Category: News

ESBL/BioBE welcomes new Associate Director of Outreach

ESBL and BioBE are thrilled to announce that Mark Fretz has joined the team as the new Associate Director of Outreach, based out of the Portland location.  Mark brings a unique combination of experience in architecture and public health service, and will help further our goal of promoting health in the built environment through research, outreach, and knowledge exchange.

Mark has a history of successful collaboration with the lab- several years ago he was a research assistant with ESBL.  He helped to develop the idea and grant for our ongoing project on the effect of weatherization on indoor air quality, human health, and the indoor microbiome.  He was also involved developing field materials and pilot studies for our study on the effect of daylight on dust communities, currently in review.

Mark helping set up data collection boxes for the home weatherization project.
Installing “lightboxes” onto the roof of Pacific Hall for a bacterial community study.

In addition to developing future research, and teaching, Mark will primarily be developing the Institute for Health & the Built Environment consortium that ESBL and BioBE initiated in May 2017 with their inaugural meeting.  The Consortium aims to dramatically reduce energy consumption and maximize human health by conducting research that transforms the design, construction and operation of built environments. Mark will help foster collaboration between innovative industry professionals and academic researchers in the disciplines of architecture, biology, chemistry, engineering, and urban design,  provide sharp focus to our research agenda, and accelerate the impact of our scientific discoveries.

Welcome to the team!

Alfred P. Sloan Foundation renews BioBE funding!

Dr. Van Den Wymelenberg, Biology and the Built Environment Center PI and Co-Director, is excited to announce that the Center has secured another two years of funding from The Alfred P. Sloan Foundation and their Microbiology of the Built Environment (MoBE) program.  Van Den Wymelenberg stated, “we are honored to have been awarded a final BioBE Center renewal.  This investment will help us transition to an alternate funding model that aims to progress this important field through both basic science and applied research.  The BioBE Center’s vision is to conduct research and apply this new MoBE knowledge in ways that will optimize the design and operation of buildings and public spaces to promote both human health and environmental sustainability.”

In 2010, The BioBE center was formally implemented with funding from the Sloan Foundation MoBE program.  The Sloan Foundation vision was that we would establish a multidisciplinary center to conduct innovative research on the built environment, while training early-career scientists, and promote the importance of this field to improve the quality of life for people.  For seven years, BioBE has brought together architects, microbiologists, ecologists, snd other researchers at the University of Oregon and a number of collaborating institutions. The Center was launched by Dr. Jessica Green, Dr. Brendan Bohanan, and Professor G.Z. “Charlie Brown”.  Co-PIs at the Center have included Dr. Rolf Halden at Arizona State University, Dr. Erica Hartmann at Northwestern University, and Dr. Curtis Huttenhower at the Harvard T. H. Chan School of Public Health.  The Center has also collaborated with Dr. Jonathan Eisen of UC-Davis in support of public outreach through microBE.net.

Previous BioBE awards have produced 16 peer-reviewed journal publications, over 80 conference and media outlet presentations, and trained over 20 researchers.  In May 2017, BioBE helped to launch the Institute for Health & the Built Environment and a knowledge-exchange industry/research consortium. We will be holding Consortium meetings at least annually, with the next meeting planned for early 2018.  Going forward,  we’ll be furthering our collaboration with the Eisen Lab to develop a sustainable outreach platform, building on microBE.net, and anticipate teaching a joint seminar series in which both architecture and biology faculty present.

With this Sloan funding renewal, we plan to progress the basic scientific research which has helped elucidate the ecological dynamics of microorganisms in the built environment, that will be the foundation for applied scientific research moving forward. Over the next two years, we will be conducting several projects to test, among other things, the effect of air, light, humidity, and materials on the indoor microbiome. We are currently building Scalar Airflow Microcosms to determine whether microbial communities will assemble in dust differently when  air from different microbial colonization sources (outdoors, indoors, or both) is provided to sterilized dust under different humidity levels. Similarly, we will be utilizing existing scalar “lightboxes” to quantify the changes in microbial community structure and viability over time in response to diurnal cycles of solar radiation exposure under different conditions.

We also have a project underway conducting room scale materials tests (wood, painted drywall, glass/concrete, strawbale) in our “climate chamber” to improve our understanding of the role that building materials have on microbial community structure, assembly, and functional profiles. Beginning with microbial community mapping of indoor spaces under different conditions, we are also developing mathematical models of indoor microbiome dynamics to characterize how spatial properties of real buildings relate to microbial population dynamics.

So long, summer!

Written by Hannah Wilson

The beginning of my summer was dedicated to moving the BioBE center’s molecular biology lab to a new location on campus.

Sue, Roo, Ashkaan, and Jeff all pitched in the help pack up the old lab!
The lab is unpacked and up and running!

I dedicated the next part of my summer to finishing the DNA extractions for ~350 swab samples collected from cohort 2 of the EPA weatherization project, and then the corresponding fungal (ITS) and bacterial (16S) library prep (nearly 700 samples in the end). I also completed the DNA extractions and metagenomics library prep for the vacuumed dust samples of the EPA weatherization project (~150 samples), the DNA extractions and 16S library prep for Gwynne’s latest Urban Air data collection effort (~60 samples), as well as finishing the library prep for the adoption study that Ashley had been overseeing (~96 samples).  

In August I took some vacation time to visit Europe, traveling with my partner, Craig. We spent the first part of our trip in the French countryside. We got to go cheese tasting in medieval villages, and visit local markets, castles, and beautiful cathedrals.

We then traveled to the south of France, to Marseille and Toulon, and took a ferry to Sardinia. Sardinia was a very interesting place full of  rich history, culture, and amazing landscapes. 

We topped off our trip with a quick stopover in Amsterdam, where we had a lovely visit with Craig’s friends that he hadn’t seen since college.I spent the last part of the summer updating protocols, troubleshooting methods, working on manuscripts, and harvesting vegetables from my garden and making tomato sauce.

I’ve also been training a new addition to the lab, Mitch Rezzonico, who just started his Masters in Bioinformatics here at UO.  Mitch has been learning common lab techniques, like DNA extraction and PCR amplification, as well as helping Sue with some data analysis.

Mitch preparing for PCR.

Report from the Mycological Society

In July, one of our own, Dr. Roo Vandegrift, went to the annual Mycological Society of America (MSA) meeting, held just outside of Atlanta, Georgia, in the college town of Athens. He went to learn what others in the field are up to, and present work from the BioBE Center. Roo live-tweeted most of the talks he went to; you can find him @MycoRoo on twitter to look back through his experience of the conference, and look up the hashtag #MSA17 or #MSA2017 to see other posts about the conference.

The meeting started with a pre-conference foray: a group of nearly one hundred mycologists loaded into three packed busses and went out to Unicoi State Park for a 3.5 mile hike; collecting mushrooms, ascomycetes, and plant pathogenic fungi all the way. It has apparently been a particularly wet summer in Georgia so far, and the fungal diversity on display was astonishing, particularly coming from Oregon, where our summers are dry and a bit mycologically deprived.

On Monday morning, the day started with the Presidential Address from outgoing president, Dr. Georgiana May, titled “Lucky: A career in mycology.” She gave a rolling account of a career full of lucky breaks and fortuitous moments, which she made the best possible use of with her sharp and grateful mind. She also included a number of historical anecdotes that had the audience in stitches of laughter, and sometimes on the verge of tears. She asked that the contents of her talk remain private, though, so that’s as much detail as I’ll give here.

The first session of talks that I went to was the Ecology & Conservation section, which started with Terry Henkel presenting some amazing work from his lab on the Thelephoralean ectomycorrhizal fungi of a monodominant tropical forest in the Guyana shield region of South America, and how these fungi may be involved in seedling survival and recruitment in this forest. The discussion of this system continued with the next talk in the session, from Terry’s graduate student, Carolyn Delevich, who gave a fascinating discussion of the community assembly of ectomycorrhizal fungi on the roots of these dominant Fabaceae trees, looking at the change in the community over time on the seedlings from one of these mass fruiting events.

There were a number of other excellent talks about mycorrhizal communities, highlighting the cutting edge of molecular techniques in fungal community ecology, host-associated dynamics, and spatial/temporal ecology. Dr. Alija Mujic’s talk on invasion dynamics in mycorrhizal communities of Nothofagus in Patagonia was particularly good.

At the end of that first day, Roo presented his talk: “Impacts of Weatherization on Indoor Fungal Communities“, co-authored with other BioBE personnel, as well as colleagues from the Oregon Research Institute and Northwestern University (Roo Vandegrift, Ashkaan Fahimipour, Jeff Kline, Alejandro Manzo, Dale Northcutt, Jason Stenson, Hannah Wilson, Ryann Crowley, Erica Hartmann, Deborah Johnson-Shelton, G.Z. Brown, Jessica Green, Kevin Van Den Wymelenberg). This talk debuted preliminary data from our EPA-funded study examining a multi-faceted, interdisciplinary dataset combining microbial ecology, indoor air quality, and an extensive survey detailing aspects of health and behavior. Feedback was incredibly positive and encouraging, including some really helpful feedback on biophysical explanations for observed trends in the data.

There were a handful of other talks that stood out as particularly important or impactful. Mara DeMers, from the University of Minnesota, Twin Cities, presented on endophytic fungi in prairie plants, and whether molecular OTUs (or ESVs, for that matter) correspond to species; she asks the question does it matter if they do? She was particularly vexed by the genus Alternaria, which made up most of her endophyte sequences, and appears to be non-resolvable into meaningful groupings via ITS alone — the region is so variable in this group (and other!), that the intra-strain variation is as great as the inter-strain variation, meaning that the same sequence may belong to totally different strains, while very different sequences may belong to extremely closely related individuals. This is an important caution for the field, and one we at the BioBE Center will certainly keep in mind!

Among the amazing talks, excellent company, and stimulating scientific conversations, Dr. Regine Kahmann (from Max Planck Institute for Terrestrial Microbiology) presented the the Karling Lecture, titled “Core Effectors in Smut Fungi: An Amazing Treasure Box.” This was an incredible summary of her life’s work on the molecular mechanisms underlying the pathogenicity and ecology of smut fungi (Ustilagomycota). The careful, methodical, innovative science on display during her talk was breathtaking, and an inspiration.

One other talk strikes me as worth explicit mention here: Jesse Uehling’s discussion of how to re-purpose archived data in new ways. I think there’s an important lesson here; we are generating sequence data much more rapidly than we are currently exhausting the ways that such data can be explored, and the techniques for exploring that data are evolving extremely rapidly. As Jesse says, there may be treasure in that trash!

One idea from her talk that struck me as particularly significant was that the “junk” reads from genomic assemblies are typically reads representing the microbiome of whatever organism was sequenced. It is certainly worth considering that there may be a large quantity of un-examined microbiome data available from a wide range of organisms, if we only go looking through the available raw data. And, the assembly of small bacterial genomes from mixed starting templates has been well demonstrated.

There were many other noteworthy aspects to this meeting; it is worth browsing the #MSA17 tweets if you’re interested. We hope for many more productive, fascinating meetings like this in the future!

~~

Roo wore a different mushroom-patterned bowtie every day of the meeting. We’re not sure why he was so pleased about this.

Congratulations to Dr. Ashley Bateman on her defense, next steps!

We made sure to send her off with some Oregon memorabilia.

Last week, BioBE said good-bye and good-luck to Ashley Bateman, who successfully defended her dissertation on May 25th.  Ashley has been with the department for 6 years, as a graduate student in the Institute of Ecology and Evolution at the University of Oregon.  She worked in the labs of Drs. Jessica Green and Brendan Bohannan, studying the human skin microbiome.  Her thesis, entitled “Moving Microbes: The dynamics of microbial transfer and persistence on human skin“, will soon be available through the University of Oregon library.

Starting in 2011, Ashley has had a very distinguished graduate career; in 2012 she received a  National Science Foundation (NSF) Graduate Research Fellowship Program (GRFP) award to conduct research on the transfer of microorganisms to human skin from contact sources, in 2013 she was named Outstanding Graduate Student by the UO Institute of Molecular Biology, in 2015 she received the William R. Sistrom Memorial Scholarship Award, and in 2016 she won a scholarship from the Women in Graduate Sciences organization at UO to attend the Pacific Northwest Women in Science Retreat.  She has already co-authored a number of cutting-edge papers, including the investigation of the human microbiome cloud, a meta-analysis on the indoor microbiome, and a review on human hygiene, as well as a number of other previously published and forthcoming articles.  Ashley has also been interviewed and has contributed blog posts on the implications of her work.  From here, she is headed to the University of California, Davis, to attend law school.  BioBE is going to miss her insight, her organizational skills and attention to detail, and her welcoming personality, but we are enthusiastic about the next step in her journey!

ESBL is seeking an Associate Director of Outreach in Portland, OR

The Energy Studies in Buildings Laboratory (ESBL) at the University of Oregon is seeking a new Associate Director of Outreach at the Portland location!

At ESBL, as part of the Department of Architecture, we research how buildings, related transportation and land use systems, climate, and human behavior, determine energy and resource use and impact human health. We develop new materials, components, assemblies, whole buildings, and communities with improved performance. We consult and develop design tools to enable professionals to design more effective buildings and communities. We educate professionals and students, so they develop the knowledge and skills necessary for improving building energy performance and human well-being. Finally, we collaborate with academia, government agencies, utilities, product developers, and the profession. ESBL works closely with the Biology and the Built Environment Center (BioBE) as ESBL Director, Dr. Kevin Van Den Wymelenberg, is Co-director of BioBE.  Examples of our collaborative work include how the shape of a building and its use affects microbial dispersal, or the effect of home weatherization on air quality and the indoor microbiome, and many other studies in our state-of-the-art climate chamber in Portland.

Together, BioBE and ESBL launched the Health+Energy Research Consortium (HERC) in May 2017 with their inaugural meeting, which brings university researchers and building science professionals together to exchange information on the built environment, assess the need for research that can provide answers related to design and health choices, and foster collaborations that benefit both the academic and industry sectors while providing a beneficial impact on human health, building design, and energy sustainability.  The Consortium aims to dramatically reduce energy consumption and maximize human health by conducting research that transforms the design, construction and operation of built environments. Collaboration between innovative industry professionals and academic researchers in the disciplines of architecture, biology, chemistry, engineering, and urban design provides sharp focus to our research agenda and accelerates the impact of our scientific discoveries.

Position Summary
The Department of Architecture seeks a creative and innovative faculty member for a faculty position to teach, secure and conduct research, oversee the Portland ESBL, and to cultivate outreach and engagement. The chosen candidate will support the ESBL director by leading the lab’s Portland-based outreach efforts by securing grants and contracts to fund the lab’s work. Specifically, the candidate will lead the effort to develop the HERC industry-university research consortium (following, in-part, the NSF IUCRC model). S/he will also be expected to contribute to ESBL’s teaching obligations to A&AA students in Portland, possibly including architectural design studios, environmental control systems, and related technical courses. The selected candidate will develop and maintain strong industry support for the University of Oregon HERC, thus this position will have a large outreach component. Finally, the selected candidate will share the obligation to secure and conduct research, technical assistance, and project based education in cooperation with ESBL faculty and staff and associated architectural and engineering professional design teams to support ESBL’s mission.

Minimum Requirements
• Terminal degree from accredited college or university.
• Three or more years of research or outreach administrative experience, or relevant transferable experience.
• Professional training or relevant transferable experience managing a budget.
• Experience in a lead or supervisory role.

The full job posting and application can be found here.

The initial review of applications begins August 1st, 2017, but the position will remain open to application until filled. We look forward to hearing from you!

Dr. Sue Ishaq joins the BioBE team!

Hello, readers! I’m Dr. Sue Ishaq, the newest Research Assistant Professor hire in the BioBE center at the University of Oregon.  I’ve been at the center for two weeks now, and I thought I’d introduce myself as I’ll soon be a regular contributor to the center’s research efforts and blog.  I’m a microbial ecologist with a focus on host-associated microbiomes. My baccalaureate and doctorate were both in animal science and nutrition from the University of Vermont, in Burlington.  As a Ph.D. student in the Wright Lab, my work focused on identifying and manipulating the bacteria, methanogens, and protozoa in the rumen of the North American moose.  For the past two years, I was a post-doctoral researcher at Montana State University, in Bozeman.  For one year, I was in the Department of Animal and Range Sciences performing the bioinformatic analyses for multiple host-associated and environmental projects in the Yeoman Lab.  My second year was in the Department of Land Resources and Environmental Sciences in the Menalled Lab, where I was part of a large project investigating the effect of climate change on wheat production.  For my part, this meant assessing the changes to soil bacteria over time and under different climate scenarios.

Here at the BioBE, I’ll be adding my experience in host-associated microbiomes, bacterial ecology, and health, to the growing collaborative research team.  Over the course of the summer, I’ll be writing several grants and organizing new projects that explore how building design, occupancy, pets, and human habits affect human health and the indoor microbiome.  If you happened to have been at the Health + Energy Research Consortium, held in Portland in May, you might have seen me around, and I’ll also be at the Ecological Society of America meeting in Portland, OR in August.  You can follow me on my personal blog and, of course, you can find me on the BioBE blog!

Multiple Positions Open at University of Oregon BioBE Center

Kevin Van Den Wymelenberg and Jessica Green, of the Biology and the Built Environment Center (BioBE), are currently seeking a microbial ecology Research Associate / Research Assistant Professor / Research Associate Professor (non-tenure track faculty) to investigate fundamental questions surrounding the role of microorganisms (bacteria, archaea, fungi, protists, and viruses) in the built environment and in relation to human health outcomes. Applicants must have a Ph.D. in biology, bioinformatics, or a related discipline.

The ideal candidate will have a combination of domain expertise and leadership potential. With regards to domain expertise, candidates should possess a demonstrated ability to generate and interpret microbiome data. Deep knowledge in data analytics, bioinformatics, and/or clinical microbiology is highly desirable. From a leadership perspective, we are seeking candidates that: are comfortable working on multiple concurrent projects with interdisciplinary scientists comprising a diverse range of experience (undergraduate through postdoc); have demonstrated a record of scientific writing and scholarly productivity; have a record of, or evidence of potential for, obtaining external research funding.

The successful candidate will have the ability to work with faculty, students, and industry partners from a variety of diverse backgrounds and the opportunity to creatively and independently engage in research at the BioBE Center (http://biobe.uoregon.edu/), funded by the Alfred P. Sloan Foundation, federal agencies, and members of industry.

The BioBE Center is training a new generation of innovators to study the built environment microbiome, including the diversity of microorganisms interacting with each other and with the indoor environment. The vision of this national research center is to understand buildings and urban environments as complex systems and to explore how urban, architectural, and building system (passive and active) design work to shape the microbiome, with the ultimate goal of designing healthy and sustainable buildings and cities.

For more information or to apply, see the full job post.

Linking antimicrobials and antibiotic resistance genes in indoor dust

Previous BioBE postdoc Erica Hartmann (now Assistant Professor at Northwestern University!), along with several BioBE researchers and members of Curtis Huttenhower’s (Harvard) and Rolf Halden’s (Arizona State) research groups, recently published a paper establishing a link between antimicrobials and antibiotic resistance genes in indoor dust. Dr. Hartmann published a post summarizing the main findings at microBEnet. The paper is freely available in the journal Environmental Science & Technology.