Meeting Report: ASM 2013 in Denver, Day 1

Posted on May 20, 2013 by

The first day at ASM was amazing.   Started off the morning by attending the “Putting ‘Omics to the Test” session which contained talks by Ed DeLong, David Stahl, Nicole Dubilier, Julia Vorholt, and Thomas Shenk.  The overall theme of this session was to look at example where ‘omics data (genomics, proteomics, transcriptomics, etc.) data was used to generate testable hypotheses.  All of the speakers then gave example of where these hypotheses were followed up in the lab.  It was nice to see the emphasis on relating ‘omics data to the lab instead of just as an overview.  I skipped out on the end of this session to see “What the Chimpanzee Microbiome Tells us About the Human Microbiome” by Howard Ochman which was cool.

Went to a special interest session before lunch called “Accomplishments and Legacy of the Soviet Bioweapons Program, 1928-1992″ by Raymond Zilinskas from the Center for Non-Proliferation Studies.  His talk was both fascinating and quite scary.

In the afternoon was our microBEnet-sponsored session called “Citizen Microbiology:  Enhancing Microbiology Education and Research with the Help of the Public”.   The goal of this session was to have a series of talks by the few folks who are actually doing citizen microbiology, with a particular focus on problems and issues they’ve encountered.   A good description of the rationale for this session can be found on Jonathan’s blog here.

First Graham Hatfull talked about his awesome phage discovery project which has now involved thousands of students and a number of institutions as well as characterized many many new phages and produced several publications.

Then Georgia Colares talked about the cell phone and shoe sampling citizen science project undertaken in Jack Gilbert’s lab.

Jack Gilbert and Dan Smith then gave a tag-team talk about the home microbiome project they’ve been working on.

Then Darlene Cavlier (founder of Science Cheerleader and SciStarter.com) gave an inspiring talk on those two organizations and on citizen science in general.  I got the feeling a lot of people were surprised at the scope of many of the (non-micro) citizen science projects out there.

This was followed by Jessica Richmond who talked about the uBiome project.

In a very similar vein was the next talk by Antonio Pena who talked about the American Gut Project.

Rounding out the session (in his trademark hysterical and informative style) was Rob Dunn who talked about the Wildlife of Our Homes project and the various “turns” in his life that lead him there.

All in all a great day.

ASM2013Day1

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Another reference genome for microbiology of the built environment studies: Curtobacterium flaccumfaciens

Posted on May 18, 2013 by

Another genome report from our microBEnet project on generating reference genomes for microbes from the built environment is out: Draft Genome Sequence of Curtobacterium flaccumfaciens Strain UCD-AKU (Phylum Actinobacteria).

From the paper:

Curtobacterium flaccumfaciens strain UCD-AKU was isolated from a residential carpet in Davis, California, as part of a project to produce reference genomes for microorganisms living in the built environment. Carpet fibers were placed in Luria broth (LB), incubated overnight at 37°C, and plated on LB agar ….

And then the genome was sequenced …

We are doing this project for many reasons not just to generate reference genomes for microbes from the built environment.  Another reason is to get students interest in microbes from the built environment and what better way than to have them isolate such microbes and work on them.  Also – we figured if we are going to write about studies of microbes in the built environment, well, it would be good to do some work on such microbes.  And for many other reasons.

Anyway – just a quick post here.  Congratulations to UC Davis undergraduate Jennifer Flanagan for this work and to the rest of the team. For more on the project see here.

Undergrad Project

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National Toxicology Program factsheet on mold

Posted on May 17, 2013 by

The National Toxicology Program (NTP) just released an updated fact sheet on mold in the built environment.   Very handy introduction to the subject, including some information on current research on the topic.   Thanks to James Scott for bringing this to our attention.

FactSheet

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Software Carpentry comes to UC Davis!

Posted on May 17, 2013 by

Last September, I watched Greg Wilson’s three-minute pitch for Software Carpentry, and I was SOLD! Do I want to get more done at the computer in less time? Absolutely! The only difficulty was waiting until this week for it to happen. Finally, this past Monday and Tuesday (May 13-14,) Software Carpentry arrived at UC Davis. The instructors were (in order of appearance) Matt Davis, Tracy Teal, Azalee Bostroem, and Chloe Lewis. Vince Buffalo showed up to help and observe, as did two members of the Eisen lab, Russell Neches and Guillaume Jospin. We were also accompanied by master assessor, Caitlyn Pickens.

photo-2

On Day 1, Tracy Teal gave a great introduction to the shell. I would describe the pace as quick baby steps, which was perfect for most of the room. Even those who use the shell all day every day, like myself, were able to pick up a few new tricks. And, Tracy has such a quick wit, that if you didn’t pay constant attention, you were going to miss something really funny. Then, Azalee introduced git, which I had heard about before, but I’d always felt was something that “real” programmers used. It never occurred to me that I could use it for version control, or even that version control was something that I should be doing. And, holy cow, I should DEFINITELY have been using git or something like it for at least the last 7 years. She made many compelling arguments for using it, but the two that stuck with me were 1) avoiding the existence of files named Dissertation_final_last_MostRecentVersion_7.doc and 2) avoiding the scenario in which you’re feeling pretty good about yourself because your new script actually does what you want it to do, so you decide that you’re going to add one minor tweak to make it even more awesome, and then it stops working, and you don’t understand how you broke it, and so you try to fix it, but you end up getting so far away from a functional script that you decide to delete it and start from scratch because, well, when you started from scratch the first time, that’s when it worked.

photo-3I made python cookies for Day 2!

On Day 2, Matt introduced us to Python using the iPython Notebook. As someone with a decent amount of self-taught experience with Perl, I originally did not understand why we were playing with colored blocks. I admittedly spent too much time trying to figure out how I was going to be incorporating colored blocks into my research. But, when we switched from manipulating colored blocks to manipulating text files, it was like the clouds parted and I was already programming in Python! It took me a while to figure out how I would use the notebook for my research (well, I’m still not 100% sure, but I’ll give it a try) but there are some things that I loved about it right away. For example, help is easily accessed while you’re writing the code, so if you can’t remember the syntax, you don’t have to do yet another Google search for: perl split syntax. The other thing I really, really like is being able to test little chunks of code without saving and running the entire script.

Chloe gave a nice introduction to making pretty figures with matplotlib. She tied in the basics that we’d learned from Matt to convince us that “Yes, we can!” plot our data! I love that there’s a gallery of plots to choose from, and I hope that the reviewers don’t mind (or notice?) when my next publication includes a figure that’s been XKCDified!

Overall, it was a great boot camp! These folks have clearly invested a lot of time into thinking about how to teach scientists to be smarter computer users, and it shows in the quality of the instruction. I would love to host a boot camp at UC Davis on a regular basis, so if you are interested in attending one in the future, please send me an email, and I will notify you when the next one is coming!

Jenna Lang

jennomics@gmail.com

 

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New funding opportunity in its Microbiology of the Built Environment (MoBE) program.

Posted on May 17, 2013 by

The Alfred P. Sloan Foundation has created a new funding opportunity in its Microbiology of the Built Environment (MoBE) program.

The Foundation seeks to further the development of talented early stage Ph.D. scientists and engineers by establishing the Microbiology of the Built Environment (MoBE) Postdoctoral Fellowship program. The program will provide support for postdoctoral researchers in laboratories engaged in research on the microbiology of the built environment in the U.S. or Canada. Eight awards of $120,000 each will be awarded over the 24 months of the program. Successful fellows will have developed an innovative project in consultation with an established advisor in the research area.

Deadline for applications: September 1, 2013

Announcement: October 2013

Research Area of Interest: Applications most likely to be of interest should describe innovative fundamental research in the microbiology of the built environment. Cross-disciplinary studies in microbial biology and engineering are encouraged.

Eligibility: Applications will be accepted from graduate students for their first postdoctoral fellowship, and the fellowship must begin within one year of completion of the Ph.D. degree. Awards are open to applicants in academic and other not-for-profit organizations, the states, districts, and territories of the United States of America and Canada. Graduate students will initiate the applications for the fellowships but these applications must include a letter of commitment from the potential postdoctoral advisor. Successful applicants must be committed to conducting research on the Microbiology of the Built Environment during their postdoctoral fellowship.

Selection Awards will be based on several factors: assessment of the proposed research, the arrangements for the interdisciplinary educational broadening of the fellow, and the previous research records of the potential fellow and advisor. Distinguished scientists and engineers who are knowledgeable in the field will review the applications. The Sloan Foundation is committed to enhancing diversity in the science and engineering communities and applications from graduate students from underrepresented groups are especially encouraged.

Budget The MoBE Postdoctoral Fellowship program provides a $120,000 award, payable in two $60,000 installments. Funds are normally expended over a period of two years after the appointment of the fellow. Charges associated with indirect costs or institutional overhead are not allowed. The stipend support for the fellow should be at least $48,000 of the total annual award amount (stipends may be supplemented from institutional or other sources). $2,000 is provided as a stipend to the fellow for travel or research expenses. Fringe benefits from this award may not exceed $10,000 per year. In the event that institutions/laboratories receiving the MoBE Postdoctoral Fellowship award have higher rates for fringe benefits, the institution must provide the difference

Application Procedure All application materials must be received electronically by the deadline of September 1, 2013. Winners will be announced in October 2013.

Application package: The application and application details can be requested from Wolf@sloan.org

If you have specific questions, please contact Paula Olsiewski at olsiewski@sloan.org.

ResearchFunding

Posted in Building science, Funding, Sloan Program | Tagged , | 5 Comments

“…antibiotic resistance genes may be transported via aerosols on local scales”

Posted on May 17, 2013 by

CAFO - USDA photo

In their just published paper in Environmental Science & Technology, “Tetracycline Resistance and Class 1 Integron Genes Associated with Indoor and Outdoor Aerosols,” Alison L. Ling, Norman R. Pace, Mark T. Hernandez, and Timothy M. LaPara have found that genes escape the indoor environment and can be found 2 km away. The abstract can be read and the article can be accessed here. (ES&T is not open access, but it is the most widely-read and respected journal in the environmental engineering community.

“…[Q]uantitative polymerase chain reaction (qPCR) was used to determine the abundance of tetracycline resistance and Class 1 integrase genes in aerosol samples collected from livestock farms, human-occupied indoor spaces, and outdoor air along the Rocky Mountain Front Range in Colorado, USA. [They] hypothesized that CAFOs and clinics may contribute significant concentrations of aerosolized resistance genes which can potentially spread via aerosol transfer.” They found that antibiotic genes escaping from two confined animal feeding operations (CAFO), one swine and one dairy, could be found in outdoor air 2 km distant from the CAFO.

“The widespread subtherapeutic use of antibiotics in animal feed has been controversial in the United States, since it has been considered a major source of antibiotic resistance to nearby soil and water, and is often considered to be unnecessary or avoidable.4,5 In general, hospitals and confined animal feeding operations (CAFOs) are assumed to be the most significant sources of antibiotic resistance because of their extremely high utilization
of antibiotics.”

While much of the Sloan Foundation’s Microbiology of the Built Environment Program focuses on characterizing microbes indoors (air, surfaces, dust, and water), this paper reports research, partially funded by the Sloan Foundation, that looked at genes escaping from the indoor environment and traveling as aerosols. The study found that CAFOs are a source of the relatively high abundance of airborne bacterial genes, “…a substantial fraction of which carry antibiotic resistance genes.”

The authors concluded that “…our recovery of antibiotic resistance genes from aerosols across different indoor environments has implications for public health, hospital quarantine measures, and indoor air quality.”

This study of airborne bacterial transport from indoors to outdoors reminds me of studies of SARS spread in the Amoy Gardens apartment complex in Hong Kong where the index case was in a building across a very large open area from a downwind building where many cases occurred. (See Ignatius et al, 2004, “Evidence of Airborne Transmission of the Severe Acute Respiratory Syndrome Virus,” NEJM:350:1731-1739.),

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Worth a look: An Introduction to Social Media for Scientists

Posted on May 14, 2013 by

At microBEnet one of our goals has been to experiment with various forms of social media and to see if / how it can be useful in general to the field of “microbiology of the Built Environment.”  For those interested in such things, as well as for anyone interesting in the interface between social media and science, I would recommend you check out this paper PLOS Biology: An Introduction to Social Media for Scientists. By Holly Bik (who is a post doc in my lab and who works on the microBEnet project) and Miriam Goldstein it has many useful bits of information, pointers, and advice.

SocialMedia

 

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Woohoo – two more genome announcement papers from our undergraduate project on built environment reference genomes

Posted on May 10, 2013 by

Two new papers out from the microBEnet Undergraduate Research: Built Environment Reference Genomes  project:

These go with two previously published ones:

And two more coming. So proud of the undergrads in my lab who did this work and David Coil for coordinating it with help from Jenna Lang and Aaron Darling.  Undergrads at UC Davis sequencing genomes of organisms they isolated. So cool.

Undergrad Project

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Asthma: pacifiers, plasticizers, and microbes

Posted on May 9, 2013 by
Jonathan Eisen wearing plastic microbes during his Ted Talk!

Jonathan Eisen wearing plastic microbes during his Ted Talk: Meet your microbes!

By 4028mdk09 (Own work) [CC-BY-SA-3.0 (http://creativecommons.org/licenses/by-sa/3.0)], via Wikimedia Commons

By 4028mdk09 (Own work) [CC-BY-SA-3.0 (http://creativecommons.org/licenses/by-sa/3.0)], via Wikimedia Commons


After some off-line dialogue related to my “Should you lick your baby’s dropped pacifier?” blog post, I have decided to post a separate comment regarding the hygiene hypothesis, mentioned in the introduction, and the plasticizer hypothesis, emphasized by some off-line correspondents.

What is clear is that in the modern, human-occupied indoor environment, there are microbes and plasticizers covering everything!

We have approximately 2,000 organisms on every square centimeter of our exposed surfaces (skin, mouth, upper respiratory). And as we shed all of our skin cells (which we repeatedly do every two to four weeks), the natural skin oils (with low volatility) and the microbes on normal skin end up covering all the surfaces exposed to the indoor environment — floors, walls, ceilings, furnishings, and dust…and of course, pacifiers!

Can you really distinguish between the two potentially important, potentially causally-related agents (microbes and chemicals) when we inhale, touch or lick objects in our environment?

What about the possibility of an adjuvant effect? Or an additive or synergistic effect of exposures to both microbes and plasticizers (and other semi-volatile organic chemicals abundant in our indoor environments such as pesticides and fire retardants)? Of course studying complex, interactive effects is extremely difficult, but absent such studies, the possibilities cannot be excluded. And there is sufficient evidence to support the interactive effects hypothesis.

A 2011 European Commission report (Kortenkamp et al ) pointed to additive effects of exposure to certain types of endocrine disrupting chemicals (EDCs).

A 1975 report of the National Academy of Sciences, Principles for Evaluating Chemicals in the Environment, highlights the potential for interactions: “It is widely recognized that in many instances the action of a toxic agent can be modified by exposure to other agents.” (page 13). The report gives examples of thousandfold potentiation of exposure to a known carcinogen by exposure to a second, non-toxic substance! (Bingham and Falk, 1969. Arch Env Health 19:779-783).

The risk of lung cancer from asbestos exposure and cigarette smoking illustrates the synergy of these two exposures: the combined risk is equal (approximately) to the multiple of the two separate risks. (see Asbestos-related diseases and smoking.)

But studies of combined effects are extremely difficult and somewhat rare in the scientific literature.

Limitations of research funding, human subjects research review committees, epidemiology, and the necessities of statistical analysis combine to impede scientific studies that can elucidate combined effects and risks. Add to the mix the potential importance of the variations in human genetics and the human microbiome, and we recognize the difficult of blending advances from various scientific disciplines to understand the complexity of modern life.

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Should you lick your baby’s dropped pacifier?

Posted on May 6, 2013 by

By 4028mdk09 (Own work) [CC-BY-SA-3.0 (http://creativecommons.org/licenses/by-sa/3.0)], via Wikimedia Commons

By 4028mdk09 (Own work) [CC-BY-SA-3.0 (http://creativecommons.org/licenses/by-sa/3.0)], via Wikimedia Commons


A story on the May 6th NPR program, Morning Edition, “Parents’ Saliva On Pacifiers Could Ward Off Baby’s Allergies” features a focus on the human microbiome, partental behavior and babies’ allergies.

“That word “microbiome” — describing the collection of bacteria that live in and on our bodies — keeps popping up. This time, researchers say that children whose parents clean their pacifiers by sucking them might be less likely to develop allergic conditions because of how their parents’ saliva changes their microbiomes.”

The NPR story is based on a small Swedish study of 184 Swedish babies. The story was based on an article published in this week’s issue of the journal Pediatrics. 65 babies whose mother or father sucked on their babies’ dropped pacifiers to clean them were reportedly far less likely to get eczema and asthma than babies whose parents did not clean dropped pacifiers by licking them.

micrbobe.net has abundant posts on the human microbiome, viewable as a search result here.

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