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“!
500 Women Scientists Eugene is hosting another Science Salon at First National Taphouse; “Hot Mess: Biodiversity in the Sky Islands and following fire.”
Carolyna Piña Páez
Graduate Student at Oregon State University
Title: “Population structure of Rhizopogon in the Madrean Archipielago: The Sky Islands of Southwestern United States and Northwestern Mexico.”
Bio: Carolyna Piña Páez is a graduate student at Oregon State university. Her adventures in Mycology began in 2005 in the Sonoran Desert, working with gasteroid fungi. Since 2011, she’s been working with truffles and other ectomycorrhizal fungi associated with true fir, pine and oak in the central part of México. In 2013, she moved to Oregon and was amazed with the diversity that this place hosts.
Fire Management Officer, a.k.a. “Burn Boss”, Nature Conservancy, Oregon
Title: “Burning for Butterflies, Birds & Blooms”
Bio: Amanda started her career in fire management as a member of a 20-person contract crew in 1999. In 2001, after finishing her BA in Philosophy at the University of Oregon, she returned to fire management, working on hotshot crews, handcrews, and engines; as a fuels technician on the Deschutes National Forest; and assistant fire management officer in fuels management on the Ochoco National Forest and Crooked River National Grassland. She studied Natural Resources at Oregon State University and completed a Masters in Natural Resources, Fire Ecology, and Management at the University of Idaho in 2012. She has since worked for the Prineville Bureau of Land Management as a natural resource specialist coordinating post-fire emergency stabilization and rehabilitation; as invasives program manager for the Deschutes and Ochoco National Forests and Crooked River National Grassland; fire management officer for The Nature Conservancy in Oregon and Washington; and chair of the Oregon Prescribed Fire Council.
500 Women Scientists Eugene would like to thank the organizations that helped make this event possible. First and foremost, First National Taphouse in Eugene, who shared their wonderful space with us and where we will be putting on future Salons, and donated a keg to the event! We are also extremely grateful to several organizations which contributed raffle or trivia items for us to raise additional funds, including Leslie Dietz and the Eugene Science Center. Our beautiful logo was crafted by Cassie Cook, our amazing event posters were designed by Serena Lim. Fertilab generously lent us a sound system. And of course, we want to acknowledge the national leadership of 500 Women Scientists, who brought us together, gave us a voice, and who suggested these Science Salons as a way to help CienciaPR, a organization which similarly supports science education and infrastructure.
I’d also like to acknowledge the powerhouse team of women who came together to organize this event: Karen Yook, Leslie Dietz, Jessica Flannery, and our wonderful speakers; Carolyna Piña Páez and Amanda Stamper. 500 Women Scientists was formed in the spirit of cooperation and support, and this team truly took that to heart. I can’t wait to organize the next one with you ladies, and the next one, and the next one, and the next one…
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.
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!
The end of 2017 marks the second year of my website, as well as another year of life-changing events, and reflecting on the past year’s milestones help put all those long hours into perspective. I reviewed my year last year, and found it particularly helpful in focusing my goals for the year ahead.
This involved another large move, not only from Montana to Oregon, which has led to some awesome new adventures, but also from agriculture and animal science to indoor microbiomes and building science. So far, it has been a wonderful learning experience for incorporating research techniques and perspectives from other fields into my work.
This year, I added fournewresearchpublications and one review publication to my C.V., and received word that a massive collaborative study that I contributed to was accepted for publication- more on that once it’s available. In April, I hosted a day of workshops on soil microbes for the Expanding Your Horizons for Girls program at MSU, and I gave a seminar at UO on host-associated microbiomes while dressed up as a dissected cat on Halloween. In November, I participated in a Design Champs webinar; a pilot series from BioBE which provides informational discussions to small groups of building designers on aspects of how architecture and biology interact.
I published 34 posts in 2017, including this one, which is significantly fewer than the 45 I published in 2016. However, I have doubled my visitor traffic and views over last year’s totals: over 2,000 visitors with over 3,200 page views in 2017! My highest-traffic day was April 27th, 2017. While I am most popular in the United States, I have had visitors from 92 countries this year!
I also added some “life” to my work-life balance; in November, I married my best friend and “chief contributor“, Lee Warren, in a small, stress-free ceremony with some local friends in Eugene, Oregon!!
I have high hopes for 2018, notably, I’d like to finish more of the projects that have been in development over the last two years during my post-docs. Nearly all academics carry forward old projects: some need additional time for experimentation or writing, some get shelved temporarily due to funding or time constraints, some datasets get forgotten and gather dust, and some which got cut short because of the need to move to a new job. This is a particular concern as grant funding and length of job postings become shorter, forcing researchers to cut multi-year projects short or finish them on their own time. After defending in early 2015, I had two one-year postings and started at UO in June 2017, making this my fourth job in three years. I’m looking forward to roosting for a bit, not only to clear out unfinished business, but also to settle into my new job at BioBE. This fall, I have been analyzing data on a weatherization project, writing a handful of grants, and developing pilot projects with collaborators. I have really enjoyed my first six months at BioBE, and Lee and I have taken a shine to Eugene. In the next few months, I hope to have more posts about my work there, exciting new developments in BioBE and ESBL, and more insights into the work life of an academic. Happy New Year!
Service can be a vaguely defined expectation in academia, but it’s an expectation to give back to our community; this can be accomplished in different ways and is valued differently by institutions and departments. Outreach is an easily neglected part of science, because so often it is considered non-essential to your research. It can be difficult to measure the effectiveness or direct benefit of outreach as a deliverable, and when you are trying to hoard merit badges to make tenure and your time is dominated by other responsibilities, you often need to prioritize research, teaching, advising, or grant writing over extension and service activities. Nevertheless, public outreach is a vital part to fulfilling our roles as researchers. Academic work is supported by public funding in one way or another, and much of our research is determined by the needs of stakeholders, who in this sense are anyone who has a direct interest in the problem you are trying to solve.
Depending on your research field, you may work very closely with stakeholders (especially with applied research), or not at all (with theoretical or basic research). If you are anywhere in agriculture, having a relationship with your community is vital. More importantly, working closely with the public can bring your results directly to the people out in the real world who will benefit from it.
A common way to fulfill your outreach requirement is to give public presentations. These can be general presentations that educate on a broad subject, or can be specifically to present your work. Many departments have extension specialists, who might do some research or teaching but whose primary function is to connect researchers at the institution with members of the public. In addition to presentations, extension agents generate newsletters or other short publications which summarize one or more studies on a specific subject. They are also a great resource for networking if you are looking for resources or collaborations, for example if you are specifically looking for farms in Montana that grow wheat organically and are infested with field bindweed.
For my new job, I’m shifting gears from agricultural extension to building science and health extension. In fact, the ESBL and BioBE teams at the University of Oregon have recently created a Health + Energy Research Consortium to bring university researchers and industry professionals together to foster collaborations and better disseminate information. The goals of the group at large are to improve building sustainability for energy and materials, building design to serve human use better, and building microbiology and its impact on human health. I have a few public presentations coming up on my work, including one on campus at UO on Halloween, and one in February for the Oregon Museum of Science and Industry Science Pub series in February. Be sure to check my events section in the side bar for details.
Even when outreach or extension is not specified in your job title, most academics have some level of engagement with the public. Many use social media outlets to openly share their current work, what their day-to-day is like, and how often silly things go wrong in science. Not only does this make us more approachable, but it’s humanizing. As hard as scientists work to reach out to the public, we need you to reach back. So go ahead, email us (please don’t call because the stereotype is true: we really do hate talking on the phone), tweet, post, ping, comment, and engage with us!!
A couple of weeks ago, I attended my first Ecological Society of America meeting in Portland, which assembles a diverse community of researchers looking at system-wide processes. It was an excellent learning experience for me, as scientific fields each have a particular set of tools to look at different problems and our collective perspectives can solve research problems in more creative ways.
In particular, it was intriguing to attend talks on the ecology of the human microbiome. Due to the complexity of host-associated microbial communities, and the limitations of technology, the majority of studies to date have been somewhat observational. We have mapped what is present in different animals, in different areas of the body, under different diet conditions, in different parts of the world, and in comparison between healthy and disease states. But given the complexity of the day-to-day life of people, and ethics or technical difficulty of doing experimental studies in humans, many of the broader ecological questions have yet to be answered.
For example, how quickly do microbial communities assemble in humans? When you disturb them or change something (like adding a medication or removing a food from your diet) how quickly does this manifest in the community structure and do those changes last? How does dysbiosis or dysfunction in the body specifically contribute to changes in the microbial community, or do seemingly harmless events trigger a change in the microbial community which then causes disease in humans? Some of the presentations I attended have begun teasing out these problems with a combination of observational in situ biological studies, in vitro laboratory studies, and in silico mathematical modeling. The abstracts from all the meeting presentations can be found on the meeting website under Program. I have also summarized several of the talks I went to on Give Me The Short Version.
My poster presentation was on Wednesday, halfway through the meeting week, which gave me plenty of time to prepare. You never know who might show up at your poster and what questions they’ll have. In the past, I’ve always had a steady stream of people to chat with at my poster which has led to a number of scientific friendships and networking, and this year was no different. The rather large (but detailed) poster file can be found here: Ishaq et al ESA 2017 poster . Keep in mind that this is preliminary work, and many statistical tests have not yet been applied or verified. I’ve been working to complete the analysis on the large study, which also encompasses a great deal of environmental data. We hope to have manuscript drafted by this fall on this part of the project, and several more over the next year from the research team as this is part of a larger study; stay tuned!
I just got back from my very first Congress on Gastrointestinal Function, a small meeting for researchers with a specific focus on the gastrointestinal tract, which is held every two years in Chicago, Illinois. The special session this year was on “Early Acquisition and Development of the Gut Microbiota: A Comparative Analysis”. The rest of the sessions opened up the broader topics of gut ecosystem surveillance and modulation, as well as new techniques and products with which to study the effect of microorganisms on hosts and vice versa. The research had a strong livestock animal focus, as well as a human health focus, but we also heard about a few studies using wild animals.
As I’ve previously discussed, conferences are a great way to interact with other scientists. Not only can you learn from similar work, but you can often gain insights into new ways to solve research problems inherent to your system by looking at what people in different fields are trying, something that you might otherwise miss just by combing relevant literature online. A meeting or workshop is also a great place to meet other similarly focused scientists to set up collaborators that span academia, government, non-profit, and industry sectors.
This year, I was excited for one of my abstracts to be accepted as a poster presentation, and honored to have the other upgraded from poster to talk! Stay tuned for details about both of those projects in the coming weeks, and be sure to check this meeting out in April, 2019.
2016 started with a bang when I launched this site and joined Twitter for the first time! For the first quarter of the year, I was a post-doctoral researcher in the Yeoman Lab in the Department of Animal and Range Sciences at Montana State University. I was working on a total of eight grants, ranging from small fellowships to million dollar projects, both as a principal investigator and as a co-PI. I was also doing the bioinformatic analysis for multiple projects, totaling nearly 1,000 samples, as well as consulting with several graduate students about their own bioinformatic analyses.
In late spring, my position in the Yeoman lab concluded, and I began a post-doctoral position in the Menalled Lab in the Department of Land Resources and Environmental Sciences at MSU. This position gave me the opportunity to dramatically increase my skill-set and learn about plant-microbe interactions in agricultural fields. My main project over the summer was studying the effect of climate and other stresses on wheat production and soil microbial diversity, and this fall I have been investigating the legacy effects of these stressors on new plant growth and microbial communities. I have extracted the DNA from all of my Fort Ellis summer trial soil samples, and look forward to having new microbial data to work with in the new year. Based on the preliminary data, we are going to see some cool treatment effects!
Over the summer, I attended the American Society for Microbiology in Boston, MA in June, where I presented a poster on the microbial diversity in organic and conventional farm soil, and the Joint Annual Meeting for three different animal science professional societies in Salt Lake City, UT in July, where I gave my first two oral conference presentations. One was on the effect of a juniper-based diet on rumen bacteria in lambs, and the other was on the biogeography of the calf digestive system and how location-specific bacteria correlate to immune-factor expression.
Thanks to a lot of hard work from myself and many collaborators, a number of research projects were accepted for publication in scientific journals, including the microbial diversity of agricultural soils, in reindeer on a lichen diet, and in relation to high-fat diets in mice, it also included work on virulent strains of Streptococcus pyogenes, and a review chapter on the role of methanogens in human gastrointestinal disease.
A whopping thirteen manuscripts are still in review at scientific journals or are in preparation waiting to be submitted! Some of those are primarily my projects, and for others I added my skills to the work of other researchers. Editing all those is going to keep me plenty busy for the next few months. I’ll also be writing several more grants in early 2017, and writing a blog post about the Herculean task that can be.
I’ll be concluding my greenhouse study by March of 2017, just in time to prepare for another field season at Fort Ellis, on the aforementioned climate change study that is my main focus. In January, I’ll be spending time in the lab helping to process and sequence DNA from my 270 soil samples, and begin the long task of data quality assurance, processing, and analysis. I’m not worried, though, 270 samples isn’t the most I’ve worked with and bioinformatic analysis is my favorite part of the project!
This year, I am hoping to attend two conferences that I have never previously attended, and present data at both of them. The first will be the 2017 Congress on Gut Function in Chicago, IL in April, and the second will be the Ecological Society of America’s Annual Meeting in Portland, OR in August. Both conferences will give me the opportunity to showcase my work, network with researchers, and catch up with old friends.
If 2017 is anything like the past few years, it’s going to be full of new projects, new collaborators, new skills, and new opportunities for me, and I can’t wait! So much of what I’ve accomplished over the last year has been possible because of the hard work, enthusiasm, and creativity of my colleagues, students, friends, and family, and I continue to be grateful for their support. I’d also like to thank anyone who has been kind enough to read my posts throughout the last year; it’s been a pleasure putting my experiences into words for you and I appreciate the time and interest you put in. I look forward to sharing more science with you next year!
For the last four days I was in Boston for the American Society for Microbiology (ASM) Microbe 2016 meeting.The meeting is held in Boston on even years, and New Orleans on odd.
The conference brings together all sorts of microbiologists: from earth sciences, to host-associated, to clinical pathologists and epidemiologists, to educators. This year, there were reportedly over 11,000 participants! Because of the wide variety of topics, there is always an interesting lecture going on related to your topic, and it was a wonderful experience to be able to talk directly to other researchers to learn about the clever techniques they are using. I posted about a tiny fraction of those interesting projects on Give Me The Short Version.
On Sunday, I presented a poster on “Farming Systems Modify The Impact Of Inoculum On Soil Microbial Diversity.” I analyzed the data from this project for the Menalled Lab last year, and it has developed into a manuscript in review, as well as several additional projects in development.
One of the best parts of ASM meetings is that you never know who you are going to run into, and I was able to meet up with several friends and colleagues, including Dr. Benoit St-Pierre, who was a post-doc in the Wright lab at the University of Vermont while I was a student, and Laura Cersosimo, the other Ph.D. candidate from the UVM Wright lab who will be defending in just a few months! I also ran into Ph.D. candidate Robert Mugabi, who is hoping to defend by March and in the Barlow lab at UVM while I was there. Most unexpectedly, I ran into a A Lost Microbiologist who had wandered in from Norway: Dr. Nicole Podnecky, who I met at UVM back when we were undergraduates!
Of course, no conference would be complete without vendor swag.
Vendor swag! And not even all of it…
Ice cream made using liquid nitrogen from the Witches of Boston.