The beginning of my summer was dedicated to moving the BioBE center’s molecular biology lab to a new location on campus.
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.
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.
EcM diversity increases as you move AWAY from the equator — counter to most other diversity trends. But some exceptions, eg Guyana. #MSA2017
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!
ITS OTUs don't map well to species or sections within Alternaria. Variation at the ITS locus doesn't match multi-locus variation. #MSA2017
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.
Mating and pathogenicity are intimately linked in U. maydis. This process happens only inside the plants. #MSA17
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.
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.
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.
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!
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.
Jessica Green and Kevin Van Den Wymelenberg are quoted in an architecture article wrote by Mark Wilson and published in the Fast Company Magazine called: “The City of Tomorrow is A Petri Dish- By Design”. Read the complete piece here.
Energy Studies lab director Kevin Van Den Wymelenberg and doctoral candidate Gwynne Mhuireach brought science and design activities to 50 seventh-grade students at O’Hara Catholic School. The students practiced swabbing indoor surfaces and learned how to test daylighting with a heliodon model.