Saturday, March 29, 2014

Why I don't like to pre-submit slides for talks - lessons from #AAASMoBE meeting

So - I gave a talk at a meeting on Thursday.  The meeting was called "Microbiomes of the Built Environment" and it was sponsored by the Alfred P. Sloan Foundation and run by AAAS.

The meeting organizers, as is often the case, wanted me to submit my slides a few days in advance, in theory to make sure they were loaded into their system and that all worked OK.  Well, as usual, I did not do this.  I like to make my talks fresh - just before the meeting so that I can incorporate new ideas into them and so that they do not have that canned feeling that a lot of talks do.

My talk was to be 15 minutes long and was to focus on my Sloan Foundation funded project "microBEnet: the microbiology of the built environment network" (see http://microbe.net for information about the project). I figured, I would work on the talk on the plane - five plus hours to edit a talk I had given relatively recently on the topic of this project.  And all would be good.  Plus, United had told me there would be WiFi on the plane so if I needed any new material I should be able to get it from the web right?  Well, the flight took off on time - 8 AM on Wednesday morning.  And I opened my laptop once allowed and paid the $15+ dollars for the WiFi and got to work.  Then, about 10 minutes later, the WiFi died and despite heroic efforts by the flight attendants, it never came back. And I plugged away at my slides doing some edits of the following presentation.




Thursday, March 27, 2014

Guest post by Jay Kaufman: A Bad Taste That Keeps Not Getting Any Better....

Guest post by Jay Kaufman.  Jay and I have been having some email discussions about a paper in PLOS One.  I offered to let him write a guest post to my blog about his concerns.

-------------------------------

Jonathan Eisen already posted on this blog about a PLoS ONE paper by Mason et.. published on 23 October 2013.  And he posted related comments on the PLoS ONE website.  I also commented at this site, in reference to his comments and the authors' response. The purpose of my comments here are just to review those concerns and comment additionally on the PLos ONE response and what this means for the journal's publication model and the progress of science.

The paper by Mason and colleagues analyzes data on 48 people in each of 4 self-identified ethnic groups (African American, Caucasian, Chinese, and Latino). These study subjects are apparently volunteers, and the paper only states that they are non-smokers over 18 years old who are free of a list of diagnosed diseases and who have not recently had their teeth cleaned. Based on the text of the published paper, there is no consideration of their age, diet, social class, or even gender. The authors culture bacterial species from the study subjects and process the data through an algorithm that maximizes the prediction of racial group membership based on these measured data.

The prediction is moderately successful, but this could result from any number of unsurprising reasons. For example, if alcohol consumption affects some particular bacterial species, and whites drink more than Asians in central Ohio, then whatever species is diminished by alcohol exposure would help predict that a sample was from a white rather than from an Asian volunteer. And likewise for any of a million possible lifestyle, social class and demographic differences.  In fact, this is a general problem with data mining exercises that Lazer et al describe in the current issue of Science.

The authors provide no information about how balanced this sample is with respect to any of these variables. Maybe the 48 Hispanics are younger than the 48 whites on average, or have more tooth decay or eat more refined sugar or any of a million other possibilities. The fact that these countless potentially imbalanced factors get represented in the oral bio-environment hardly seems surprising, and the fact that these behaviors and exposures might be differential by race is an observation that is completely trivial from a sociological perspective.

My concern here, however, the authors assert in the published text that these differences do not arise from any of these myriad environmental factors, but from some innate genetic characteristics of the groups. In the Discussion section on page 3 they state that "ethnicity exerts a selection pressure on the oral microbiome, and...this selection pressure is genetic rather than environmental, since the two ethnicities that shared a common food, nutritional and lifestyle heritage (Caucasians and African Americans) demonstrated significant microbial divergence." Here is a remarkable statement, that Caucasians and African Americans experience no differential dietary or lifestyle factors. It is directly contradicted by thousands of published papers in sociology, epidemiology and anthropology that document these differences for reasons of culture, geographic origin, social class and discrimination.

Jonathan Eisen's post directly confronted the authors on this point, and they responded with the following explanation:

"Subjects were selected based on extensive questionnaire surveys and clinical examinations to ensure homogeneity. These questionnaires evaluated educational level, socio-economic status, diet and nutritional history, systemic health status, oral hygiene habits and dental visits, among other things."

This is surely an important statement about the research design, but the problem is that it appears nowhere in the peer-reviewed text of the published paper. What exactly do the authors mean when they insist that the study subjects were perfectly balanced on factors such as socio-economic status and nutritional history? These complex social and lifestyle variables are notoriously difficult to define and measure. While the authors describe the laboratory techniques in baroque detail, they do not even mention in the published paper that they measured these factors, let alone how these variables were defined and considered in the analysis. This represents a profound limitation for the reader in assessing the validity of these measures and adjustments, and therefore the adequacy of the claimed "homogeneity". The complete omission of these crucial aspects of the analysis in the paper prevents the reader from investing much confidence in the boldly stated claim that observed differences are "genetic rather than environmental" in origin.

I expressed these concerns in my own post at the journal website on 14 November 2013, but the authors did not respond.  Therefore, at Jonathan's suggestion, I addressed this concern to the PLoS ONE editors in an e-mail on 22 November 2013. I got passed along from one editor to another, and finally I got a very nice response from Elizabeth Silva on 4 December 2013. She wrote:

I wanted to let you know that I am discussing this article and your concerns with both the Academic Editor and the authors, as well as with my colleagues. We take such concerns very seriously and will ensure that appropriate measures are taken to correct any errors or discrepancies. 

Then I waited.  After 2 months I had heard nothing, so I wrote to Dr. Silva again asking for any word on progress, but received no reply.  So I waited another month.

On 4 March it had been 3 months since the note from PLoS ONE promising appropriate measures to correct any errors or discrepancies, so I wrote again, this time a bit more insistently.  This did message did finally generate a quick and reassuring response from Dr. Silva:

I really am very sorry for the extended delay in replying to you, and for my neglect in providing you with an update. Following your correspondence I contacted the authors to ask them for additional information relating to their statement that they corrected for confounding factors, and details of these methods. They promptly replied with a table of details of the baseline variables that they corrected for, and that they described in the comment on their article (see attached), as well as an additional correction to one of their figure legends. I then contacted the Academic Editor, Dr. Indranil Biswas with the full details of your concerns, as well as the table sent by the authors and the correction they requested for their figure legend. We asked Dr. Biswas to revisit the manuscript, in light of this new information, and he has informed us that he feels the conclusions of the manuscript are sound. We will now work with the authors to draft and issue a formal correction to the published article to update the methods to include the table, and to amend the figure legend in question.

The table that Dr. Silva forwarded displayed a list of variables and a p-value for some kind of test between the values in the 4 race groups. The test is not specified (t-test? chi-square test?) but presumably it is for any difference in means or proportions between the 4 groups.  Most of the p-values are large, indicating little evidence for any difference between the groups in income, age, education, or frequency of tooth-brushing, etc.  Based on this table, the populations differed only in their diets, which were characterized as "Asian Diet", "Hispanic Diet" and "American Diet".  Not unsurprisingly, the Asians were significantly more likely to report an "Asian Diet" and the Hispanics were significantly more likely to report a "Hispanic Diet".  The Blacks and Whites had similar reported consumption of the "American Diet", which presumably was the basis for the authors' assertion that these groups have identical social environments.

To date, there has been no correction made to the Mason et al paper at the PLoS ONE website.  Therefore it is perhaps somewhat premature to speculate on how the authors will address the concern voiced by Jonathan Eisen's posted comment and blog post that balance across a handful of measured covariates does not in any way imply balance across all relevant factors except for genetics. Indeed, it has long been argued in the epidemiology literature that one cannot make indirect inferences about genes by measuring and adjusting for a few environmental exposures and attributing all remaining differences to genes.  The argument that Blacks and Whites in Ohio experience identical environments is clearly false, even if a handful of measured covariates are not significantly different in their small convenience sample, the exact origin of which is still obscure.

There are many observations that can be made from this episode. I offer just a few:

  1. These authors are assiduous in describing their lab techniques, but regarding the study design and analysis they are quite cavalier.  Presumably the reviewers were not population scientists, and so they failed to point out these embarrassing flaws. This raises the question of whether a multidisciplinary journal such as PLoS ONE has the relevant expertise to screen out scientifically invalid papers. The fact that Dr. Silva suggested that the authors' table of covariates and p-values solves the issue demonstrates a wide gap of understanding.  Specialty journals that handle a narrow disciplinary range are not faced with this kind of crisis of competence.
  2. PLoS ONE is such a large operation with so many papers, that quality control seems to suffer. These beleaguered editors are responsible for an enormous publishing volume. Has quantity overwhelmed quality to the extent that gross errors of logic slip through? Months later, the Mason paper has been accessed thousands of times and generated a great deal of media attention, and yet no correction or erratum has appeared, despite the fact that the authors freely admit that the methods in their published paper are not accurate. 
  3. The publishing model gives PLoS ONE a big incentive (almost $2000) to accept a paper, but once it is published, little incentive to correct or withdraw it. 

Sadly, this is not an isolated example.  This week, PLoS ONE published a paper by Wikoff et al which makes a similar logical gaffe about observed racial difference proving a genetic difference.  We could post a comment online, but it seems that nobody (neither the authors nor the editors) has much time to spend monitoring such comments, nor much incentive to care about them.  The authors have their publication, the journal has its $2000, and another tiny piece of horrific misinformation has been released into the world.  The basic philosophy of PLoS ONE is to reduce the gate-keeper role of scientific publication. I am starting to become convinced that a little gate-keeping is not such a bad idea.

Tuesday, March 25, 2014

Wrap up of Twitter chat on the human microbiome with a high school bio teacher

It started with this
And eventually we worked out a date, which was yesterday. Now I note I had no idea who these people are/were. But it seemed like a good chance to do some some outreach. So I said yes. And yesterday it happened. OK it was chaotic. But it was fun. Here is a Storify of the Tweets.

Sunday, March 23, 2014

Microbiome topic of the day: radiation therapy and the microbiome

Just saw this interesting story in the Observer: Cancer scientists to classify gut bacteria to prevent the side-effects of radiotherapy | Science | The Observer.  It discusses an effort to give more consideration to protecting and / or repopulating the microbiome in relation to radiation therapy.  I think this is critically important.  I want to note - people should give some credit to DARPA for being ahead of their time on this issue.  I went to a workshop in 2004 organized by Brett Giroir and Manley Heather.  The topic was "Radiation Protection" and one of the points of discussion was the gut microbiome and the effect of radiation on it.

Anyway - since that meeting I have been following this topic on and off.  And I do think thinking about the microbiome in relation to radiation therapy (and any radiation exposure) is critically important.


Saturday, March 22, 2014

Simple microbiome quiz and then mapping function from PGED

Just did this: Map-Ed Genetics: Pin Yourself on Our World Map! (the microbiome one - there are two right now - the other is personal genomics - and others coming).  Best part is browsing the map of other participants afterwards.

mBio - home of some really cool, #openaccess microbiology papers

Am really enjoying the suite of papers coming out in mBio - the Open Access PLOSOne like journal from the American Society for Microbiology.  Here are some examples of recent papers that caught my eye:
And many many more.  Kudos to ASM and mBio.

Thursday, March 20, 2014

is Sexxing up your scientific journal OK? The Journal of Proteomics seems to think so

I saw a Tweet from a college classmate of mine -  Jillian Buriak - that pointed me to this article from the Journal of Proteomics in January 2012.

Harry Belafonte and the secret proteome of coconut milk

And this is what one sees when one goes there:
A "Graphical Abstract" with the text "Here is your coconut woman, as perhaps envisioned by Harry Belafonte. For its proteome, though, have a look at the report inside!".  I guess this is an attempt at a joke about breasts and coconuts?  And how is it appropriate for a scientific paper?

Want to guess about the gender balance of the people who run the journal? Here are the pics from the web site of the main executive editors and officials








Tuesday, March 18, 2014

Postdoc Position in Innovating Communication in Scholarship

3/17/2014

Postdoc Position in Innovating Communication in Scholarship

A new UC Davis initiative on "Innovating the Communication in Scholarship" (http://icis.ucdavis.edu/) is hiring a 2 year postdoctoral fellow, starting July 1, 2014. This is a cross-disciplinary project to study the future of academic publishing, involving faculty from the Center for Science and Innovation Studies, the Library, the Genome Center, and the School of Law (with additional collaborators in Computer Science, English, Philosophy, and the Graduate School of Management). Research topics include open access models, peer review, new forms of quality metrics, data publication, use of social media, and new forms of academic misconduct.
The successful candidate will conduct research, collaborate on or lead organization of conferences, workshops, participate in pedagogical activities, and assist in grant writing. A Ph.D. or equivalent degree is required in Science and Technology Studies, Library and Information Sciences, Communication, Law, Science, or Literature. Other disciplines will be considered depending on the specific focus of the candidate's research and other experience. Qualified applicants will have experience working successfully in teams and managing multi-year projects. He or she will possess excellent written and oral communication and administrative skills.
We encourage applicants from historically under-represented groups, as well as individuals who can contribute to the diversity and excellence of the academic community through their research, teaching, and/or service.
Salary is based on experience and qualifications according to UC Davis guidelines.
To apply: E-mail a PDF file containing your CV, short description of your research experience relevant to this position, and contact details for three references to Mario Biagioli (mbiagioli@ucdavis.edu), MacKenzie Smith (macsmith@ucdavis.edu), Jonathan Eisen (jaeisen@ucdavis.edu).
Applications are due by April 15, 2014.

Saturday, March 15, 2014

Collecting my posts from various blogs, all in one place ...

Trying to just compile my posts from various blogs I contribute to all in one place so decided to do it here.  These are posts for the last month or so

From the Innovating Communication in Scholarship blog and Website


Posts of mine at the microBEnet blog

UC Davis ADVANCE

Wednesday, March 12, 2014

Overselling the microbiome award of the week: Science News on "Bacteria that Trigger Crohn's"

Well, this is just a terrible, terrible, very misleading headline: Bacteria that trigger Crohn's disease identified | Science News.  The headline relates to a story by Ashley Yeager on a new paper in Cell Host and Microbe.  The paper is "The Treatment-Naive Microbiome in New-Onset Crohn’s Disease" and it seems very interesting on first glance and very very very careful in the wording about what they have shown in the paper.  And all that care is wasted with news headlines like this.  The paper does not identify any bacteria that "trigger" Crohn's.  They do identify microbial signatures with various aspects of Crohn's and find some very interesting things.  But no triggering is shown.  Nor claimed.  And then Science News misleads people into thinking this article will be about what triggers Crohn's.  Lame.  Annoying.  And a winner of the Overselling the Microbiome Award of the week.

Wednesday, March 05, 2014

Guest post by Lizzy Wilbanks: Story behind the paper "Microscale sulfur cycling in the phototrophic pink berry consortia of the Sippewissett Salt Marsh"

Here's another entry in the "Story behind the paper series".  This one is from Lizzy Wilbanks, a co-advised PhD student in my lab (Twitter: @LizzyWilbanks)


A sulfurous symbiosis: Microscale sulfur cycling in the phototrophic pink berry consortia of the Sippewissett salt marsh 

Here's the story behind my recent publication (with many talented coauthors) on the pink berries, the marvelous, macroscopic microbial aggregates of the Sippewissett.

A bit of background:

The wild microbe rarely eats alone. The microbial world is a jungle far more exotic than those we can see (metabolically and phylogenetically, at least), one rife with fierce competition, intimate cooperation, and intricately inter-dependent food webs. Eavesdropping on the metabolic conversations of uncultured microbes, though, remains a major technical challenge.  It requires tools to navigate the world from the microbe's-eye view.
     
 Your binoculars just aren't gonna cut it...  (image source )
In our recent paper, my co-authors and I describe how we were able to tune in to one such metabolic conversation, and look at a nutrient ('biogeochemical') cycle on the microbial scale. Here's the back-story on how this project got started, and why I'm so excited to share our work with you!

Let's get one thing straightened out:

'Pink berries' are a nickname for these pink colored microbial aggregates.  We're not talking about fruit or frozen yogurt here.
(image source: my own, here, and here)

My first encounter....

I first encountered these eye-popping pink wonders in 2010 when I was as a second year grad student attending the Microbial Diversity summer course at the Marine Biological Laboratory in Woods Hole, MA.  Exploring the nearby Little Sippewissett Salt marsh for our first field trip, I stomped through the marsh grass into a muddy, sulfidic pool.
And people wonder why I think sulfide smells like beautiful summers and nostalgia?
(image source: my own)
Below the surface of the pool's water, scattered across the sediment, was a truly magnificent carpet of pink blobs. 
(image source: my own)
After a bioinformatics-heavy start to grad school at UC Davis, I was dying to get my hands dirty with some fieldwork.  I was transfixed by the stinky, sulfidic marsh mud and these slimy pink aggregates. 
Me, awfully excited and really "diving-in" to the project.
Can't remember how many times TA Annie Rowe and others had to fish me out of the mud that summer!

(image source: Melissa Cregger :) 

Course directors at the time, Dan Buckley and Steve Zinder, told me that these were the pink berries, balls of uncultured bacteria found in the Sippewissett marsh (and, so far as they knew, nowhere else). Summer students had been looking at the berries ever since the course was founded 40 years ago, they said, and they pointed me towards a pile of old course reports back at the lab.  

Berries: an MBL Microbial Diversity legacy.

These reports (now digitized and freely available) tell the tale of many happy, hard-working summers where students took a crack at these exotic looking blobs during their independent research mini-projects.  One of the most fun parts of this project has been meeting all of these "berry alumni", both via email and in person, who are now scattered throughout the world. From helpful discussions, to sharing data and suggestions, and even digging up never-published 16S rRNA gene sequences from over a decade ago (thanks Bruce Paster and Jarrod Scott!), the berry-alums have helped lay the groundwork for our project and have been an amazing network of friends and collaborators.  

Our paper is a sequel, 20 years in the making, to the first and only other paper describing the pink berries.  Published in 1993 by MBL summer students Angelica Seitz and Tommy Nielsen with course faculty Dr. Jörg Overmann, this work described the berries as aggregates dominated by uncultured purple sulfur bacteria, anoxygenic phototrophs that oxidize hydrogen sulfide to sulfate (unlike cyanobacteria and green plants that oxidize water to oxygen). By spearing berries with oxygen microsensors, they found that the berries were such hot-spots of microbial activity that all oxygen was consumed just a few micrometers below the surface, creating a haven for anaerobic microorganisms.  
My obviously-not-to-scale cartoon of berry spearing with oxygen microsensors.
The purple sulfur bacteria give the berries their rosy hue with their photosynthetic pigments that have evolved to capture lower-energy, longer wavelength light (compared that used by green phototrophs). 
Peering into the pink berries with a dissection microscope (real color!).
Pink blobs are islands of purple sulfur bacterial cells.

(image source: Verena Salman) 
With the introduction of 16S rRNA gene sequencing to the course in 1997, students discovered that, in addition the conspicuous purple sulfur bacteria, the berries also harbored an abundance of an uncultured species related to sulfate reducing bacteria (sulfate -> sulfide).  The co-occurrence of putative sulfide-oxidizing purple sulfur bacteria and sulfate reducing bacteria spawned the hypothesis that these species might be metabolically interdependent, creating a "cryptic" sulfur cycle within the berries.  
The hypothesis! Purple sulfur bacteria in pink, sulfate reducing bacteria in green.
(image source: my own, modified version of Figure 9 from our paper) 
These sulfate reducing bacteria, though, had remained elusive, uncultured, and their activity, undetected. This intriguing hypothesis about an "intraberry" sulfur cycle and metabolic cooperation ('syntrophy') remained untested like so many other questions about the secret lives of uncultured microbes.

Project launch: Team berry 2010

Resolved to work on the pink berries for my mini-project, I banded together with fellow students and co-authors Ulli Jaekel and Parris Humphrey, and with the help of TAs Cristina Moraru and Rebekah Young - formed Team Berry 2010.  We began investigating the pink berries using DNA sequencing (16S, metagenomics), microscopy (FISH, TEM) and other incubation studies. 

The first few weeks at the MBL course were bonanza of microbial excitement for me as a huge metabolism geek.  My mornings were spent trying to drink from the fire hose of information in lecture, followed by afternoons of lab, then dinner, more lab, and finally trying to piece together the day's ideas over beers.
"Drinking from a fire hose" - another gem from PhDComics
Coming back from Dan Buckley and Victoria Orphan's lectures about the uses of stable isotopes in microbial ecology (reviewed here), I wondered if there was a way to use sulfur stable isotopes to track the cryptic sulfur cycle in the pink berries.  Brainstorming with Victoria, we devised a plan to conduct incubations with the pink berries using isotopically heavy sulfate (34SO42-) as a stable isotope label.  The purple sulfur bacteria in the berries had abundant intracellular sulfur reserves, which typically come exclusively from reduced forms of sulfur (e.g. sulfide).  Our hope was that the sulfate reducing bacteria would reduce the heavy sulfate we added to heavy sulfide, which would then be oxidized by the purple sulfur bacterial and incorporated into their cells.

To track the flow of our isotopically labelled sulfur, we planned to image thin sections of the incubated berries using nanometer scale secondary ion mass spectrometry (nanoSIMS), an instrument commonly used by the Orphan lab for studying anaerobic methane oxidizing consortia.
Using the nanoSIMS to blast sections of pink berries with  focused cesium beam (~50nm spot size)
and generate spatial maps of isotopic and elemental abundance.  
(image source: my own)
At that time, there was no precedent in the literature for using 34S-isotope labeling in this way (most stable isotope probing experiments focused on carbon or nitrogen compounds), but Victoria's group was interested in exploring this area for studying other tightly coupled sulfur-cycling.  The berries were an accessible testing ground. After a madcap two weeks of rush-orders, late nights, midnight berry slicing, and help from so many wonderful, patient TAs, our samples made a cross-country journey to the Orphan lab at Caltech where they, and thankfully the nanoSIMS, survived a minor earthquake.  
The nanoSIMS beast in its subterranean lair @ the Caltech Microanalysis Center.
(image source: my own)
It was a wild ride during those final weeks, but just before the end, we got exciting results from Victoria's nanoSIMS run that suggested our experiment had worked.  The preliminary nanoSIMS data showed accumulation of our sulfur isotope label (enrichment in 34S compared to controls), and also found evidence for carbon fixation (13C enrichment from labeled bicarbonate additions).

Can't stop, won't stop... the side-project that ate my thesis.

After returning to Davis, passing my qualify exam and wrapping up prior projects, I was determined to get back to berries but wasn't sure exactly how.  Victoria suggested that she could include berries in a collaborative NSF proposal on the biogeochemistry of tightly coupled sulfur cycling consortia (along with David Fike, Greg Druschel and Jesse Dillon).  When their funding came through, it held out the safety net I needed to work on berries full time.  With approval from Victoria and my co-advisers at Davis, I jumped!

Returning as a TA to the MBL Microbial Diversity course in 2011, I had a chance to conduct follow up isotope experiments, and collaborate with course student and co-author Verena Salman on developing species-specific FISH probes to identify the spatial arrangements of the two berry symbiotic.  Since then, I've followed up on our initial metagenomic sequencing to reconstruct near-complete genomes for the two berry symbionts, demonstrating the genetic potential for a complete sulfur cycle.

Figure 4 from our paper showing:
the sulfate reducing species (green rods, 16S rRNA gene FISH probe)
snuggled up with their metabolic partners,
the purple sulfur bacteria (pink/purple cocci, autofluorescence),
but not in the exopoylmer matrix with  
other cell types  (blue, DNA stain: DAPI).
In 2012, the final pieces of this project came together during a week of Sippewissett fieldwork with biogeochemistry collaborators  David FikeGreg Druschel, and their groups.  With high resolution geochemistry equipment aboard our homemade raft, we were able to link our existing microbiological measurements with microscale geochemical signatures in the berries.
(image sources: my own)


Conclusions:

Using the pink berries, we demonstrate how an integrative microbiological and microgeochemical approach can be used to decrypt the microbial metabolic partnerships that drive sulfur cycling at the microscale. This methodology, which may ultimately be used to examine more complex ecosystems, offers direct evidence of syntrophic interspecies sulfur transfer. 

For more details on how all these different pieces came together, you'll just have to check out our paper yourself!   

FAQ:

What do they taste like?
Mostly just salty, and a bit sandy :)

Are the pink berries found anywhere else?
Not really!  I've looked through the literature and chatted up loads of people, but no one's ever reported seeing pink berry-type macroscopic consortia of purple sulfur bacteria and sulfate reducers.  There's a description of a microscopic type pink berry-like aggregates in the chemocline of Lake Cadagno, and interestingly those aggregates' sulfate reducing isolate (Cad626) is closely related to our PB-SRB1 sulfate reducing species.   Should you find berries somewhere else during your marshly peregrinations, email me!

Have you tried culturing them?
Yes!  My undergraduate students recently confirmed that we have an enrichment culture of the purple sulfur bacterial strain, and are working to purify it, and submit it to a culture collection.  If you're interested in working on it, I'm happy to send you a sample of the culture.  The sulfate reducer has, so far, resisted my efforts to coaxing it into culture but hasn't really been a major focus of my project (I'd wager it's possible).

So wait, why are you studying them again?
  • My naturalist's answer is: because they're the pink, charasmatic macrofauana of the microbial world. They're nifty, and we don't know what they do. But seriously... 
  • Microbial metabolism is the engine that drives the nutrient (biogeochemical) cycling that shapes the health of both our planet and our bodies.
  • However, many key transformations in these cycles are carried out by microbial consortia over short spatiotemporal scales that elude detection by traditional analytical approaches. 
  • The berries provide a tractable, reproducible model microbial consortia for developing methods to eavesdrop on these otherwise cryptic metabolic conversations between the wild microbes.
  • Understanding the biosignatures (e.g. sulfur isotopic fractionation) produced by microbial communities like the pink berries improves our ability to interpret the rock record and construct models of ecosystem function in both ancient and modern environments.

Thank you:

Through this project, I've had the privilege of working with truly amazing people and making life-long friends.  The author list and acknowledgement are just the tip of the iceberg in terms of people who have contributed to this project in one way or another.  You all know who you are; I feel so lucky to have gotten to know and work with you. THANK YOU!

This project was started as grass-roots style, curiosity-driven student research, and as such, the funding for it has been fairly eclectic.  I want to take a moment to acknowledge those organizations that have supported this kind of research and made my work possible.

Funding to the MBL Microbial Diversity course from:
  • Howard Hughes Medical Institute
  • Gordon and Betty Moore Foundation (#2493)
  • National Science Foundation (DEB-0917499)
  • US Department of Energy (DE-FG02-10ER13361)
  • NASA Astrobiology Institute (NAI)
Grants to collaborators Victoria Orphan and David Fike from:
  • NSF (EAR-1124389 & EAR-1123391)
  • Gordon and Betty Moore Foundation (#3306)
Grad-student grants and fellowships supporting my work at UC Davis from:
  • National Science Foundation Graduate Research Fellowship
  • UC Davis Dissertation Year Fellowship
  • P.E.O. Scholar Award
  • NAI/APS Lewis and Clark Fund in Astrobiology
  • NSF Doctoral Dissertation Improvement Grant (DEB-1310168)

Full citation:

Wilbanks EG, Jaekel U, Salman V, Humphrey PT, Eisen JA, Faccioti MT, Buckley DH, Zinder SH, Druschel GK, Fike DA, Orphan VJ. (2014) "Microscale sulfur cycling in the phototrophic pink berry consortia of the Sippewissett Salt Marsh." Environmental Microbiology,  doi:10.1111/1462-2920.12388,  http://dx.doi.org/10.1111/1462-2920.12388.




What to do when kicked out of my own lab meeting?

Thought some would enjoy a bit of comic relief.


Monday, March 03, 2014

A must read: How to Level the Playing Field for Women in Science by Mary Ann Mason

This is a must read for anyone interested in Science / Academia: How to Level the Playing Field for Women in Science - Advice - The Chronicle of Higher Education.  By Mary Ann Mason, who is a professor at UC Berkeley and has extensive experience on studying issues relating to women in science and academia.  She details in this article four key things that can be done to reduce the "baby penalty":
  • Better (and more) child-care options
  • Effective dual-career policies
  • Childbirth accommodations
  • Compliance with Title IX 
Definitely worth reading.  And worth checking out some of the web material from her including
(Thanks to Madhu Katti - who posted this to Facebook)

Another Mostly Male Meeting from UCSD- should be called "Food and Fuel for the 19th Century"

Well, just when I thought meeting organizers from UCSD had learned their lesson regarding mostly male meetings - this comes along.  Check out "Food and Fuel for the 21st Century" (I was pointed to this by a comment on a blog post of mine). The speakers are
That a ratio of 18:2 or 10% female.  

Not that I know the cause of this but here are some other pieces of information to consider.

The Food and Fuel for the 21st Century Program lists 5 people on their Executive Committee.  Any guesses on the # of these that are men?  Well it is 5.
Fortunately they have an Advisory Committee too and that must have some women on it right?  Nope.
Reminds me a bit of the QBio meeting from 2013 organized by many from UCSD which I wrote about last year: Q-Bio conference in Hawaii, bring your surfboard & your Y chromosome because they don't take a XX.  I note - this years Q-Bio meeting is much better.  But one can ask - does nobody at UCSD think about these issues when planning conferences and Advisory / Executive Committees.  I personally don't think one should choose women to just choose women.  But as with the Q-Bio meeting from last year, I think there are an enormous number of highly qualified women working on topics directly related to "Food and Fuel for the 21st Century" and thus I am both surprised and disturbed by the gender ratio of this meeting and this organization.


UPDATE 3/4 7:21 AM

It took me a bit but I found details on the 2013 symposium from the same group.  The web site for the 2013 meeting is not active as far as I can tell.  However it is available in the Internet Archive.  For example, here is a snapshot from June 1, 2013.  From that snapshot here are the listed speakers
  • David Kramer, Michigan State University
  • Susan Golden, University of California, San Diego
  • Julian Schroeder, University of California, San Diego
  • Stephen Mayfield, University of California, San Diego
  • Steven Briggs, University of California, San Diego
  • Matteo Pellegrini, University of California, Los Angeles
  • Donald Weeks, University of Nebraska--Lincoln
  • Michael Burkart, University of California, San Diego
  • Chancellor Pradeep Khosla, University of California, San Diego
  • Farzad Haerizadeh, Life Technologies
  • Ben Hueso, California State Assembly
  • Bill Gerwick, Scripps Institution of Oceanography
  • Eric Mathur, SG Biofuels
  • James Van Etten, University of Nebraska--Lincoln
  • Fred Tennant, Heliae
  • David Dunigan, University of Nebraska--Lincoln
  • Xuemei Bai, Cellana
  • George Oyler, University of Nebraska--Lincoln
  • Gerry Mackie, University of California, San Diego
  • Mark Hildebrand, Scripps Institution of Oceanography
  • Lawrence Johnson, Salim Group
  • Craig Behnke, Sapphire Energy
  • Rebecca White, Sapphire Energy

For a ratio of 20:3.

Sunday, March 02, 2014

Save the dates / preliminary program for Lake Arrowhead Microbial Genomes Meeting

UPDATE 3/13/14 - Official Web Site now up


------------------------------------------------------------------
Preliminary information for the The Lake Arrowhead Microbial Genomes - which is going to be great (note - I am on the planning committee) is below.  Registration information and Abstract Submission details will be coming soon.

Preliminary Program of Confirmed Speakers
Lake Arrowhead International Microbial Genomics Conference
September 14-18, 2014

Keynote Speaker: 
  • Julia A. Segre, National Human Genome Research Institute, NIH, Bethesda, MD (skin microbiome; tracking outbreaks through genomic sequencing)
Mirobial Communities I: Microbiomes
  • Peter Turnbaugh, Harvard University, Cambridge, MA (human microbiome)
  • Noah Fierer, University of Colorado, Boulder, CO (human microbiome; soil microbial communities)
  • Sarkis K. Mazmanian, California Institute of Technology, Pasadena, CA (gastrointestinal microbiota)
  • Andrew Goodman, Microbial Diversity Institute, Yale University, West Haven, CT (human microbiome; pathogens)
Microbial Communities II, Metagenomics, Biodiversity, Natural Products, Evolution
  • Nancy Moran, University of Texas, Austin Texas (Symbiosis between multicellular hosts and microbes)
  • Tanja Woyke, DOE Joint Genome Institute, Walnut Creek, CA (metagenomics; single cell genomics)
  • Eric J. Alm, Massachusetts Institute of Technology, Cambridge, MA (evolution of microorganisms)
  • Michael Fischbach, UCSF, San Francisco, CA (Insights from a global analysis of secondary metabolism: Small molecules from the human microbiota)
  • Jessica Green, University of Oregon, Eugene, OR (metagenomics; built environment)
  • Karyna Rosario Cora, University of South Florida, St. Peterburg, FL (Exploring the viral world through metagenomics)
  • Susannah Green Tringe, DOE Joint Genome Institute, Walnut Creek, CA (Microbial communities and the carbon cycle)
  • Nicole Perna, University of Wisconsin, Madison, WI (Evolution of the response to oxygen availability in enterobacteria: a complex trait in a model family)
  • Katie Pollard, UCSF, San Francisco, CA (Metagenomics; evolutionary genomics)
  • Jenna Morgan Lang, University of California, Davis, CA (Citizen microbiology)
Pathogens, Antibiotic Resistance
  • Julian Parkhill, Welcome Trust Sanger Institute, Cambridge, UK (genomics of pathogens; tracking outbreaks through genomic sequencing)
  • Lance B. Price, George Washington University, Washington, D. C. (foodborneurinary tract infection studies)
  • Gautam Dantas, Washington University, St. Louis, MO (reservoirs of antibiotic resistance)
  • Jeffrey T. Foster, Northern Arizona University, Flagstaff, AZ (genomic epizootiology of white-nose syndrome in bats)
  • Timothy D. Read, Emory University School of Medicine, Atlanta, GA (S. aureus antibiotic resistance genomics)
  • Evgeni Sokurenko, University of Washington, Seattle, WA (Pathoadaptive mutations in microbial genomes)
  • Jennifer Gardy, University of British Columbia, British Columbia, Canada (Genomics and epidemiology)
  • Ashlee Earl, The Broad Institute of Harvard and MIT, Cambridge, MA (Pathogen and Comparative Genomics)
Systems Biology, Metabalomics, Synthetic Biology
  • Fiona Brinkman, Simon Fraser University, Greater Vancouver, British Columbia, Canada (Using genomics and network analysis to characterize disease outbreaks)
  • Mallory Embree, University of California, San Diego, CA (Deciphering dynamic community interaction using systems biology)
  • Fuzhong Zhang, Washington University, St. Louis, MO (producing biofuels and pharmaceuticals with synthetic biology)
  • Sri Kosuri, University of California, Los Angeles, CA (synthetic biology, TBA)
  • Michele C. Chang, University of California, Berkeley, CA (expanding fluorine chemistry of living systems by genetic engineering)




Saturday, March 01, 2014

When to "defend" on Twitter and when to listen #scio14 #scicomm

So - by Friday morning I was dying for the weekend to come. It had been a rough week.  Without getting too much into my saga, suffice it to say that "The saga of my pancreas..feet..microbiome ..blood.. liver - part 1" is not turning out so well right now and medical issues are on my mind a lot. With a little help from my family, friends, colleagues, and cats I have been getting by.
And as Friday went by things were not getting better. And then another medical issue and I had to head home early. Fun. I was just starting to recover, getting ready to watch a movie with my wife and kids when, well, the Twitter world intervened. I started to see some posts from Science Online 2014 making not so positive comments about the SpaceMicrobes project in which I am involved. Oh - and they were coming from people like Madhu Katti, who I deeply deeply respect.
It took me a few minutes to figure out that there was a microbial swabbing "event" going on at Science Online connected to the Space Microbes project. And there were many many questions being posted to the Twittersphere about the project by Madhu and a few others (e.g., see one below).
Hmm. This did not look good. But for perhaps the first time in a very very long time I felt like somehow I should not respond online. I am not sure why I felt this. I think partly I felt that, since the Space Microbes project is a collaboration in which many people from my lab are involved (and help run) that somehow I should let this play out without my "interference". I think somehow I thought that once I got involved it could become more about me and not about how the people involved handled the questions in real time. Now - I say "I think" and "somehow" and such because this was going on while I was reading books to my son (my phone was just sitting next to me, and I really did not want to look at it or follow what was going on). So - anyway - I did not do anything directly, but I sent an email to some of the people from my lab who are involved in the SpaceMicrobes project. It included an intemperate title line and the following text:
You should look at Twitter What exactly is happening at Science Online? Who is doing sampling there and what is the purpose?
Anyway - after I wrote this it was about time for movie night to start with my wife and kids and things were getting complex. My son did not want to watch the same movie as my daughter. Important decisions had to me made. And now I was getting sucked into Twitter. And I started to try to answer some of the questions Madhu and DocRicky and others had. Madhu made a Storify of much of the exchange.

Now - I personally believe that we can answer all the questions Madhu and others had about the project. And I started to try and explain some of the goals and aims of the project and the reason things were done in the way they were done. However, I was also explaining bits of Star Trek II to my son.  And I started thinking - was "defending" the project really the right thing to do here? I thought not actually.  And I decided that this was an important moment to listen and learn (and step away from the keyboard a little) and not to defend. The event that was happening (or happened - I was not sure if it was live or after the event) was what it was. If the people there could not answer the questions coming up, and if our materials on the web and in the handouts could not answer the questions, then we had, well, failed. And my explaining things on Twitter was, in a way, a cheat only made possible because I was willing to ignore family time and be online.

So - I did not completely put away the keyboard but I stopped trying to explain it all away and started trying to just listen and to accept that things had gone a bit awry. Anyway - clearly those of us involved in SpaceMicrobes need to do a better job in multiple areas. I will not try to defend or explain or justify everything here either. But I will say - thanks. To the people who are willing to ask questions and have high expectations. I will just end this post with a few of my last Tweets



Wrap up of recent posts of relevance on microBEnet

I have been doing a lot of blogging at microBEnet and don't always do a good job of cross posting or even posting here to let people kno...