What I do for a living Part 5: The Indoor Microbiome

Last June, I started a position as a Research Assistant Professor of Microbial Ecology at the Biology and the Built Environment Center at the University of Oregon.  The BioBE Center is a collaborative, interdisciplinary research team investigating the built environment – the ecosystem that humans have created for themselves in buildings, vehicles, roadways, cities, etc.  With my background in host-associated microbiology, I am concerned with how the built environment interacts with biology.

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Humans shed microorganisms constantly – every itch, every cough, every minute.  In fact, our buildings are littered with the biological material shed from our bodies and our microbiomes (1, 2, 3, 4).  Pets (1, 2) and plants (1, 2) also contribute, and so does outdoor air (1, 2).  In fact, the indoor environment is full of microorganisms.

 

In addition to knowing how our presence, our behaviors (ex. cleaning), and how we run our buildings (ex. ventilation) creates the indoor microbiome, I want to know how the indoor microbiome affects us back.  Not only can “sick buildings” negatively affect air quality, but they can harbor more microorganisms, especially fungi, or pathogenic species which are detrimental to our health.

My first indoor microbiome data is one that I have inherited from an ongoing project on weatherization in homes, and hope to present some of that work at conferences this summer.  Since June, a large amount of my time has gone into project development and grant writing, most of which is still pending, so stay tuned for details.  It has involved read lots of articles, going to seminars, networking, and brainstorming with some brilliant researchers.

As research faculty, I am not required to teach, although I have the option to propose and teach courses by adjusting my percent effort (I would use the teaching salary to “buy back” some research salary).  As I am not currently tenure-track, I am also limited in my ability to hire and formally mentor students.  However, I have been teaching bioinformatics to a student who recently graduated with his bachelor’s and is pursuing a masters in bioinformatics later this year.

I’ve also been keeping up with my science outreach.  I gave a presentation on my host-associated microbiome work, I marched, I volunteered for a few hours at Meet A Scientist day at the Eugene Science Center, and I’m hosting a Science Pub on “A crash course in the microbiome of the digestive tract” at Whirled Pies in Eugene this Thursday, February 8th!

 

 

Anyone can Science, step 3: show your support

The political climate of 2017 has already raised several causes for concern among U.S. scientists: from politicians who reject current scientific theory, to dramatic cuts proposed to federal or state budgets for research (and jobs), to enacting hiring freezes and stopping grant payments, to policy changes which would allow for governmental oversight on which and how results were disseminated (a gag order).  Certainly, other administrations have suggested or enacted scientific budget cuts, or called for hiring freezes and gag orders, but never before has a president and White House administration so clearly come out against scientific literacy, education, research, and policy.

This change of political tone has encouraged many scientists to voice their concerns, but we scientists also need the support of the general public.  After all, science is largely designed to improve the lives and economies of everyone.  According to the U.S. Bureau of Labor Statistics, STEM jobs accounted for 8.6 million US jobs in 2015 in the U.S., but an estimated 26 million jobs (20% of jobs in 2011) require knowledge of a STEM field, a sector that consistently has low rates of unemployment, and expands the US economy.  Thus, even without thinking about the politics of science, we can agree that scientific research is a vital part of the U.S. economy.  Additionally, 93% of STEM occupations have wages above the national average.  If you are a scientist, know a scientist, or generally want to show your support, here are some ways you can get involved.

March for Science

Signing petitions, wearing slogans, and being vocal to legislatures and the public about your support is wonderful, but a show of solidarity can bring people together to effect change.

On Saturday April 22, 2017, people will March for Science in cities across the United States to peacefully show their support for scientific literacy, education, policy, and freedom of speech.  Please consider joining them.

You can find a march near you, here.  A number of scientific organizations have endorsed the March for Science, including (in no particular order) the Union of Concerned Scientists, the Georgia Academy of Science, the National Science Teachers Association, the American Public Health Association, the American Geophysical Union, the American Chemical Society, the American Association for the Advancement of Science, and others.  And if you need inspiration for a sign or an outfit, there are lots of places that are ready to help you out.

Financial Support

As I discussed in a previous post about research grant money, financial support of science is always welcome.  There are lots of ways to contribute, whether it’s donating to organizations to fund research for specific medical conditions, participating in a crowd-funding campaign to raise money or get equipment donated, becoming a member or donating to scientific advancement organizations, or even just taking a grad student out to lunch.

Rock the Vote

Support for scientific funding, education, and policy may not be at the top of your list of reasons for supporting political candidates, but it should be on there somewhere.  After the first few months of 2017, a number of scientists have decided to hang up their lab coat and run for public office, so you’ll have plenty of options in the coming elections.


I would like to acknowledge Drs. Irene Grimberg and Fabian Menalled for their edits to this post, as well as the ongoing efforts of my editor, Mike Haselton, MA, towards improving my writing.

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Anyone can Science, step 1: get your education on

Co-written by Dr. Irene Grimberg, Affiliate Associate Research Professor at Montana State University.


Science may seem like an exclusive club, what with the complicated technical jargon, quirky inside jokes that only seem funny to science people, daunting entrance and exit exams, and years of study and self-improvement.  And it doesn’t help that many scientists would rather hole up in their lab than give a public presentation or figure that “social media thing” out.  But we scientists get coffee stains on our lab coats and use spell-check just like everyone else.  And as with ice cream, science comes in a tremendous variety of flavors and sizes of commitment.  So, let’s talk about some ways that you can involved today!

Education

Getting acquainted with the vast field of science seems daunting, but it’s actually easy and fun.  There are hundreds of museums out there that are eagerly waiting to broaden your perspective on science, technology, engineering, and mathematics (STEM), and will let you give it a try with hands-on activities.  Wikipedia has conveniently made some lists on science museums in the US and around the world.  In fact, there are organizations like the American Alliance of Museums and the Association of Science-Technology Centers that can help to get you connected to the museum that catches your eye.  Many US National Parks also have strong science education programs and information in the visitor centers or around the park (at least, as of January 19th, 2017 they did).

All colleges and universities host daily talks (seminars) on current research and they are open to the public, they just aren’t advertised widely in local media.  If you search online for your local university and “seminar”, you can find public presentations for nearly every department or subject, not just the STEM ones.  Some presentations are available as webinars and can be found online to watch remotely in real-time so that you can ask questions, or can be replayed later at your leisure.  There are many outreach STEM programs sponsored by non-profit organizations, sometimes in collaboration with universities.  For example, Farm Days or Field Days are public presentations at university research facilities on issues related to local and national agriculture, food production, and food safety.  In fact, most university farms and greenhouses are open to the public and offer free tours and other events on a regular basis.  There are also “ask an expert” shows on local public radio and TV in which viewers can call in and ask questions to university researchers.  Or you can simply email your questions and get connected to someone in a relevant field.  Even NASA has a program in which you can ask questions to an astrophysicist!

Other educational options include science festivals, robotic competitions and shows, Science Olympiads, The National Chemistry Week, and programs that specifically aim to recruit girls to science, such as Expanding Your Horizons and Girls for a Change.  As an undergraduate at the University of Vermont, I participated in a service-learning course in spring of 2008 in which we designed a public presentation at the ECHO Center in Burlington, VT.  The purpose of the all-day workshop was to educate kids and adults on wolf ecology and potential reintroduction into New England.  Our Wolfwise presentation was incredibly fun to host, and it was a huge hit: we were invited to come back and present again the next weekend!

 

If leaving the house isn’t your thing, there are an overwhelming amount of resources available online.  An increasing number of scientific and research journals are available free of charge online, known as open access.  Over 26 million journal articles are available through PubMed, a database for medically-relevant research studies which is curated by the National Center for Biotechnology Information (NCBI).  Science News hosts a huge variety of STEM articles compiled from the most prestigious science journals, as well.  And any subject under the sun (or inside the sun) has an educational video out there somewhere.  There are science shows on TV, a dedicated cable channel, and documentaries including several outstanding educational series with high-definition video footage from around the globe (Plant Earth, Life, and The Blue Planet).  There are podcasts, such as Science, Star Talk Radio, and many others that allow you to listen to recorded audio shows on your own time.  You can find interactive websites to learn a variety of things, both academic and practical.  Or teach yourself computer coding in C++, Java, Ruby, Python, or Perl.

Just be sure that you are getting your information from a credible source.  Many online bloggers or websites sound great, but they often have no formal training in what they peddle, or are heavily sponsored by companies to promote an unsubstantiated lifestyle or discredit scientific work.  A good rule of thumb is to look for qualifications, citations, and motivations.  Does this person or organization have formal education or training?  Do they cite their sources for information?  And what is their reason for doing this?  Here are my qualifications, you’ve seen how much I enjoy citing sources, and since I am (and have always been thus far) federally-funded through different grants, I consider it part of my job to share my work and my experiences free of charge.

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Field bindweed study sampling

Field bindweed (Convolvulus arvensis) is an invasive plant related to morning glories.  Their winding vines grow into a tangled mass which can strangle other plants, and a single plant can produce hundreds of seeds.  The plants can also store nutrients in the roots which allow them to regrow from fragments, thus it can be very difficult to get rid of field bindweed.  It will return even after chemical or physical control (tilling or livestock grazing), but it does not tolerate shade very well.  Thus, a more competitive crop, such as a taller wheat which will shade out nearby shorter plants, reduce the viability of bindweed.

First seen in the US in 1739, Field bindweed is native to the Mediterranean. By 1891, it had made its way west and was identified in Missoula, Montana.  As of 2016, it has been reported from all but two counties in Montana, where it has been deemed “noxious” by the state department (meaning that it has been designated as harmful to agriculture (or public health, wildlife, property).  In the field, this can be visually striking, as pictured below.  In the foreground, MSU graduate student Tessa Scott (lead researcher on this project) is standing in a patch of wheat infested with bindweed. Just seven feet away in the background, undergraduate Lazarro Vinola is standing in non-infested wheat, with soil core samplers used for height reference.
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In agricultural fields, bindweed infestations severely inhibit crop growth and health.

 

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Last week, Tessa, Lazarro, and I went to several farms in and around Big Sandy and Lewistown, Montana in order to sample fields battling field bindweed. To do so, we harvested wheat, field bindweed, and other weed biomass by cutting all above-ground plant material inside a harvesting frame.  These will be dried and weighed, to measure infestation load and the effect on wheat production.

The sampling locations are consistent with previous years to track how different farm management practices influence infestations.  This means using GPS coordinates to hike out to spots in the middle of large fields.

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It also means getting very dirty driving and walking through dusty fields!

I Accepted a New Position in Soil Microbiology and Agroeconomy!

As my current post-doctoral position winds down in the Yeoman Lab in the Department of Animal and Range Sciences, I am pleased to announce that I have accepted a post-doctoral position in the Menalled Lab in the Land Resources and Environmental Sciences Department! Dr. Menalled’s work focuses on agricultural weed ecology and management, particularly with respect to plant-plant interactions, changing climate (water and temperature changes), and now plant-microbe interactions!

I’ll primarily be working on a new two-year project that recently got funded through the USDA, entitled “Assessing the vulnerability and resiliency of integrated crop-livestock organic systems in water-limited environments under current and predicted climate scenarios”, but I’ll also be working collaboratively on several other similar projects in the lab.

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A little pre-job job training: I’m helping to make structures to keep rain out (rain-out shelters) of plots to simulate drier climate conditions.  Photo: Tim Seipel

My new responsibilities will include comparing agronomic performance and weed-crop-pathogen interactions between organic-tilled and organic-grazed systems, evaluating the impact of management and biophysical variables on soil microbial communities, and collaborating in modeling the long-term consequences of these interactions under current and predicted climate scenarios.  It’ll mean a lot more field work, and a lot of new skills to learn!  In fact, to help me study for my new job working with agricultural plants, my mentee and her friend made me flash cards:

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My mentee made my study cards so I could learn to identify common crop and weed species.

In addition to my new skills, I’ll be integrating my background in microbial ecology and bioinformatics, in order to study agricultural ecosystems more holistically and measure plant-microbe interactions.  In the same way that humans eat probiotics to promote a healthy gut microbiome, plants foster good relationships with specific soil microorganisms. The most exciting part is that I will act as an interdisciplinary bridge between the agroecology of the Menalled lab and the microbial ecology of the Yeoman lab, which will allow for more effective collaborations!

 

 

Improving a child’s life is as easy as wearing a paper turkey-hat.

Encouraging girls to go into STEM fields is really important; studies show that female STEM high-school teachers and even online mentors increase the probability of female students following a STEM education.  Moreover, any child benefits academically and psychologically from having positive role models in their life, especially when they were role models that they interacted with as opposed to celebrity role models.  And the benefits don’t just extend to children, adults benefit from positive role models, too.  Certainly I have benefited from strong female role models in my life, from high school art teachers, to undergraduate lecturers, to family (happy birthday, Mom!).

This past fall I started putting my money where my mouth was- I started mentoring an elementary school-aged girl in Bozeman, MT through the Thrive Child Advancement Project (CAP).  So far, we have mostly been making art projects and talking about archaeology.  But we have been talking about trying to learn the Java programming language together!

There are lots of opportunities to mentor kids, either through CAP programs, Big Brother/Big Sister, Girls and Boy Scouts, etc., just a quick internet search brings up dozens of local options.  For less of a time commitment, you can also volunteer for community workshops, like the Girls for a Change summit in Bozeman or the Girls-n-Science in Billings.

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Citizen Science- volunteering for the microplastics study

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Sampling in September, when the stream wasn’t frozen and we could see the trail. Credit: Lee Warren

Yesterday was the winter sampling time point for a large research project I’m volunteering for: Adventurers and Scientists for Conservation is managing sample collection for the ASC Gallatin Microplastics Initiative in the Gallatin Valley watershed. The project samples various streams and lakes, both where they converge with the Gallatin River and at their headwaters.  The project is part of a much larger project looking at microplastics in water around the world, the ASC Worldwide Microplastics Initiative.  ASC recruits volunteers who have the outdoors-man skills (like hiking, tracking, or boating) and enthusiasm to get to hard to reach places to collect samples, then trains them in how to collect water samples and metadata (like weather, temperature, what we’re wearing during collection), coordinates sample collection times, and makes sure to safely send the samples back to a laboratory in Maine.

 

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A lovely view of the Spanish Peaks.

Lee and I sample Deer Creek, just north of Big Sky, Montana.  To do this, we hike 13 miles round trip to Moon Lake, with a 3,288 foot elevation gain up to around 9,000 ft above sea level. This time, the trail was covered in 1-2 feet of undisturbed snow, luckily we had snowshoes that kept us from sinking into all but the most soft of snowdrifts. On the way up it was snowing heavily, though visibility was fine, and on the way down it was raining. In many areas of the trail, drifts meant that the trail was at a 45 degree angle, and we had to break our own trail for nearly all of it. Despite the arduous trek, the views were beautiful, it was wonderful to be out of the office, and it was fun helping a large coordinated study.  You can get involved in studies like this through organizations like ASC, or through research universities- volunteers are always needed for all different types of studies.

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Moon Lake…so where do we start digging?

The Reluctant Interplay of Science and Social Media

Recently, I had another in a long series of conversations with scientists about how they got into science so that they wouldn’t have to use any of their rusty social skills, only to find that social interaction, meetings, and now online communication were a huge part of their daily routine. The myth of the curmudgeon scientist holed up their lab seems to persist despite the current age of social media, perhaps because we scientists don’t seem to understand the appeal of Twitter (how do you include the p-value when you only have 140 characters?!). But in reality, a great deal of our time involves communication, and having practiced social etiquette can make or break you in an interview, at a conference, or at a project pitch meeting.

Many researchers wait until they are hired as assistant professors before they reluctantly make a website, start a blog, or even set up an email account for the lab. How disappointing it must be to wait all those years as a graduate student and a post-doctoral researcher, only to find that a website with your last name has already been taken! And what a hassle to have to generate blog posts, update project and personnel pages, and keep up with social media when you have just landed a professorship and are swamped with grant proposals, manuscripts from old projects that keep hanging around, comparison shopping for equipment to set your lab up, generating coursework for one or several courses, recruiting students…. It’s such a hassle that a friend of mine created an entire business around helping new professors create and manage an online presence: Tenure Chasers.

It really got me thinking, shouldn’t I be starting this?  It’s a little preemptive, after all, I’m a post-doctoral researcher without a lab of my own.  But it makes sense to start it now; for one thing, I have the time to devote to creating the mainframe.  For another, as a new researcher, I sometimes need to prove that I exist.  It seems like a silly thing to think about, but sometimes you need to prove that you are, in fact, a real researcher will real work experience and not just an email scam targeting disused academic email servers (happens quite often).  And hiring someone is a serious consideration, as research funds are limited, indirect costs for personnel make total personnel costs high, you are trusting this person with your research and your career reputation, and you may need to work with this person for several to many years.  It’s a commitment to hire a scientist, and you need to be sure about them.  Thus, having at least one thorough online profile, or better yet- connections to other well-known researchers, can give employers more confidence in you.

Finally, having an online presence improves your communication skills, and shows a commitment to outreach, which is a component in any career level of academia.  It helps to get your work out to other scientists, especially those outside your field whom you wouldn’t run into at a conference or seminar, and more importantly, it disseminates it to the general public.  Graduate school and post-doctoral positions are designed to teach and refine skills, and the skill of communication is no different.  So don’t wait until you really need it, start early and improve the quality of your social media presence, before anyone is paying attention.