, Darling AE, Eisen JA, Coil DA. 2013. Draft Genome Sequence of Microbacterium sp. Strain UCD-TDU (Phylum Actinobacteria) Genome Announc. 1(2):e00120-13. doi:10.1128/genomeA.00120-13.

Congratulations to all involved especially Jonathan Lo and Zack Bendiks, the undergrads who are first authors, and to David Coil who coordinated all the work.

More information about the project can be found on blog posts from my lab blog (https://phylogenomics.wordpress.com/category/undergraduate-genome-project/) and on a page here on microBEnet (http://www.microbe.net/undergraduate-research-built-environment-genomes/) and the YouTube video below:

In summary, the point of the project was to (1) start generating some reference genomes for microbes from the built environment and (2) to engage undergraduates at UC Davis in genome sequencing and microbiology of the built environment projects.

The papers are published in a new open access journal from the American Society for Microbiology called “Genome Announcements”.

Thanks also to the Alfred P. Sloan Foundation which funds microBEnet and to the UC Davis Genome Center DNA Technologies Core facility which ran the sequencing. More papers are coming. Stay tuned.

Wanted: examples of family friendly policies for tenure review

I am on a committee at UC Davis that is part of an National Science Foundation “ADVANCE” grant that UC Davis’ Chancellor Linda Katehi and others at UC Davis received last year. The goal of the project is “increasing the participation of women, especially Latinas, in academic science, technology, engineering and mathematics careers.”

More about the UC Davis ADVANCE program

One of the things the committee I am on is charged with is looking into how the policies and practices of tenure review might differentially impact women and minorities. So – related to that I am writing to ask if people out there have examples of what one might call “family friendly” policies relating to extending the amount of time one is allowed before tenure review occurs. Some questions I would love answers to for various institutions:

What are the policy guidelines for tenure review?
Can the tenure clock be extended for family related issues (e.g., birth of a child, adoption of a child, dependent medical care, etc)?
What is the specific wording of such policies?
How are such policies explained to tenure review committees and letter writers?

For UC Davis here is what I have been able to find (well, with help from the other people on the committee)

UC Davis Academic Personnel Manual

APM 210 has guidelines directly related to this

UC Davis Work Life Balance

I posted a quick request to Twitter earlier.

Wanted: examples of wording / guidelines for tenure review that encourages / allows for family leaves to extend time clock #ADVANCE
— Jonathan Eisen (@phylogenomics) March 18, 2013

//platform.twitter.com/widgets.js And got some responses

@phylogenomics Our wording is more on the ‘allows’ than ‘encourages’ end of the spectrum. Pg3 section 1.4 subsec 4 usu.edu/hr/files/uploa…
— weecology (@weecology) March 18, 2013

//platform.twitter.com/widgets.js

@phylogenomics Here’s a page that describes cases of family leave for stopping tenure clock @uwmadison:secfac.wisc.edu/newfac/tenure/…
— Eve Emshwiller (@EveEmshwiller) March 18, 2013

Any other information would be great. I am hoping to make this an “open discussion” of such issues rather than just an internal UC Davis discussion …
//platform.twitter.com/widgets.js

QIIME workshop at UC Davis (May 2-4, 2013)

UC Davis will be hosting a 2.5 day QIIME workshop following the SMBE Satellite Meeting on Eukaryotic -Omics, running Thursday afternoon May 2nd through Saturday May 4th. Meeting participants and local Bay Area researchers are encouraged to attend.

Due to space constraints, this workshop will be strictly limited to 32 participants.

Click here to complete the application form (form closes March 22, 2013, and this deadline will not be extended)

PLoSOne paper: Parallel polymorphisms for pepper population phylogenetics, from #UCDavis, not #Pepperspray

Interesting new paper from colleagues at UC Davis: PLOS ONE: Characterization of Capsicum annuum Genetic Diversity and Population Structure Based on Parallel Polymorphism Discovery with a 30K Unigene Pepper GeneChip.

Press release is here: http://www.news.ucdavis.edu/search/news_detail.lasso?id=10497

Good to see something on peppers from UC Davis not about spraying.

SimplyThick food thickener, necrotizing enterocolitis, and microbiomes

Wow. I have not heard anything about this issue until this NY Times article: Warning Too Late for Some Babies – NYTimes.com. The article summarizes some recent FDA and other medical warnings about a product called SimplyThick. This product has been connected to cases of necrotizing enterocolitis (NEC) in premature infants. NEC is a horrible horrible ailment with an incredibly high death rate. I am familiar with NEC mostly because some colleagues at UC Davis are involved in clinical trials to use probiotics and prebiotics as a preventative therapy for NEC (see more on the project here: Premie NEC — Foods For Health Institute and UC Davis Medicine – Helping Premature Infants Thrive). NEC seems to have some general connection to “microbiome health” although it is not entirely clear (to me at least) whether the connection is correlative or causal in any way. The NY Times article simple serves to remind me that we seem to know very very little about the connection between diet and general microbe-related health in infants (or for that matter, adults). We desperately need to accelerate the pace at which we determine / study how foods, food additives, and diet affect our microbial communities …

Lesson of the week from this article is captured in this quote

“You try not to put anything in a baby’s intestine that’s not natural.” If you do, he added, “you’ve got to have a good reason.”

I am not by any means convinced that everything has to be “natural” (I am not sure I even know what that means) but stuffing preemies full with some food thickener simply because it has been marketed to speech pathologists as something to use seems like a pretty bad idea.

SMBE Meeting on Eukaryotic -Omics: April 29-May 2 at UC Davis

I’m leading the organization of an SMBE Satellite Meeting focused on Eukaryotic -Omics at UC Davis this spring. The meeting dates have been set as April 29-May 2, 2013, and the meeting description is as follows:

The SMBE Satellite Meeting on Eukaryotic -Omics will bring together an interdisciplinary pool of researchers to discuss current efforts, challenges, and future directions for high-throughput sequencing approaches focused on microbial eukaryotes (environmental studies of non-model organisms). The meeting program will encompass investigations of eukaryote biodiversity, ecology, and evolution, using approaches such as rRNA marker genes, shotgun metagenomics, metatranscriptomics, and computational biology tools and software pipelines.

See the meeting website (http://www.smbe.org/eukaryotes/) for program announcements, registration details, and travel award information. We’re currently in talks to tack on a QIIME workshop at the end of the meeting (tentative dates May 2-4), so keep an eye our for further details. The official conference hashtag will be #SMBEeuks on Twitter.

Our call for travel award applications includes a heavy focus on diversity–encouraging early-career applicants as well as those from underrepresented groups. Please pass on this meeting announcement to anyone who might be interested in attending. Deadline for abstract submission and travel grant applications is Feburary 22, 2013.

Storify/Tweet Notes from Noah Fierer’s talk at UC Davis

//storify.com/phylogenomics/noah-fierer-talk-at-ucdavis-on-biogeography-of-soi.js?template=slideshow[View the story “Noah Fierer talk at #UCDavis on biogeography of soil microbes” on Storify]

Noah Fierer talk at #UCDavis on biogeography of soil microbes

Storified by Jonathan Eisen· Thu, Jan 10 2013 22:44:52

At #UCDavis tomorrow: Noah Fierer @NoahFierer on “Exploring Terra Incognita: the biogeography of soil microorganisms” http://shar.es/44O44Jonathan Eisen

Reminder – today 4 PM #UCDavis Seminar by Noah Fierer #microbes #microbiomes #biogeography #evolution #soil http://wp.me/ph9ob-RvJonathan Eisen

Awaiting talk at #UCDavis by @NoahFierer- starting in a few minutes “Exploring terra incognita – the biogeography of soil microorganisms”Jonathan Eisen

Introduction for @NoahFierer talk at #ucdavis refers to him as a self described expert on cooties .. this has to be goodJonathan Eisen

@noahfierer Did you ever play the Cooties game? I did, now I’m an entomologist. Trapped.Jack C. Schultz

For more on work of @noahfierer (whose talk at #UCDavis I am live tweeting) see http://www.colorado.edu/eeb/EEBprojects/FiererLab/Jonathan Eisen

Now tweeting from @NoahFierer ‘s #UCDavis seminar “Exploring terra incognita: the biogeography of soil microorganisms” No eukaryotes tho :(Holly Bik

Fierer at #UCDavis defends referring to plants and animals as “macrobes” as better than calling small things microbesJonathan Eisen

Fierer at #UCDavis: 4000-2000 kg microbial biomass per hectare (from Fierer et al. 2009 Ecology letters)Jonathan Eisen

Fierer at #UCDavis: vast majority of soil microbial diversity undescribed, quotes Donald Rumsfeld as “patron saint of microbial ecology”Jonathan Eisen

Fierer at #UCDavis: example of Acidobacteria – up to 30% of bacteria in soil from this phylum yet only 5 described generalJonathan Eisen

Fierer at #UCDavis: using microbes to test principles of biogeography/ecology; using biogeography to learn about poorly understood microbesJonathan Eisen

Fierer at #UCDavis: in 2006 $10K = 400 bacteria IDd in each of 5 samples; 2012 $10K = > 10K bacteria IDd in each of 500 samplesJonathan Eisen

Fierer at #UCDavis: reduction in sequencing cost / increase in capacity allows 1st time biogeography studies of microbes on large scaleJonathan Eisen

Fierer: You can’t do ecology with 5 samples (old methods) – now costs have dropped, we can sequence 100s of samples to look at ecologyHolly Bik

Fierer at #UCDavis: dealing with this: “There is no biogeography of anything smaller than 1 millimeter” Bland Finlay Science 2005 vol 310Jonathan Eisen

Fierer at #UCDavis: collected soil samples from diverse biomes (tundra, desert, prairie, forest) & asked what calls “19th century” eco ??sJonathan Eisen

If the bacterial/archaeal people are doing 19th century ecology (as says @NoahFierer), then us eukaryote people are stuck in the dark ages..Holly Bik

Fierer at #UCDavis discussing Lauber et al. 2009 http://www.ncbi.nlm.nih.gov/pubmed/19502440 – ~1000 sequences per sample x 80 + samplesJonathan Eisen

Fierer at #UCDavis discussing this figure http://aem.asm.org/content/75/15/5111/F4.large.jpg from 2009 paper – where simple ordination did not distinguish samples wellJonathan Eisen

Fierer at #UCDavis now discussing Figure B from http://aem.asm.org/content/75/15/5111/F4.large.jpg saying that soil pH shows strong association w/ microbe Beta diversityJonathan Eisen

“@Dr_Bik: Fierer: You can’t do ecology with 5 samples costs have dropped, we can sequence 100s of samples 4 ecology” SORT OF. Whoo R U? $$$Jack C. Schultz

Fierer et al. refs http://aem.asm.org/content/75/15/5111/F3.large.jpg from 2009 paper that shows good relationship between soil pH and alpha diversityJonathan Eisen

Fierer at #UCDavis: their soil data did not show any obvious relationship to latitude, mean annual temp, or other variables looked atJonathan Eisen

Fierer at #UCDavis: their data showing relationship between pH and microbial diversity could have been due to some feature related to pHJonathan Eisen

Fierer at #UCDavis: looked at soil microbes in one biome in arctic and still had correlation with pH and diversityJonathan Eisen

Fiere at #UCDavis: refs. http://www.nature.com/ismej/journal/v4/n10/full/ismej201058a.html where even in controlled system (Rothamsted Research) pH & microbial diversity correlatedJonathan Eisen

Does pH itself drive soil microbial assemblages, or aluminum toxicity (Al and pH closely linked)? We don’t know yet says @NoahFiererHolly Bik

At #UCDavis @NoahFierer: discussing PNAS 2012 Soil paper http://www.pnas.org/content/early/2012/12/05/1215210110.full.pdf – metagenomics of VERY different soil samplesJonathan Eisen

At #UCDavis @NoahFierer: in soil metagenomic data only ~ 20% of reads could be annotated (i.e., function predicted)Jonathan Eisen

At #UCDavis @NoahFierer: in soil metagenomic data there is a weak ++ correlation between 16S PD and functional diversityJonathan Eisen

At #UCDavis @NoahFierer: desert soils VERY different from other soils in beta diversity of taxa & functionsJonathan Eisen

At #UCDavis @NoahFierer: looked are which genes were driving the major differences beta. soils in deserts & other locationsJonathan Eisen

At #UCDavis @NoahFierer quotes Willa Cather “elsewhere the sky is the roof of the world but here the earth was the floor of the sky”Jonathan Eisen

. @NoahFierer heads to 19th century graveyards to sample native prairie grass habitats for soil microbes. One of least disturbed sites..Holly Bik

At #UCDavis @NoahFierer refs paper that modelled distributions of Sasquatch http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2699.2009.02152.x/abstractJonathan Eisen

At #UCDavis @NoahFierer discussing collaborative work w/ Josh Ladau from UCSF http://docpollard.com/jladau/index.html (who I collaborate w/ too)Jonathan Eisen

At #UCDavis @NoahFierer says “Microbial ecology needs more Ecologists” (emphasizes the capital EJonathan Eisen

At #UCDavis @NoahFierer: Ecology needs more microbial ecologyJonathan Eisen

Pleas frm @NoahFierer: Microbial ecology needs more Ecologists–lots of data out there, not being fully used, & lots of reinvention of wheelHolly Bik

At #UCDavis @NoahFierer: ecological restoration projects need to consider microbes as part of the storyJonathan Eisen

“: @NoahFierer: ecological restoration projects need to consider microbes as part of the story” or quit stupid reconstructionJack C. Schultz

“: At #UCDavis @NoahFierer says “Microbial ecology needs more Ecologists” (emphasizes the capital E” ) Brilliant!Jack C. Schultz

Lots of reasons reconstruction is purely subjective, starting with “which era do we reconstruct?”. Not “science”Jack C. Schultz

For a different take (e.g., why is YOUR reconstruction THE reconstruction?) see http://www.amazon.com/Invasion-Biology-Oxford-Mark-Davis/dp/0199218765Jack C. Schultz

Both true! – MTs: “: At #UCDavis @NoahFierer: Ecology needs more MICROBIAL ecology” &”Microbial ecology needs more Ecologists”Gavin Collins

@jackcschultz sure some restoration projects have issues but the “not science” accusation makes you sound sillyJonathan Eisen

Some fun holiday reading about the UC Davis Medical Center neurosurgeon saga

Well, here are some new news stories to read:

For some background see my detailed post with much of the history in the story here.

I must say, it certainly seems time to replace the administration at the UC Davis Medical Center. The Dean is stepping down, but not for some months (see Amid controversy, Claire Pomeroy to step down as UC Davis med). The main administrator Ann Madden Rice is still there. I wouldn’t expect her to stay for long.

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Noah Fierer talk at #UCDavis on biogeography of soil microbes

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