The Microbes and Social Equity Working Group is delighted to make its published debut, with this collaboratively-written perspective piece introducing ourselves and our goals. You can read about us here.
This piece also debuts the special series we are curating in partnership with the scientific journal mSystems; “Special Series: Social Equity as a Means of Resolving Disparities in Microbial Exposure“. Over the next few months to a year, we will be adding additional peer-reviewed, cutting edge research, review, concept, and perspective pieces from researchers around the globe on a myriad of topics which center around social inequity and microbial exposures.
Ishaq, S.L., Parada, F.J., Wolf, P.G., Bonilla, C.Y., Carney, M.A., Benezra, A., Wissel, E., Friedman, M., DeAngelis, K.M., Robinson, J.M., Fahimipour, A.K., Manus, M.B., Grieneisen, L., Dietz, L.G., Pathak, A., Chauhan, A., Kuthyar, S., Stewart, J.D., Dasari, M.R., Nonnamaker, E., Choudoir, M., Horve, P.F., Zimmerman, N.B., Kozik, A.J., Darling, K.W., Romero-Olivares, A.L., Hariharan, J., Farmer, N., Maki, K.A., Collier, J.L., O’Doherty, K., Letourneau, J., Kline, J., Moses, P.L., Morar, N. 2021. Introducing the Microbes and Social Equity Working Group: Considering the Microbial Components of Social, Environmental, and Health Justice. mSystems 6:4.
2020 has … gone in a very different direction than the way we probably all thought that it would back in early January. The emergence of the SARS-CoV-2 (COVID-19) pandemic has dramatically altered the way we live our day-to-day lives, and the way we think about ourselves as a global community. To reduce the transmission of the virus, the University of Maine, and many other schools and institutions, made significant alterations to their operating policies over spring 2020. This included sending students home (where possible), moving classes to online instruction only, asking faculty to work from home, and restricting laboratory and field work. This has resulted in some disruption to my plans, so here’s an attenuated post about updates over the last few months.
Teaching
The courses I am teaching this spring lent themselves well to being taught strictly online, with some modifications. Naturally, the presentations class works better in person where the stress of having an audience present promotes in situ training. The students were able to give an elevator speech, a regular short presentation for a peer-level audience, and a peer-level audience presentation with random technical challenges introduced by me into the slides. The remaining portion of the semester was devoted to giving presentations to a public-level audience, which requires a different presentation style and a good deal of thought into how much info is condensed and what you can and can’t expect your audience to already know. It was going to be too logistically challenging to organize public presentations remotely with short notice, so instead I had students create annotation notes for someone else’s slides, described here.
What was a technical challenge you had during a presentation? I'm teaching a presentation course and one assignment I mess with the students' PPT to introduce tech problems I've encountered before. Like videos don't play, slides in wrong order, screen flickers, PPT won't play…
The data analysis class was easier to adapt, but required adjustment nonetheless. Instead of hosting a three-hour video meeting each week, I recorded the remainder of my lectures and made them available well in advance, so that students could watch and listen when they had time and internet access. During the class period, the class met to collaboratively work through data, which was always the goal, but with the challenge of remote work some re-imagination of the assignments was needed to allow students to opt-in to some of the work at times convenient to them.
To simplify the work, instead of having students independently perform similar analyses on different sets of data, I had them perform similar, somewhat independent, analyses on the same dataset, allowing them to all work collaboratively. As a bonus, this unpublished dataset was one that I have been working on collaboratively over the past year, so the students will be able to opt-in to participating in the publication of this work. This is in addition to the two manuscript which are slated to be submitted for review in the next few months, and two more under development. Because that’s still in development, I won’t share more detail now, but stay tuned to those results, and a more in-depth discussion on integrating student data analysis education with research.
My DNAseq data analysis students had 10 wks to learn R, amplicon seq processing/analysis, re-purposing stats knowledge to microbial data, and manuscript writing. These were new to most students, but I'm blown away by their quality. #IntegratedResearchAndTeaching#SoMuchGrading
Since starting at UMaine in September 2019, I have been working on establishing my lab. Most of that effort thus far has revolved around rearranging my lab spaces and acquiring specialized lab equipment. This aspect hasn’t been negatively impacted, outside of the new logistical challenges of delivering large pieces of equipment to locked buildings without coming into contact with delivery drivers.
However, acquiring supplies has been impacted, as certain materials are suddenly in extremely high demand, while production of others has dramatically reduced for the time being. Although I hadn’t begun any wet lab research which needed to be halted, I was just about to start culture work and training students on laboratory protocols, which has now been delayed for at least two months. Instead, I am in the process of transitioning student projects from benchtop-based to data analysis-based, at least for those students planning on graduating between now and spring 2021.
I am also focusing on trying to get previously completed projects written up and sent out for review, including a study on bacterial communities around window components in hospital rooms with the BioBE lab, a few collaborations on gut microbes in different animal species with the Yeoman Lab, and two more papers on the effect of climate, farming system, weed competition, and plant health on wheat production and wheat-associated soil bacteria with the Menalled/Seipel Lab. You can read the pre-print (meaning it hasn’t been peer-reviewed yet) on the soil microbes one here.
I do have some concrete exciting news, though, two graduate students will be joining my lab this summer/fall to start work on master’s of science degrees! Johanna Holman will be working on diet and gut microbiome in humans, for a master’s in Nutrition and Food Science, and Sarah Hosler will be working on new methods for investigating gut microbial communities in animals, for a master’s in Animal Science.
Looking forward, I’ll be changing my plan for training students on laboratory work, to facilitate social distancing measures while ensuring that students aren’t alone in the lab. Luckily for me, my labs and soon-to-be-office have windows between them so I can hover from a different room entirely.
Outreach
Social distancing has temporarily impacted my outreach activities, particularly in the short term as we try to adjust. A lecture I had planned for the Maine Organic Milk Producers annual meeting was canceled in April, although I’ll now be able to talk about Microbes and Social Equity at the Institute for Health in the Built Environment Industry Consortium annual meeting in May since it has been moved from in-person to online. Similarly, I am participating in a few discussions for other summer events and whether they might be transitioned to online formats. In the mean time, I’ve been practicing coming up with pithy interactions on Twitter.
I know a number of scientists who have gotten tattoos visualizing their science. For me, though, I think the most on brand science tattoo would be a simple line of code with a typo in it.
A number of scientific conferences which I was planning to attend and/or have research presented at have made the decision to postpone, including the American Society for Microbiology’s Microbe 2020, International Society of Microbial Ecology’s ISME18, the Gordon Research Conference’s Microbiology of the Built Environment (MoBE) 2020 meeting, the American Society for Nutrition 2020 meeting. Other scientific conferences are attempting to switch to online formats, such as the Ecological Society of America (ESA) 2020 meeting, but bringing thousands of participants together in an interactive way is an extremely ambitious adaptation in such a short period of time.
Looking forward, I hope that many organizations will adjust and maintain their commitment to online accessibility of conferences, meetings, talks, and other outreach events, as well as making these resources available after the event. Attend a conference or public presentation is important to building you research program and improving the impact of your work, but financial, physical, logistical, or familial considerations often make it impossible to participate. Maintaining remote-accessibility, and making content available after the event, are important steps in making science more inclusive and allowing a broader audience to participate.
The journal is called Frontier for Young Minds, and pairs a young scientist with an established scientist to review your articles, a ~1,500 word summary version. The journal provides cartoon illustrations that help bring your science to life.
Ours was written by an undergrad I was mentoring at UO, Sam Rosenberg, and architecture grad student Julia May helped us with our Figures. I wasn’t involved with the original article, but along with Ashkaan, I helped Sam draft the summary as non-technical summaries of highly-technical science can be a real challenge. Check it out!
Rosenberg, S., Ishaq, S., May, J., Fahimipour, A.K. 2020. How light exposure changes bacterial communities in household dust. Frontiers for Young Minds.Article.
The Nature Lab at Rhode Island School of Design is presenting an exhibition on the interface of biology and art; Biodesign: From Inspiration to Integration. Curated in collaboration with William Myers, the show is part of their 80th anniversary celebrations. The exhibition runs from Aug 25—Sept 27 at the Woods Gerry Gallery, and will feature photos and sampling equipment from the Biology and the Built Environment Center.
Biodesign: From Inspiration to Integration
OPENING RECEPTION
An exhibition curated by William Myers and the RISD Nature Lab, this show features the following works:
Hy-Fi and Bio-processing Software—David Benjamin / The Living
Mycelium architecture, made in collaboration with Ecovative and 3M.
Zoa—Natalia Krasnodebska / Modern Meadow
Leather grown using yeasts that secrete collagen, and grown completely without animal derivatives.
The Built Environment Microbiome—BioBE Center / Jessica Green, Sue Ishaq and Kevin Van Den Wymelenberg
The BioBE conducts research into the built environment microbiome, mapping the indoor microbiome, with an eye towards pro-biotic architecture.
Zea Mays / Cultivar Series—Uli Westphal
Newly commissioned corn study, this project highlights maize’s evolution through interaction with humans.
Harvest / Interwoven—Diana Scherer
Artist coaxes root systems plant root systems into patterns.
Fifty Sisters & Morphogenesis—Jon McCormack
Artist algorithmically generates images that mimic evolutionary growth, but tweaks them to include aesthetics of the logos of global petroleum producing corporations.
Organ on a Chip—Wyss Institute
Wyss Institute creates microchips that recapitulate the functions of living human organs, offering a potential alternative to animal testing.
AgroDerivatives: Permutations on Generative Citizenship—Mae-Ling Lokko
This project proposes labor, production criteria and circulation of capital within agrowaste/bioadhesive upcycling ecosystems.
New Experiments in Mycelium—Ecovative
Ecovative makes prototypes of mycelium items such as insulation, soundproofing tiles, surfboards, lampshades.
Bistro in Vitro—Next Nature Network
Performance with speculative future foods samples. The installation will include video screens and a cookbook on a table display.
Raw Earth Construction—Miguel Ferreira Mendes
This project highlights an ancient technique that uses soil, focusing on how soil is living.
Burial Globes: Rat Models—Kathy High
This project presents glass globes that hold the ashes of the five HLA-B27 transgenic rats, each one named and remembered: Echo, Flowers, Tara, Matilda, Star.
To Flavour Our Tears—Center for Genomic Gastronomy
Set up as an experimental restaurant, this project places humans back into the foodchain — investigating the human body as a food source for other species.
Blood Related—Basse Stittgen
A series of compressed blood objects—inspired by Hemacite objects made from blood/sawdust compressed in a process invented in the late 19th century—highlights bloodwaste in the slaughterhouse industry.
Silk Poems—Jen Bervin
A poem made from a six-character chain represents the DNA structure of silk, it refers to the silkworm’s con-structure of a cocoon, and addresses the ability of silk to be used as a bio sensor, implanted under people’s skin.
Zoe: A Living Sea Sculpture—Colleen Flanigan
Zoe is an underwater structure, part of coral restoration research, that regenerates corals in areas highly impacted by hurricanes, human activity and pollution.
Aquatic Life Forms—Mikhail Mansion
Computationally generated lifeforms animated using motion-based data captured from Arelia aurita.
Algae Powered Digital Clock—Fabienne Felder
By turning electrons produced during photosynthesis and bacterial digestion into electricity, algae will be used to power a small digital clock.
A Place for Plastics—Megan Valanidas
This designer presents a new process of making bioplastics that are bio-based, biodegradable AND compostable
Data Veins & Flesh Voxels—Ani Liu
This project explores how technology influences our notion of being human from different points of view, with a focus on exploring the relationship between our bodies as matter and as data.
Pink Chicken Project—Studio (Non)human (Non)sense/ Leo Fidjeland & Linnea Våglund
By changing the color of chickens to pink, this project rejects the current violence inflicted upon the non-human world and poses questions of the impact and power of synthetic biology.
August 24
5:30 pm – 7:30 pm
Woods Gerry Gallery, 62 Prospect Street, Providence, RI 02903
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.
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!
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.
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.
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.
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!
The Wolfwise Team
Here I am as an undergraduate presenting on wolf behavior and how it isn’t so different from human behavior.
We presented information to the public on wolves and their reintroduction.
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.
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.
Bindweed wraps around other plants.
This patch goes all the way to Lazarro.
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.
In agricultural fields, bindweed infestations severely inhibit crop growth and health.
Â
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.
This slideshow requires JavaScript.
It also means getting very dirty driving and walking through dusty fields!
Thalspi, or pennycress, which is dropping seeds even in my shoes!
The van did very well on rocky, uneven field roads!
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.
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:
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!
The Ishaq Lab 