research

Challenge and Imagination: Working Science at K

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Kalamazoo College alumnus Parker de Waal
Parker de Waal ’13

Parker de Waal ’13 had a wish: he wanted to work on a computational chemistry project.

Laura Furge, the Roger F. and Harriet G. Varney Professor of Chemistry, had a challenge: she needed models of the variants of an important human enzyme. (Some background: The aforementioned enzyme, found in the liver, helps the body process medicines, but it’s not exactly the same–hence, variants–in all individuals. Such variability means some people react differently (including adversely) to important medicines. That’s a serious health problem, and part of Furge’s current grant from the National Institutes of Health calls for the study of these variants. And for such study a model of the variants’ structures would certainly be useful!)

In spring 2013, wish met challenge, and, one year later, the two researchers (along with co-author Kyle Sunden ’16) have published a paper in PLoS ONE, the online journal of the Public Library of Science.

That culminating publication traces back to a laboratory question: Could de Waal (a student in Furge’s “Advanced Biochemistry” class) make computational models of the variants? “I suggested some different ways to approach the problem,” says Furge, “and those approaches took Parker all of about two days!” It was at that point that de Waal suggested to Furge some different, more powerful computational approaches–specifically, molecular dynamics using more sophisticated software. “I said, ’Let’s go for it!’” says Furge. “And we both started on the journey to learn more about Molecular Dynamics approaches.”

The journey included consulting with other scientists around the country and the world (Germany, the Czech Republic) both by email and in person at various scientific conferences. Furge and de Waal used a supercomputer at the University of Texas for the computational work. Analysis of the resulting structures was completed by Furge and Sunden during the winter and spring terms of 2014. “The project is a beautiful example of how research and teaching go together at K,” says Furge. The work has been presented at two major medical meetings.

The paper includes 21 figures and tables. Parker de Waal performed all the experiments that led to the figures; Sunden did the experiments and analyses for two of the figures. Furge did the majority of the analysis. In true liberal arts fashion, the cross-disciplinary work combines computer science and biochemistry. Furge taught Sunden, a chemistry and computer science double major, the relevant biochemistry as they progressed with the project. Sunden hopes to continue the work for his Senior Individualized Project after he returns from study abroad in Australia. The work may one day contribute to personalized solutions for people who have adverse drug reactions to important medicines. The paper has had more than 300 views in the six weeks since it’s been published.

Great academics, cross-disciplinary collaboration, research at the edge, and science that matters! Science education at Kalamazoo College: a double helix of challenge and imagination.

Mara Richman ’14: Have Research, Will Travel

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Senior psychology major Mara Richman in front of a projection screen
Mara Richman ’14 presenting her research in Rome

Mara Richman ’14 recently cut classes for an entire week. But the senior psychology major wasn’t goofing off. Rather, she attended the International Borderline Personality and Allied Disorders annual conference in Rome—at their invitation—to deliver her research paper “Reading the Mind in the Eyes Test in Major Depression and Borderline Personality Disorder: A Meta-Analysis”

She was the conference’s youngest oral presenter.

“There were researchers from all over the world on this topic and I presented before a huge audience,” said Mara.

“I have a passion for meta-analysis and this is one of several that I have done on my own. This one looked at differences in mental state decoding between borderline personality disorder and major depressed patients.”

The National Institute of Mental Health defines borderline personality disorder (BPD) as a serious mental illness marked by unstable moods, behavior, and relationships. Most people with BPD suffer from problems with regulating emotions and thoughts, impulsive and reckless behavior, and unstable relationships with other people.

Mara’s paper was based on independent research she conducted while on study abroad at Kalamazoo College’s Budapest Semester in Cognitive Science, under the mentorship of Zsolt Unoka, M.D., Ph.D. She visited with Dr. Unoka during the Rome conference.

One of her K professors, Luce Professor of Complex Systems Studies Peter Erdi, Ph.D., helped her arrange the research project. Help with funding for her Rome trip came from K’s Office of the Provost, Department of Psychology, and Arcus Center for Social Justice Leadership.

“The conference truly shaped me and it was great to network with people in the field to learn more about the BPD,” said Mara.

Mara completed her SIP this past summer at Harvard University where she moved forward her BPD research by studying identity disturbance. She currently has 12 peer-reviewed journal articles in review or awaiting publication. Previously, she received an award from the American Psychological Association for outstanding research.

“My K advisor, Visiting Assistant Professor of Psychology Jennifer Perry, Ph.D., has been a huge help in guiding me and helping me make these decisions.”

Mara, who came to K from Tampa, Fla., completed all of her graduation requirements early and will leave campus at the end of this fall quarter. She hopes to land fulltime work in a clinical facility in order to gain more clinical experience before pursuing a Ph.D. in clinical psychology with a focus on BPD.

K Professor and Students Publish Important Chemistry Research

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K students Rina Fujiwara, Erran Briggs and Amanda Bolles with Professor Laura Furge
Medicinal researchers and members of the Furge Lab (l-r): Rina Fujiwara, Erran Briggs, Amanda Bolles, and Laura Furge

Laura Furge, the Roger F. and Harriet G. Varney Professor of Chemistry at Kalamazoo College, is the senior and corresponding author of an important scientific paper that includes three Kalamazoo College student co-authors: Amanda Bolles ’14, Rina Fujiwara ’15, and Erran Briggs ’14. The paper is titled “Mechanism-based Inactivation of Human Cytochrome P450 3A4 by Two Piperazine-containing Compounds” and appears in Drug Metabolism and Disposition, a highly regarded, high impact international journal published by the American Society for Pharmacology and Experimental Therapeutics. The research the paper describes, which was conducted in the Furge Lab on K’s campus, contributes the understanding of how some drugs “apply the brakes to” the activity of an enzyme–in this particular case, an enzyme important to the metabolism (or processing) of about half of all medicines! What are the human implications of the work? “Many individuals take multiple medicines each day,” said Furge. “Multiple-drug regimens can lead to unwanted side effects, including drug-induced inhibition of the very enzymes responsible for the metabolism and clearance of other co-administered drugs.” In fact, side effects from drug interactions of polypharmacy therapy are the number one cause of hospitalization in the U.S. “This paper adds in understanding of how certain classes of drugs may cause this type of unfavorable medical event,” said Furge. “New insights will hopefully lead to better prevention in the future.”

The paper includes 13 figures and tables. Furge noted that Bolles, Fujiwara, and Briggs performed all the experiments that lead to those figures, and “all the work was done on the campus at Kalamazoo College. We had all the equipment here needed to complete these studies, and we have already started full swing on another set of experiments for a future publication.” The students have presented parts of the preliminary data at national meetings in the past year, and the research forms of basis of the Senior Individualized Projects for Bolles and Fujiwara.

Such research, and the extraordinary educational opportunities it provides for K students, requires the cooperation, coordination, and collaboration of many funding sources. “This is so important,” Furge stressed. The Richard Cook Fellowship and the Alan and Elaine Hutchcroft Fund (endowments created and supported by alumni gifts) paid for the summer stipends of Fujiwara and Bolles, respectively. The mass spectrometer essential to the experiments was paid for in part by the Hutchcroft Fund and a grant from the Howard Hughes Medical Institute. The research also was funded by grants Furge secured from the National Institutes of Health.

“Drug Metabolism and Disposition is an international journal with a high impact factor,” added Furge. Impact factors measure how frequently manuscripts in a journal are referenced by other authors.

With/Out ¿Borders? Opens Thursday

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Two social justice advocates attend Without Borders ConferenceMore than 500 social justice advocates, scholars and leaders ranging from civil rights icons and eccentric artists to young organizers and poet laureates will be on the Kalamazoo College campus, as well as locations throughout the city, this weekend, Sept. 25-28 to participate in the Arcus Center for Social Justice Leadership (ACSJL) “With/Out ¿Borders?” conference.

Attendees will engage in questioning–and openly attempt to complicate –the political, ideological, cultural, and social barriers that make up our world. Thought-provoking plenary sessions, participatory think tanks, and moving and entertaining artistic performances are just some of the diverse and engaging platforms that will be used to question the borders that surround so much of our world today–and develop paradigms and strategies to break them down.

Well-known performance artists and cultural workers Guillermo Gómez-Peña and Michèle Ceballos Michot, whom make up the performance troupe La Pocha Nostra, will be on stage on Friday afternoon with Adriana Garriga-López, the Arcus Social Justice Leadership Assistant Professor of Anthropology. The trio will discuss, instigate, and agitate on the meaning of border politics, performance, and the role of art in the process.

Later that day, the conference will take on a more poetic note, as two well-known poets read form their work and engage with local poet and activist Denise Miller and Lisa Brock, academic director of the ACSJL.

Nikki Finney, winner of the 2011 National Book Award for Poetry, and Keorapetse “Willie” Kgositsile, former poet laureate of South Africa, will bear witness to history and exile and set the stage alive with “truth telling” and love poems crafted out of the struggles of black people from both the southern areas of the United States and South Africa.

Civil rights icon Angela Davis will take to the stage on Saturday morning, along with distinguished African American studies expert Robin D. G. Kelley, peace activists Lynn Pollack and Leenah Odeh and academics Alex Lubin and Saree Makdisi, to discuss the Boycott, Divest and Sanction (BDS) Movement emerging globally in support of the Palestinian people, who live in walled, or “bordered” territories.

Participants in this plenary session will ask if the BDS movement is the next critical solidarity movement of our time, who it’s for, who it’s against, and why.

Cities will take center stage later Saturday, when a plenary of scholars and organizers examine resistance movements in cities today. Organizer and writer Kali Akuno, Detroit-based activist shea howell and David Stovall, professor of African-American studies, will discuss teacher protests in Chicago, water rights issues in Detroit, city planning strategies in Jackson, Miss., and minimum-wage increase advocacy efforts nationwide at this plenary moderated by Rhonda Williams, associate professor of History at Case Western University.

The future of various social justice movements will be on display in the Hicks Center Banquet Room Sunday morning, where a host of young social justice advocates and organizers will discuss their own projects, talk about the need for more youth to become involved and analyze the New Youth Movement.

Civil rights organizers Phillip Agnew and Charlene Carruthers, undocumented immigrant advocate Lulu Martinez, climate change organizer Will Lawrence, sexual assault awareness organizer Zoe Ridolfi-Starr and voting rights advocate Sean Estelle will be in on the discussion, moderated by the Mia Henry, executive director of the ACSJL.

For a full list of events, go to the conference’s schedule page.

Small School; Big Experiments

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Professor of Chemistry Jeff Bartz in the laser labThis past spring Professor of Chemistry Jeff Bartz (pictured at left with two students in his laser laboratory) received word that the National Science Foundation would provide a three-year grant to Kalamazoo College so that Bartz’ lab could conduct new experiments to evaluate how the shape of a molecule influences the mechanics of its dissociation into smaller fragments. The work began this summer and involved four students: Mara Birndorf ’16, Jeremy Lantis ’16, Braeden Rodriguez ’16, and Marlon Gonzalez ’17. And there’s nothing quite as effective as complementing classroom work with hands-on real-world experience. “My chemistry classes taught me the fundamentals, but the research is giving me an idea of what a physical chemist does,” said Birndorf. Bartz agrees: one of the great benefits of the NSF grant is its effect on students, who “move from seeing themselves as students to seeing themselves as scientists.” On a typical weekday morning these young chemists are using lasers in the type of experiments that Bartz long ago thought were unlikely to ever be performed here. After all, smaller schools do face the challenges of getting their research swallowed up by larger institutions with more resources (not to mention graduate students) to conduct a project. Despite those challenges, Bartz finds an angle for K to contribute to new scientific work. “We have to evolve if we want to continue to work at the forefront.” Like most new science, what’s going on in Bartz’ lab derives from previous work. Niclas West ’12 presented a talk, “Velocity-mapped ion imaging of methyl nitrite photodissociation,” in 2010 at the 65th International Symposium on Molecular Spectroscopy. Researchers from Texas A&M found the abstract online and approached the K team about the similarities between the two teams’ experimental techniques. The two groups decided to collaborate on the publication of a paper, “A method for the determination of speed-dependent semi-classical vector correlations from sliced image anisotropies,” which included K student co-authors West and Kelly Usakoski ’14. After this paper came out in The Journal of Chemical Physics, Bartz began work on the proposal the NSF funded last spring. “We are looking at information gaps in previous work that our current experimental techniques can help fill,” Bartz said, “sort of testing old experiments in new ways. It’s kind of a K niche we’ve carved out.” (text by Colin Smith ’15)

Making Research Click

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Michael Finkler uses a pencil to point as Bel Da Silva looks on
Michael Finkler and Bel Da Silva study the embryonic development of snapping turtles.

Michael Finkler ’91, Ph.D., “pays forward” the kind of hands-on research opportunity he had at K (thanks to his mentor, Associate Provost Paul Sotherland, who was teaching biology when Finkler was a student). Finkler is a professor of biology at Indiana University Kokomo. This past summer he hosted in his lab Brazil native Bel Da Silva, an undergraduate student (Federal University of Amazonas) participating in an exchange program called Science Without Borders. She assisted in Finkler’s ongoing research of snapping turtle embryo development. IU-Kokomo posted a story about the collaboration in its online newsletter, and in the interview for that story, Finkler paid tribute to Sotherland: “’I had a really great mentor as I completed my undergraduate thesis, and that’s when research really clicked for me,” he said. “That’s why I’m a professor now, because of that mentoring. In Bel’s case, I also saw an opportunity to get experience working with an international student.’” Sotherland served as Finkler’s SIP advisor. In fact, their SIP work (a productive collaboration that included John Van Orman) eventually led to the 1998 publication of a paper titled “Experimental manipulation of egg quality in chickens: influence of albumen and yolk on the size and body composition of near-term embryos in a precocial bird” in the Journal of Comparative Physiology. Seems that the seed of a K experiential opportunity like the Senior Individualized Project grows across time and borders. After all, the IU-Kokomo article notes that Da Silva intends to become a professor and researcher, the kind of scientist and teacher who will provide hands-on research opportunities for students from Brazil and other countries.

Young Scientist

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Mara Richman standing by her research posters
Mara Richman presented research at the North America Society for the Study of Personality Disorders.

Mara Richman ’15 has built an impressive scientific résumé in three short undergraduate years–and she has yet to reach her Senior Individualized Project (SIP) term!

During her study abroad in Budapest, Hungary the psychology major collaborated with Dr. Zsolt Unoka on research in depression and borderline personality disorder. She presented that work, titled “Mental state decoding deficit in major depression and borderline personality disorder: a meta-analysis,” at the North America Society for the Study of Personality Disorders. Think the age of David (when he confronted Goliath) or of Joan of Arc … Mara was the youngest presenter at NASSPD! And she will be one of the youngest oral presenters at the prestigious International Congress on Borderline Personality Disorder and Allied Disorders (Rome, Italy), where her paper was accepted and where she will detail the meta-analysis she completed with Unoka. Their research also has been submitted in manuscript form to Clinical Psychology Review.

To date, Mara has six manuscripts published or in review for publication on research into schizophrenia, drug courts, and borderline personality disorder. She has presented research (or had research accepted for presentation) at Stanford University, the Association for Psychological Science, the Midwestern Psychological Association, the Mid America Undergraduate Research Conference, and the Michigan Undergraduate Psychology Conference. And she will present her work at the American Psychological Association in August. Most of this BEFORE she begins in earnest her SIP work. That will happen this summer at Harvard University Medical School’s Department of Psychiatry under mentor ship of one of the world’s foremost experts on borderline personality disorder, Dr. Mary Zanarini.

Given her youth and her accomplishments so far, it may not be too surprising that Mara will graduate after her senior fall term. She hopes to work in a lab for nine months or so and then apply to graduate school. She plans to earn a Ph.D. in clinical psychology and focus her research on borderline personality disorder.

Four in More Than 15,000

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Three female students who presented at the 2014 Experimental Biology Meeting
K student researcher/presenters at the 2014 Experimental Biology Meeting included (l-r): Amanda Bolles, Rina Fujiwara, and Virginia Greenberger. Not pictured is Michael Korn.

Four Kalamazoo College students attended at the 2014 Experimental Biology Meeting: Amanda Bolles ’14, Chemistry; Rina Fujiwara ’15, Chemistry; Virginia Greenberger ’14, Chemistry; and Michael Korn ’14, Biology. Experimental Biology is a joint meeting of six different societies including the American Association for Biochemistry and Molecular Biology (ASBMB) as well as societies for physiology, nutrition, pharmacology, pathology, and anatomy. The meeting provides a great opportunity for students to present their work and attend a variety of engaging scientific talks. More than 15,000 scientists attended the event in San Diego, Calif.

Bolles and Fujiwara presented their research findings during the Undergraduate Poster Competition and during the regular scientific session for ASBMB. Their research involves recent work completed in the laboratory of Professor of Chemistry Laura Furge. That work has shown that two different (but related) compounds inactivate P450 3A4, an enzyme in the liver and intestine that metabolizes (or processes) a major pharmaceutical drug. The titles of the Bolles and Fujiwara posters were, respectively, “5-Fluoro-2-[4-[(2-phenyl-1H-imidazol-5-yl)methyl]-1 piperazinyl]pyrimidine is a mechanism based inactivator of CYP3A4” and “Mechanism-based inactivation of human CYP3A4 by a piperazine-containing compound.” The ASBMB competition includes posters of some 300 students from a variety of college and universities across the country. One grand prize award was presented to a student in each of four research categories (bioenergetics/protein structure, cell biology/developmental biology, DNA/gene regulation, and immunology/microbiology/neurobiology). Bolles won the $500 grand prize in the bioenergetics/protein structure category and was recognized the next day before an audience of hundreds of scientists, educators, and students at the award lecture for outstanding contributions to education. Bolles’s presentation derived from her Senior Individualized Project (SIP), which will be published later this year along with results from co-author Fujiwara.

Greenberger conducted her SIP research in the laboratory of Professor of Chemistry Regina Stevens-Truss. The abstract she presented at the meeting was titled “Bacterial Action of Novel Cationic Peptide Sequences.” As more antibiotic resistance is observed in patients, new sources of antibiotics are being investigated, including short peptide sequences. Greenberger’s work in the Truss lab was aimed at determining the antibiotic activity (and the precise mechanisms of action that yielded the activity) of two newly studied peptide sequences.

Dr. Furge also presented a poster in the ASBMB regular scientific session based on work started last year by Parker de Waal ’13. The work began as part of a course assignment in Furge’s “Advanced Biochemistry” course and grew into an elegant computational study of structural differences between select variants of the drug-metabolizing enzyme P450 2D6. de Waal used molecular dynamics methods to show how subtle differences in the enzyme structure can help explain differences in the metabolizing abilities of the enzymes. The study is being completed by Kyle Sunden ’16. While in San Diego, Furge spent an afternoon at the Skaggs School of Pharmacy at the University of California-San Diego discussing the implications and approach of the study with other scientists in this field.

Korn attended the American Physiological Society (APS) portion of the Experimental Biology meeting. He presented the results of his SIP work (conducted in the laboratory of Dr. Christopher Mendias at the University of Michigan) in the APS Student Poster Competition. Korn’s abstract received the David Bruce Outstanding Undergraduate Abstract Award. The title of his presentation was “Simvastatin reduces myosteatosis following chronic skeletal muscle injury.”

The future is promising for all four of these outstanding student researchers. In the fall, Bolles will enter the University of Michigan Graduate Program in Biomedical Sciences; Greenberger will matriculate to the chemistry department at Pennsylvania State University to begin work on her Ph.D; Korn will attend the University of Michigan Medical School; and Fujiwara will complete her SIP with Furge this summer. She plans to attend graduate school after her June 2015 graduation from K.

Professors Furge and Truss are both members of the ASBMB and attend the annual meeting each year. Truss also directs a National Science Foundation (NSF)-funded workshop for area high school science teachers in connection with the annual ASBMB meeting. This year’s workshop attracted more than a dozen local teachers who learned science and teaching strategies to use in their classrooms. Attendees at the workshop are also eligible for mini-grants to support further development of their teaching after the workshop. A recent article describes the impact of this workshop (which is in its fourth year).

In other meeting news, the Ruth Kirschstein Diversity in Science Award was given jointly to President Freeman Hrabowski III and Professor Michael Summers of University of Maryland-Baltimore County. Professor Summers was the SIP mentor to Erran Briggs ’14 and has worked closely with Professor Truss on the Professional Development and Minority Affairs Committees of ASBMB. Professor Summers also visited K’s campus in 2010 as a Howard Hughes Medical Institute Guest Scholar Lecturer. Given the connections, and important work of Summers and Hrabowski, Professor Truss arranged for Bolles, Fujiwara, and Greenberger to interview Summers for Kalamazoo College’s Arcus Center for Social Justice Leadership’s Praxis Center. Following the interview, Summers treated the students and Truss to lunch overlooking the San Diego Harbor marina! Notes from the interview will be posted on the Praxis website.

Travel to ASBMB for Bolles, Fujiwara, and Greenberger was supported by grants from the Provost Office, the Heyl Foundation (Greenberger), and the ACSJL. Korn’s travel to the meeting was sponsored by grant funds from his SIP advisor and the University of Michigan. Furge and Truss were supported by the Hutchcroft Endowment as well as their NIH and NSF grants, respectively. Next year’s Experimental Biology Meeting will occur in Boston, Mass.

Four Share Research on Japanese Culture

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Four students sharing their research on Japanese cultureFour Kalamazoo College students presented their research at the annual Michigan Japanese Heritage and Culture Conference. The conference was sponsored by Grand Valley State University’s Japanese Cultural Association, and attendees–some 50 students and teachers–shared their studies in Japanese culture, including Japanese relations within Michigan and contemporary issues affecting Japan and the United States. Several presenters were members of the Japanese community, including employees of government agencies, colleges and universities, and university organizations. The K presentations focused on food, fabric dyeing, cinema, and nontraditional romantic relationships. The four K students were classmates in Assistant Professor of Japanese Noriko Sugimori’s winter term class, “Intermediate Japanese II,” when most of their research was done. The students (and the titles of their research presentations) are (l-r): Anh Lam ’17 (“Mochi: Where Cultures Meet”), Jamie Heywood ’16 (“Shibori: Re-visitation, Reinvention, and Revival”), Penelope Owen ’16 (“Alternative Love”), and Edwin Salvatierra ’16 (“Kitano’s Gokudou: Reinventing the Yakuza Film Genre”). The three sophomores will study abroad in Japan during their entire junior year–Heywood and Owen in Kyoto, Salvatierra in Hikone.

The Bees’ Needs

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K alumna Rachel Mallinger holds a visual presentation for Wisconsin’s Wild Bees
Rachel Mallinger

The power of science in large part is the power of great storytelling. When the stories lead into mystery … well, that’s when science continues, generating more stories and encountering more mysteries. The University of Wisconsin-Madison’s Genetics/Biotech center harnesses the power of stories during a public series called Wednesday Nite @ The Lab, occurring every Wednesday, 50 times a year. Attendance is high, and K alumna Rachel Mallinger ’05 will be the featured presenter on Wednesday, March 26. Her topic: “Wisconsin’s Wild Bees: Who Are They, What Do They Do, and Why Should We Conserve them?” Rachel earned her B.A. in biology at K, her M.S. in entomology and agroecology (UW-Madison) and is currently pursuing her Ph.D. in entomology at UW-Madison. Wisconsin has more than 500 species of native wild bees, and their contributions to pollination are becoming more and more important as honey bee populations decline. Mallinger’s talk will focus on effect of land use change and farm management on the abundance and diversity of wild bees. “I will also discuss the role of wild bees in crop pollination, and address whether or not they can fulfill our food needs,” she wrote. Mallinger wants to learn more about the roles of insects in agricultural ecosystems and how insects can be managed to enhance the sustainability of farming. She currently studies wild bees and pollination services within fruit orchards. She enjoys working with farmers, experimenting in her own vegetable garden, and cross-country skiing during the winter. At K, Rachel studied abroad in Thailand, and she also mentored a SIP student supervised by Ann Fraser, associate professor of biology. According to Fraser, that student is now applying to Ph.D. programs to work on wild bees. “That will make at least four grads in the last eight years who have done to work on wild bees,” adds Fraser. “I’ll be working with three students this summer on another bee project (looking at the impacts of honey bees on wild bees), and a student organization on campus is starting work on constructing ’buzz boxes’ on campus to improve foraging and nesting habitat for wild bees. Maybe,” grins Fraser,” we need a new college mascot.” The hornet’s probably safe for now.