Field Work in the Bofedales

Note: This guest post was co-authored by Brandon Byrd ’18 and Alex Fazioli ’19

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Alex Fazioli ’19 and Brandon Byrd ’18

A large part of our research in Professor Fennessy’s lab has been spent behind a computer screen analyzing gas samples from the ‘Bofedales’ or high-altitude peatlands in Peru and high-latitude peatlands in Alaska. When Alex Fazioli and I were given the opportunity to travel down to Peru and into the Andes, it wasn’t something that Alex and I were going to pass up.

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It took three days of travel to get to the Andes and our field sites. When we got to our lodge in Ocangate, we both were in awe of the backdrop of the mountains where we would do field work for the next couple of days. The dramatic landscape changes in Peru made for seemingly endless number picture opportunities. The sites where we did our work were situated below a glacier that feeds a stream that runs for about 3 miles through the wetland and empties in a lake.

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The goal of our trip was to characterize the carbon budget of the Bofedales through sampling for gas emission, soil coring, and measurements of the plant communities and peat depth. Our lab was specifically tasked with collecting gas samples for greenhouse gas analysis. For the trip, we needed to bring specialized gas chambers, vials, and other materials to properly collect gas samples from each site we visited.

The Bofedales are inhabited by locals who herd Alpacas and farm potatoes and other crops. The locals were extremely interested in everything we were doing and would follow us around as we did our work in the peatland. The terrain around the peatlands, while beautiful, was extremely rough, especially when hiking with 50 pounds of equipment. Furthermore, navigating the terrain often required hopping from one cushion of vegetation to the next which became a surprisingly fun but tiresome game.

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Overall, our experience in Peru was thrilling. When in the Bofedales, it is difficult to overlook the large scale of these ecosystems. These peatlands are breathtakingly beautiful! Currently, we are aiming to contribute to the literature to help characterize the relatively understudied Bofedales and their ecosystem services. Generally, we would recommend any research student to take an opportunity to pursue field work related to their project. It can take them to amazing places and help them gain invaluable experiences.

Spring in Gambier

Spring semester at Kenyon doesn’t feel like spring until independent projects are over (really- it snowed on April 1st). Here’s a little of what it looks like:  

Wright Lab members Hannah Wedig, Sarah McPeek, and Jess Kotnour got a behind-the-scenes tour of the Smithsonian Museum of Natural History as part of the lab’s effort to understand how flight affects the evolution of birds.

Professor Schulz and Ben Berejka took blood samples of song birds at the BFEC to investigate the innate avian immune response.

Students in the introductory biology lab course worked with a range of organisms such as mosquitos, Lumbriculus, E. coli, and sorghum seedlings for their independent projects.

Professor Gunning documented the banks of Wolf Run in early spring.

Roadkill was the topic of my most recent digital photography project. As a biology student, I wanted to find a way to draw attention to the issues of roads that we often take for granted. We lose literally countless (because the U.S. doesn’t count hard enough) numbers of individual animals to roadkill every year and the environmental effects are vastly understudied. Roads divide habitats and restrict population movements in extreme ways and hopefully in the future (with the help of science!) we can create innovative solutions to these issues.

– Ben Berejka

 

An Interview with Dr. Arianna Smith

I recently had the pleasure of interviewing Dr. Arianna Smith who has returned to Kenyon as Assistant Professor of Biology this spring after her 3 year postdoc at Michigan State University.

Anna: Let’s start at the beginning: how did you get into science?

Dr. Smith: I grew up in the US Virgin Islands, in Saint Croix, and my mom was sort of a pet person. She went to college for animal science and kept us in the pet world. I thought for a very long time that I was going to be a vet. The summer before I started my freshman year in college, I was admitted to a program funded by the HHMI called the RISE Program. That was my first brush with research where I worked in a small animal genomics laboratory. The project that I was most invested in was trying to find genes that contributed to litter size in pigs.

I went to undergrad at North Carolina State University. Somewhere in my freshman year, I thought “yeah, maybe I’m not going to go to vet school.” I had already found an alternative that was quite fulfilling and, in retrospect, I don’t think I could have ever been a vet. I don’t think that would have been a career that I would have loved long term, but I loved being in that lab.

I went from NC State to Michigan State University. I got my PhD in genetics and I worked in a cranio-facial development lab, so looking at how the face comes together. Mutations in the gene that my lab worked on caused cleft lip and palate. I worked on how this gene affected fertility and egg development in mice. I also taught a lot in graduate school and felt like I had a very enriching experience in the classroom.

Dr. Arianna Smith

The times that I was teaching were as informative to my science as my science was informative to my teaching and so I pursued a number of teaching opportunities when I was in graduate school.

I know that you taught at Kenyon 3 years ago. What did you do in your time away from Gambier?

I felt like in order to be successful at Kenyon, I needed more training so I decided to take a postdoc. I went back to MSU, but this time I was at the College of Human Medicine. I spent my time thinking about how what happens during pregnancy to the mom affects and reshapes fetal development, ultimately leading to long-term adverse health outcomes. I did that for two and a half years and now I’m back here.

Are there challenges you have faced as a woman of color in STEM?

There have been some cultural disconnects that have existed for me where I felt it difficult to build certain networks because of a very obvious difference in background. I think it’s probably also true to say that the difference in background was not appreciated from both directions. So that is one of my larger challenges in the field. I am devising my own mechanisms to help me outgrow that. There was a time where there was much less confidence in myself as a scientist. I think that this might be a true statement for a lot of people of color in science and women in science. I am growing out of that everyday but does take effort. It also helps that I’m in an environment where people are just more conscious of what they’re saying, what they’re doing, and asking “are we being inclusive”, so, I’m being nurtured.

What kind of research will you be doing here?

I’m really interested in continuing to think about the maternal environment and how that translates into changes in the offspring. I am particularly interested in atopic disorders in offspring. Atopic disorders are diseases that are characterized by production of IgE (immunoglobulin E). Things that fall into this category are atopic dermatitis, allergy, and asthma. We’ve seen a significant increase over the last 30 years in the prevalence of these diseases and so, we have to ask ourselves why is that happening?

We know about the genetics of these disorders but we also know that genetics cannot account for all of the risk that we see. There has to be some environmental component. I’m interested in how the maternal environment during pregnancy restructures microbial communities which can lead to the onset of these diseases more frequently. I want to look at how the microbial community of the lung is different or not different based on whether or not an offspring has been stressed in utero or is experiencing atopic disorder.

Will you have students, or do you have students that are going to work for you? Is it a work in progress?

It’s a work in progress. I have a couple of students interested whom I am keeping in communication with. It’s just hard to start a lab right now. I’m still buying pipettes!

So if anyone is interested, come talk!

Yeah! It’d be great to have more students reach out. I look forward to mentoring students in the lab and want to build a productive lab environment. I’m going to have mice in the mouse house, so there could be opportunity for students to help manage animals.

 

Avoid the flu. Catch the feels.

It’s that time of year again. Some (many) of us are sick, some of us are lovesick, some of us are watching Lovesick, and some of us are sick of love. Happy Valentine’s Day!

I asked members of the Biology Department for Valentine card submissions related to their biological interests/areas of study. It’s up to you to figure out who wrote them!

Send an email to kenyonbiology@gmail.com with your guesses. Get them all right and you could win candy!

Check out our instagram (@kenyonbiology) for hints throughout the day of the 14th. Answers come out February 14th at 10 PM, so get your guesses in before then!

valentinetreehugger

#1

tempsensitive

#2

valentine

#3. photo by Amit Mogha

CrabValentine

#4

PandaValentine

#5

Crossbillvalentine

#7

lichen

Bonus – Can you guess which professor took a lichen to this cartoon?

KSTEM’s Course Registration Tips

It’s that time of year again where clicking, typing, and being a human at 11:15AM has never seemed more stressful. That’s right: it’s course registration. I asked KSTEM president Rachel Arens to gather the best registration tips around.

Note: The following is a guest post from KSTEM, a club on campus with a mission to develop a strong and supportive scientific community. Email stem@kenyon.edu for more information!

  1. Register in the science quad with as few people as possible! Registration works smoothly if there aren’t many people per router.
  2. Make sure you have at least two classes that you are genuinely excited about.
  3. If there’s one class that you really need/want and is difficult to get into just put that class in first and hit submit; you don’t have to waste time filling up the slots before you hit submit the first time!
  4. Make an excel sheet or Google Sheet so you can copy and paste!
  5. Minimize your windows so they’re side by side and you don’t have to click between
  6. Tell Duo NOT to remember you for 10 hours so it’s easier to log in and log out.
  7. If there’s a popular class you really want, email the professor ahead of time asking to be in the class/put on the waitlist!
  8. IT’S ALL GOING TO WORK OUT! Don’t panic! Everything will be ok.

Know Before You Go – Metagenomics Edition

Today (yes, October 12th!) at 4 PM, Dr. Heidi Andersen from Cincinnati Children’s Hospital Medical Center will be presenting her bioinformatics research. Computational genomics is a rapidly advancing field that uses and develops software to detect patterns in biomolecules like DNA, RNA, and proteins. Our guts host many different bacterial species, and Dr. Andersen pieces together their DNA sequences to determine which are present. She is especially interested in tracking the microbes that are multi-drug resistant (those that survive many of the antibiotics we throw at them) across pediatric patients in the hospital. 

A quick brush up on some computational biology vocab before the presentation never hurts:

Metagenomics – the study of the many genomes present in a given environmental sample

Microbiome – the community of microbes in a given environment

Shotgun sequencing – a method of determining the order of nucleotides (A, C, T, G) in a given DNA sequence by breaking it into short fragments, sequencing these, then piecing them back together computationally

Contiguous sequence (“Contig”) – After sequencing the separate DNA fragments in shotgun sequencing, we need to assemble them back together for a longer, more complete sequence (a contig)

16S rRNA gene (“16S”) – a ribosomal RNA gene that is used to identify bacteria and archaea at the genus level

Extra credit – Understanding PCA
If you want to know all the gory details of Principal Component Analysis, a method you will see often in computational biology, check out this post here

 

The Very Hungry Hornworms

This week, intro bio lab students geared up for their Manduca sexta dissection. These tobacco hornworms had grown significantly since students placed them in their plastic “bachelor pad” cages last week. While all hornworms at least doubled in size, the largest of the group were almost 100 times their weight from last week. Thank goodness that’s pretty impossible for humans to do or Kenyon would need to invest in a better health plan now that Marco’s Pizza accepts K-Cards.

Hornworm fact #1: Time to expand your insult dictionary – the genus Manduca literally means glutton. Try that one at Thanksgiving.

Hornworm fact #2: After a good chomp on a tobacco leaf, Manduca have “toxic halitosis” aka poisonous bad breath from the nicotine which deters spiders from eating them.

Hornworm fact #3: Adult Manduca hawkmoths can eavesdrop on the sonar clicks of bats and drop out of the air to avoid being bat food.

If you know the story of The Very Hungry Caterpillar by Eric Carle, the life of a Manduca is quite similar. Rather than eating sausages and ice cream turning into a beautiful butterfly, though, Manduca hornworms eat the leaves of tobacco, tomatoes and other members of the nightshade family (Solanaceae), then metamorphose into a hawkmoth that can hover like a hummingbird. Reared in the lab, however, the Manduca is a beloved model organism with ease of care, rapid growth rate, and accessible anatomy.

This year, the bio lab sections are testing the effect of diet nutrition on overall growth of the organism. Some Manduca will have less nutrition per bite in their food for 48 hours, perhaps affecting how much they eat, absorb nutrients, or grow in a 48 hour period. After this diet change, students hit the microscopes to investigate.

Whether they named their Manduca after their TA (shoutout to Jeremy Moore ’19), took beautiful anatomical pictures under the microscope (see above), or made a video in their hornworm’s honor like Patrick Olmstead ’21 (below), students found a way to connect with their lab-reared pe(s)ts.

Intro biology lab students share snapshots from their independent research projects

As the culmination of the year-long introductory biology lab course, all students undertake a large independent research project to apply the skills they’ve learned through a wide array of lab exercises, and begin to specialize in their own interests within the broad field of biology. Whereas in the past students worked with their laboratory section instructors on their projects, this year, the course allowed students to select faculty mentors outside of their lab section so they could receive more specialized help in their particular field of interest.

“We aren’t all Renaissance people,” said Dr. Jennifer McMahon, lead instructor and director of introductory labs. In past years, faculty had a difficult time assisting students on projects that fell outside their areas of expertise, so allowing students to pick their own mentors alleviates some of the pressure on the faculty, and lets students find subjects they are truly passionate about. Additionally, the close partnership between students and faculty mentors who share their interests can turn short, 6 week projects into multi-year research endeavors.

“The recruitment component of this new approach is very important,” notes department chair, Dr. Drew Kerkhoff. “We want to help students identify potential faculty mentors as early as possible. Hopefully, the changes will break down the barrier for students who otherwise might hesitate to approach one of their professors about research opportunities. It also helps faculty identify talented young students who share their research interests.”

Student research proposals must be approved by both their lab instructor and their faculty member. At the end of the semester, after designing and conducting their research, the students write scientific papers on their project and present their work to their lab mates and instructors, joining a long line of young researchers stretching back 25 years. You can even read papers from past years via Digital Kenyon. And each year, the latest papers are added to the collection, giving students their first taste of scientific publication.

Check out a sample of our students’ diverse and exciting projects!

Congratulations to the 2017 Honors Students!!

On Monday, May 8th, Honors students in Biology, Molecular Biology, and Neuroscience successfully defended their honors theses, bringing to a triumphant close what was, for many of them, years of work.

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The 2017 Honors Students in Biology, Molecular Biology, and Neuroscience. Back row, L-R: Kenny Viel, Jiayu Chen, Lauren Michael, Adam Berndt; Front row, L-R: Taylor Jamil, Sarah Mohr, Sarah Naguib

The students had presented their research to peers, faculty, parents, and friends last week, but on Monday, they hosted their outside examiners, established academic researchers in their field who had generously agreed to read and critique their theses, and to come to campus for the day. Researchers came from the University of Dayton, University of Cincinnati, and the Ohio State University, among others.

Each student gave a short presentation to their examiner, then the two of them sat down for an hour to discuss their thesis in detail, as well as the broader area of science to which their work contributes. The examiners asked questions and probed for the limits of the student’s knowledge, but they also shared stories and provided valuable points of reference. The research mentors and other departmental faculty attended the exams, but the conversation is purely between the student and their examiner. One of the students captured the spirit of the event, calling it “intense, but really fun!”

Once the exams were complete, the students, examiners, mentors, and other faculty and staff gathered at Weaver Cottage to celebrate the students’ achievements and to enjoy a wonderful, relaxing lunch.

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2017 Honors Students with their mentors. Back row, L-R: Kenny Viel, Jiayu Chen, Prof. Siobhan Fennessy (Biology, mentor to L. Michael), Lauren Michael, Prof. Andrew Engell (Neuroscience, mentor to S. Mohr), Adam Berndt, Prof. Joan Slonczewski (Biology, mentor to A. Berndt); Front row, L-R: Prof. Chris Gillen (Biology/Molecular Biology, mentor to K. Viel, J. Chen, and T. Jamil), Taylor Jamil, Sarah Mohr, Sarah Naguib, Prof. Hewlet McFarland (Neuroscience, mentor to Sarah Naguib).