Category: Updates

Spring Updates

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It’s been a really busy spring so far, so much so that I haven’t had much chance to write about it!  Here is a brief overview of what I’ve been up to.

Research

This past year has easily produced the largest number of research topics I have been working on concurrently.  In addition to publishing a paper on the rumen in cattle last September, I have been working on a paper on the rumen of yearling rams which is currently in preparation and due to be submitted to a scientific journal for review soon.  I still have several small projects in development from my post-doc in the Yeoman lab, as well as a number of grad-student-led papers that are still pending, and was invited to contribute to a scientific review which is also in preparation.

I’ve been working through the large dataset of soil samples from my post-doc in the Menalled lab.  That large project has blossomed into four papers thus far, two of which I’m writing on the soil bacteria, and one of which I am co-authoring on the legacy effects of climate change.  Those four are also due for submission to scientific journals for review soon.  The Menalled lab just received a grant award from USDA AFRI NIFA, on which I am a (subaward) PI and to which I will be contributing soil bacterial community analysis.

The rumen and soil work over the past year has been entirely in my spare time, however, as my position in the Biology and the Built Environment Center has kept me delightful busy.  I have been collaboratively processing a large and complex dataset on weatherization, home operation and lifestyle, indoor air quality, and microorganisms in dust, which I will be presenting at two (possibly three) conferences this summer.  I have also been collaboratively writing grant proposals, and while those are still in development or pending review, they span everything from light, to chemistry, to plants and living machines, to hospitals, to social networks in buildings.  I hope to further develop some of these collaborations with a short trip at the end of June to the University of Austin, Texas’ Test House.

In addition, I have been assisting in the planning, development, and launch of the University of Oregon’s Institute for Health in the Built Environment.  The Institute will facilitate collaboration and information sharing between researchers and industry professionals, with the goal of researching, building, and promoting healthier built environments.  The Institute just hosted its #BuildHealth2018 Consortium meeting in Portland, OR, at which I presented some of the results from that large weatherization study regarding indoor plants.  The meeting was fantastic, and spurred in-depth discussion on problems facing industry professionals, innovative research goals, and a wealth of new possibilities.

Outreach

In the past few months, I’ve spent a lot of my spare time helping to develop the Eugene Pod of 500 Women Scientists, an organization created to promote diversity, equity, and inclusion in science, and to promote education and interactive between scientists and the general public.  We have focused on hosting monthly Science Salon events, four to date, to do just that.  I presented at the first one, and have helped organize and MC the others.  The Eugene Pod’s activities were just featured on the central 500 WS page, as Pod of the Week, and you can also follow our updates and events on our Facebook page.

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Running trivia on fire and fungi.

 

While it has been a struggle to maintain regular contributions, I still maintain Give Me the Short Version, along with a few intrepid contributors, which summarizes scientific articles for easier consumption.  This spring, I spent several days judging STEM and robotics competitions for several local Eugene middle and high schools, which has been a lot of fun.  The student projects are enthusiastic and creative, and I appreciate the chance to assist in these programs in some small way.

 

I have continued to mentor UO students.  The post-bac student from the BioBE lab that was learning bioinformatics with me, Mitch Rezzonico, was accepted to the University of Oregon’s Bioinformatics and Genomics Master’s Program!  Mitch wrapped up his work this spring to prepare for the intensive program, and with his interest in health research, BioBE hopes to work with him again in the future.  BioBE recently hired an undergraduate student for science communication, Mira Zimmerman.  Mira has been making some upgrades to the BioBE and ESBL websites which will continue to be rolled out over the next few months.  In addition, she will be helping me develop informative blog posts on the built environment, and helping to grow our information dissemination capabilities.  Hiring a student as a science communicator was something I had been hoping to test out, and so far it’s been a smashing success.

Teaching

My course proposal for “Introduction to Mammalian Microbiomes” was accepted by the University of Oregon Clark Honor’s College for the fall term!

In April, I gave a guest lecture to Mark Fretz’s Design the Unseen course at the University of Oregon, on the Indoor Microbiome.  The class was populated by architecture students, who were learning about integrating health considerations into design strategies.  As a final project, students design a brief field experiment or intervention strategy for a design assistance project with Portland firms. I assisted one group in designing a small experiment on natural daylighting in an office and the effect on E. coli growth on culture plates – more on those results soon!

 

Later that same day, I have a lecture at the Oregon Museum of Science and Industry in Portland, as part of their OMSI After Dark series which opens the museum after-hours to adults for hands-on activities and lectures.  The lecture was on the gut microbiome, and I was able to present in the Planetarium!

It’s almost time!

 

 

OMSI After Dark Presentation on the gut microbiome

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Last night I participated in the Oregon Museum of Science and Industry (OMSI) After Dark event: “It’s Alive! (Mind and Body)”.  OMSI regularly puts on After Dark events, where adults can check out the museum, listen to lectures in the planetarium, and engage in interactive science experiments and activities, all while enjoying an open bar.  Last night, I had a great time giving a short presentation on “Ishaq OMSI After Dark 20180425“!

 

OMSI After Dark presentation set

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Following my OMSI Science Pub presentation in February, I was invited to present at the OMSI After Dark event: “It’s Alive (Mind and Body)!” on April 25th!

I’ll be presenting a shorter, 20 minute version on the Microbiome of the Digestive Tract!

I’ll be teaching “Introduction to Mammalian Microbiomes” this fall!

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I’m very pleased to announce that I’ll be teaching a course this fall on “Introduction to Mammalian Microbiomes”, with the University of Oregon Clark Honors College.  I hope that this will be the first of many courses taught at UO, beginning with my background in “host-associated”, and expanding out into “house-associated”.

Course Description: Introduction to mammalian microbiomes.

The learning objectives of this course are to introduce students to basic concepts in host-associated microbiomes. Some background in microbial ecology, genetics, anatomy, bioinformatics, or immunology would be helpful, but is not required. While difficult concepts will be discussed, the course is intended to teach students about the basic principles: what is a microbiome? How does host anatomy drive microbial ecology? How does that community develop over time? How does it change? How does technology inform our understanding of these systems, and what limitations does that technology introduce? When we read about host-associated microbiomes in the news, especially regarding health, how can we assess if the study is rigorous and how should be interpret the scope of the findings? The skill-set objectives include learning to review complicated journal articles, distilling their findings while understanding their limitations, and developing science communication skills in a variety of formats.

Upcoming presentations at Indoor Air 2018

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This summer, I’ll be presenting a talk at the Indoor Air 2018 conference in Philadelphia, on some of the work I’ve been doing on bacteria in homes!

Biology and the Built Environment Center

Source: Upcoming presentations at Indoor Air 2018

Tour of the Baker Lighting Lab

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For the past two months, I’ve been spending quite a bit of time writing grant proposals.  In particular; those which expand our understanding of indoor lighting on human health and behavior, the indoor microbiome, and energy usage in buildings.  These project proposals are collaborative efforts between several University of Oregon research labs: Biology and the Built Environment Center, Energy Studies and Buildings Laboratory, and the Baker Lighting Lab.  I’ll have more updates in the next few months as those are reviewed.

Siobhan “Shevy” Rockcastle, Chair of the Baker Lighting Lab, and I have been brainstorming ideas, and today I went over to the Baker Lab to check it out in person.  The Lab is decorated with concept-design lighting projects from previous students, which are not only beautiful, but extremely creative.  Here are a few of my favorites!

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A collaborative project got published on the biogeography of the calf digestive tract!

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Most studies that examine the microbial diversity of the gastrointestinal tract only look at one or two sample sites, usually the mouth, the rumen in ruminant animals, or the feces.  It can be difficult, expensive, invasive, or fatal to get samples from deep inside the intestinal tract; however many studies have pointed out that anatomical location and local environmental factors (like temperature, pH, host cells, nutrient availability, and exposure to UV light) can dramatically change a microbial community.  Thus, the microbes that we find in feces aren’t always what we would find in the stomach or along the intestines.  On top of that, certain microorganisms have been shown to closely associate with or attach to host cells, and the diversity of microbes next to host tissues can be different from what’s at the center of the intestines (the digesta).

This large, collaborative project took samples from nine different sites along the digestive tract of calves over the first 21 days of life to determine how body sites differed from each other, how sites changed over time as the calf matured, and how the lumen-associated bacteria would differ from the digesta-associated bacteria.  Samples from the mothers were also taken to understand how maternal microbial influence would affect body sites over time.

This paper was just published in  Scientific Reports, and was something I had previously presented on at the Joint Annual Meeting of the American Society for Animal Science, the American Dairy Science Association, and the Canadian Society for Animal Science in Salt Lake City, UT in 2016.

Biogeographical Differences in the Influence of Maternal Microbial Sources on the Early Successional Development of the Bovine Neonatal Gastrointestinal tract. Carl J. Yeoman, Suzanne L. Ishaq, Elena Bichi, Sarah K. Olivo, James Lowe, Brian M. Aldridge. 2018. Scientific Reports.

Abstract

The impact of maternal microbial influences on the early choreography of the neonatal calf microbiome were investigated. Luminal content and mucosal scraping samples were collected from ten locations in the calf gastrointestinal tract (GIT) over the first 21 days of life, along with postpartum maternal colostrum, udder skin, and vaginal scrapings. Microbiota were found to vary by anatomical location, between the lumen and mucosa at each GIT location, and differentially enriched for maternal vaginal, skin, and colostral microbiota. Most calf sample sites exhibited a gradual increase in α-diversity over the 21 days beginning the first few days after birth. The relative abundance of Firmicutes was greater in the proximal GIT, while Bacteroidetes were greater in the distal GIT. Proteobacteria exhibited greater relative abundances in mucosal scrapings relative to luminal content. Forty-six percent of calf luminal microbes and 41% of mucosal microbes were observed in at-least one maternal source, with the majority being shared with microbes on the skin of the udder. The vaginal microbiota were found to harbor and uniquely share many common and well-described fibrolytic rumen bacteria, as well as methanogenic archaea, potentially indicating a role for the vagina in populating the developing rumen and reticulum with microbes important to the nutrition of the adult animal.

500 Women Scientists and the equity in science movement

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At a conference this summer, I attended a lunch discussion on gender equality in science, and diversity and equity in the workplace in general, hosted by the activist group; 500 Women Scientists. What was planned to be a small meeting of 20-30 women very quickly turned into a standing-room-only event as an unexpected number of women and allies arrived; a momentum which has been gathering since the inception of 500WS. Following the 2016 presidential election, four women decided it was time to act and founded the organization with the goal of getting 500 women in STEM to sign an open letter in support of science. As of writing this, more than 20,000 supporters from over 100 countries have joined the movement, which has sparked a number of actions.

500WS

First, 500WS seeks to spread awareness of issues and provide resources towards improving life in the workplace. In particular; recognizing, preventing, and providing justice for sexual harassment in the workplace has been a large focus of the 500WS group, among many other organizations and individuals in the #MeToo movement.

Second, 500WS aims to create gender equality in STEM and the workplace in general, by promoting inclusion, by advocating for employee-friendly practices, and by reducing bias. These policies not only help women, for example; they help working parents of all genders through the implementation of policies like parental leave. One of the 500WS measures is providing an online resource for people to Request A Scientist, to promote the visibility of women in STEM and support their inclusion in news articles, on panels, as speakers, and in leadership positions. This visibility in the media reinforces the idea that women are actively working in STEM, are making important contributions to it, and can help dispel gender stereotypes and bias which lead to pay discrepancies and missed career opportunities. Along with similar resources like the Diverse Sources Database, 500WS seeks to reinforce the idea that scientists come in all sorts of formats.

Third, 500WS is an activist group. In addition to promoting the March for Science movement last year and this year, they regularly post actionable items for women in STEM and supporters on their Take Action Tuesday blog posts. Most recently, 500WS is also launching a Science Salon campaign to raise money for Puerto Rico, which has yet to recover from catastrophic hurricane damage due to insufficient US recovery funds and a lack of media attention.

501 Women Scientists

Those of you following my blog know that I am a firm supporter of equity in science (although largely from the point of view of women in STEM – write what you know, after all); I have debated the existence of the pay gap with others online; I have written about the lack of women in STEM, the disparity between what women are expected to do at work and how their performance is judged, the awkward problem of name changes and publication records, and not missing out on brilliant researchers because of bias; I have hosted a STEM workshop for girls, been a mentor to an elementary student, attended Meet a Scientist day at the Eugene Science Center; and I have marched for science, equality, and human rights when I could.

I am thrilled to announce that I’m also joining the 500 Women Scientists Eugene Pod as a co-coordinator! The Eugene Pod leadership has been working hard to develop a Eugene Science Salon, and we hope to make it a reoccurring event which will promote local women in STEM, increase public engagement and education in STEM, and raise money for a variety of causes.

Connect with 500WS

You can find the Eugene Pod online on Facebook and Twitter and both women in STEM and supporters of any gender, sexuality, ethnicity, nationality, age, career path, field, and preferred Oregon college sports’ mascot are welcome to join. If you are a woman (the inclusive definition of woman) in the Eugene area who would like to join the group and attend meetings to plan larger events, please join our Meetup group.

The national 500 Women Scientists is here: Organization | @500womensci | Facebook

OMSI presentation: A crash course on the microbiome of the digestive tract

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Last night, I gave my first “science stand-up” as part of the Oregon Museum of Science and Industry (OMSI) Science Pub series at Whirled Pies in Eugene, OR.  I really enjoy giving public presentations of my work, and while I’ve been on stage with a microphone before, it was the first time I got a stool to put my drink on.

I gave a talk which encompassed much of my previous work on host-associated microbiomes in moose and other ruminants, as well as more current research from others on the human gut.  It’s difficult enough to fit the field of host-associated microbiomes into a semester-long class, nevermind an hour (I digress), so I kept it to the highlights: “A crash course on the microbiome of the digestive tract“.   You can find the slides here: Ishaq OMSI SciPub 20180208, although there is no video presentation at this time. I was honored to have such a well-attended lecture (about 120 people!) with an engaged audience, who had some really on-track questions about the intersection of microbial diversity and health.

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Photo Credit: Al Lebovitz

As I’ve discussed here before, academic outreach is a sometimes overlooked, yet nevertheless extremely important, aspect of science.  The members of the general public are a large portion of our stakeholder audience, and outreach helps disseminate that research knowledge, facilitate transparency of the research process, and engage people who might benefit from or be interested in our work.  As I told the audience last night, scientists do like when people ask us about our work, but “we’re more scared of you than you are of us”.  I encourage everyone to add science to their life by getting informed, getting involved, and getting out to vote.

Thanks again to OMSI for inviting me to participate, and to Whirled Pies for hosting!

 

As a thank you, I received this awesome pint glass!

Featured Photo Credit: Al Lebovitz