A monument to experimental success in microbial evolution (and a pretty dandy learning experience)
Talk about making the most of an opportunity! Sophomore Tanush Jagdish took the initiative to contact microbiologist Richard Lenski (Michigan State University), who had visited Kalamazoo College last spring as the biology department’s Diebold Symposium keynote speaker. Tanush inquired about research possibilities in Lenski’s lab over the December break. Tanush has been working in Assistant Professor of Biology Michael Wollenberg’s microbiology research lab at K since his first year, so he was already familiar with techniques he would need to work in Lenski’s lab. Lenski graciously extended an offer to Tanush and paired him up with a postdoctoral fellow to work on microbial evolution. Tanush loved the work (that’s probably an understatement).
“This experience becomes the most intensive and profound one in my (extremely short) research career,” he wrote. “Through a very fortunate set of events, I got to work on the strain of E-coli that famously learned to eat citrate after 20 years of evolution. Essentially, in order to trace the potentiating mutations back through time, I was trying to figure out the set of genes that are required for citrate consumption in the evolved strain.
“Everything went amazingly well–my experiments worked, the yields were great! I transformed and scanned through more than 1,600 strains from a mutant library, consuming over 3,500 agar plates. As is Lenski lab tradition with large experiments, I got to build my own tower from the plates.” (see photo). Tanush also expressed his appreciation for the opportunity to work with the post-doc with whom he was paired, Dr. Zachary Blount.
“Dr. Blount was extremely kind and generous with his time when he mentored me,” said Tanush. “He is very well regarded in the evolutionary biology community (he characterized the citrate consuming bacteria after conducting what is still the largest genetic screen in academic history).”
Congratulations, Tanush, a beautiful example of leveraging the opportunity of a break between terms.
Justin Horowitz ’05 is a graduate research assistant in bioengineering at the University of Illinois at Chicago (UIC). He’s also the first author of a study that describes the development a of mathematical algorithm that can ascertain intention even when the act of carrying out that intention is interrupted.
The study article is titled “I Meant to Do That: Determining the Intentions of Action in the Face of Disturbances,” and it appears in the online journal PLOS ONE. The article’s co-author is James Patton, professor of bioengineering and principal investigator of the study, which occurred at the Rehabilitation Institute of Chicago and was supported by the National Institute of Neurological Disorders and Stroke.
Horowitz and Patton call the discovery a “psychic robot” and its potential applications may turn out to be profound. Imagine a car diverted from its course that could restore the driver’s intended direction faster than the driver could do so. ““The computer has extra sensors and processes information so much faster than I can react,” Horowitz said in a UIC press release (October 6, 2015, by Jeanne Galatzer-Levy). “If the car can tell where I mean to go, it can drive itself there. But it has to know which movements of the wheel represent my intention, and which are responses to an environment that’s already changed.” The algorithm can make that distinction.
The algorithm also may have potential application in treatment of stroke patients. Imagine a prosthetic device that can restore a patient’s intended course of action before that intent was changed by after-effects of the stroke, such as interruptions in motor coordination. “If you know how someone is moving and what the disturbance is, you can tell the underlying intent,” said Horowitz, “which means we could use this algorithm to design machines that could correct the course of a swerving car or help a stroke patient with spasticity.”
Horowitz earned his bachelor’s degree at K in biology.
Three Friends Talking: (l-r) Kim Chapman ’77, Jim Armstrong, and Lad Hanka ’75 (photo by Susan Andress)
Kim Alan Chapman ’77 is co-author of “Nature, Culture, and Two Friends Talking,” a collection of essays addressing the complex relationships humans have with the natural world. The book is in part the story of a 30-year friendship between Kim, an ecologist living in St. Paul, Minn., and James Armstrong, a poet and English professor at Winona State University in Winona, Minn. Their story centers on love of nature and a shared quest to understand how to save what they love. At turns literary and scholarly, their essays, poems, and public presentations document the evolution of their ideas and expressions of this love. They also reflect American culture’s own dialogue about nature and conservation.
One section of the book, “From the Darkness, Light: What an Ecologist and Poet See in an Artist’s Work,” revolves around the two writers reacting via email to etchings of rural scenes set in southern Michigan by Kalamazoo-based artist Ladislav Hanka ’75, their longtime mutual friend. That exchange also led to a live—and lively—discussion at the Kalamazoo Institute of Arts about how Lad’s work creates a dynamic confrontation between art and science, wildness and civilization, beauty and ugliness, darkness and light. All three friends joined in the conversation before a large audience at the KIA.
Kim has worked as a conservationist, consultant, teacher, and ecologist for 30 years. In addition to his B.A. degree in biology from Kalamazoo College, he holds a M.A. degree in biology (ecology) from WMU, and a Ph.D. degree in conservation biology from University of Minnesota. His other publications include “Valley of Grass” (North Star Press), winner of a Minnesota Book Award.
Joel Hutson ’02 with Ceratosaurus Carnotaurus at the Dinosaur Discovery Museum of Kenosha, Wisc.
Kalamazoo College alumnus Joel Hutson ’02 was quoted in the July 15, 2015 issue of popular scientific magazine Scientific American about dinosaur research that he and his wife, Kelda Hutson (Colgate University ’02), published in the March 2015 issue of Journal of Zoology.
Joel is a biologist who did research in the Department of Biological Sciences, Northern Illinois University, in DeKalb, Ill. He and Kelda, a geologist in the Department of Earth Science, College of Lake County, in Grayslake, Ill., compared the forelimb mechanics of alligators with fossils from Postosuchus — a relative of early dinosaurs and present day alligators and crocodiles to learn more about joint mobility. All dinosaurs once pranced, strolled or lumbered about on two legs, but over time many evolved into quadrupeds. The Hutsons’ research illustrates how dinosaurs may have made the transition from two-legged to four-legged mobility.
Their journal article is titled “Inferring the prevalence and function of finger hyperextension in Archosauria from finger-joint range of motion in the American alligator.” Joel said: “I was inspired to study dinosaurs because of Jeff Wilson ’91 who was featured in Kalamazoo College news when I was a biology student at K.” Wilson is a paleontologist at University of Michigan in Ann Arbor and has visited the K campus to speak to students and faculty about his work.
Joel said he hopes also to “inspire a future generation of paleontologists at Kalamazoo College.”
The Hutsons’ Journal of Zoology article and Scientific American interview will be available free online after an embargo.
Trace Redmond and Eeva Sharp at Roak Brewing Company
Half a dozen years ago first-year student Eeva Sharp ’13 was baking banana bread in the Trowbridge Hall kitchen when classmate (though, at the time, complete stranger) Trace Redmond ’13 walked in.
“Oh, you’re doing it wrong,” he said. Lucky for him there were beginnings of a chemistry other than that happening in the bread. Eeva and Trace have been together since freshman year, and currently you can find them both working (still “in the kitchen” so to speak) at the recently opened Roak Brewing Company in Royal Oak, Michigan.
The morphing of their love of bread to beer started long before Roak, even before Trowbridge. Eeva did a gap year prior to K during which she lived in Belgium. “Beer is a big part of the Belgian cultural identity. It’s a gastronomic experience that I really came to appreciate.” Trace was already home brewing as a student. Eeva soon joined him in that enterprise.
Eeva and Trace during homebrewing student days
After graduation they moved to Grand Rapids. Trace worked at Founders Brewery; Eeva worked in communications and development for The West Michigan Center for Arts and Technology. This past spring Trace got an offer he couldn’t pass up: director of quality control and partner brewer at Roak. By the way, his new employer queried, did he know anyone who could tackle the new venture’s social media and marketing functions. Eeva interviewed a few weeks later. Her new title: director of marketing at Roak.
Both are excited to be part of a new microbrewery. Eeva enjoys the creativity of the craft beer industry and, the sense of shared community in Royal Oak. Trace, with head brewer Brandon MacClaren, loves making beers that are clean, crisp and fresh with the best ingredients and a custom brewing system that was built around the process that he and Brandon have developed to craft their brews.
Roak makes six core beers (Powerboat, Around the Clock, Means Street, Live Wire, Devil Dog and Kasmir) and just released their first seasonal (Melonfest). You can visit the 30-barrel custom brewhouse and taproom (330 E. Lincoln Street) from 4 p.m. to 10 p.m. (Monday through Wednesday), 11 a.m. to 11 p.m. (Thursday through Saturday), and noon to 10 p.m. on Sunday. But be sure to get there early! Seats fill and lines form quickly in the recently opened taproom. Text by Mallory Zink ’15; Photos by Chandler Smith ’13 and Mallory Zink
Nicolette Hahn Niman ’89 has written a second book: Defending Beef: The Case for Sustainable Meat Production. Her first book was Righteous Porkchop: Finding a Life and Good Food Beyond Factory Farms.
Kalamazoo College alumna Nicolette Hahn Niman ’89 is an environmental lawyer, rancher, food activist, author, and vegetarian who has published Defending Beef: The Case for Sustainable Meat Production, published by Chelsea Green. It’s her second book.
Wait…a vegetarian who has written a book in defense of beef? Oh, yes!
Hahn Niman’s first book, Righteous Porkchop: Finding a Life and Good Food Beyond Factory Farms (William Morrow, 2009), took on big factory farms, charging them as major polluters and a detriment to global climate. That book also described how she met, married, and went into business with California cattle rancher Bill Niman.
In Beef, which she subtitles “The Manifesto of an Environmental Lawyer and Vegetarian Turned Cattle Rancher,” she addresses health issues, climate change, water supply, biodiversity, overgrazing, world hunger, the morality of eating meat, and more, the result of meticulous research and day-to-day life on an active livestock ranch.
Beef, Hahn Niman believes, can play an important role in ending world hunger and help restore a balanced climate.
Nicolette Hahn Niman earned B.A. degrees in biology and French at K before earning a aw degree (cum laude) from the University of Michigan.
She served two terms on the Kalamazoo City Commission, worked as an attorney for the National Wildlife Federation, and was senior attorney for Robert F. Kennedy Jr.’s Waterkeeper Alliance, an environmental organization where she was in charge of the organization’s campaign to reform the concentrated livestock and poultry industry.
Recently, Nicolette Hahn Niman was interviewed by Kalamazoo-based WMUK (FM 102.1) writer and book reviewer Zinta Aistars (a former K staffer!) on her program Between the Lines that airs every Tuesday at 7:50 a.m., 11:55 a.m., and 4:20 p.m. Listen to the interview and read more about Hahn Niman here: http://wmuk.org/post/between-lines-defending-beef.
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.
Scientist, science writer, professor of science, and K alum Rob Dunn
Scientist and science writer Rob Dunn ’97 (also an associate professor in the Department of Biological Sciences at North Carolina State University) traveled to the Gulf of St. Lawrence in 2012, on assignment for National Geographic Magazine to write about the area’s ecosystem. He fulfilled his obligation and wrote a very fine article (great verbs!) titled “The Generous Gulf.”
Only months later did Rob learn some back story to his National Geographic story–specifically, that he wasn’t the first in his family to make a “tourist” voyage to the Gulf of St. Lawrence. His forebear, one Thomas But (or Butt or Butts), son of the doctor to King Henry VIII, set sail for the Gulf in April of 1536. The voyages of the two relatives, separated by nearly five centuries, nevertheless shared a few similarities. And, THANKFULLY, the voyages differed in other (significant) ways. For example, Rob didn’t kill and eat any of his fellow travelers.
What Rob did do is write the fascinating back story for the Blog, Your Wild Life. It’s a great read, and we recommend it to our readers.
Brielle Bethke ’16 did an independent internship at the University of Louisville Center for Neurological Surgery. There she assisted with physical therapy, conducted data analysis, shadowed physicians and researchers, and met people with a unique outlook on life. Her work is connected to a recent CNN Health Report story about a study of the applications of electrical stimulation in spinal cord injury. Two people with whom Brielle worked are featured in the story. She worked with Dustin, a patient in the study who, at age 18, suffered a spinal cord injury in a car accident that left him paralyzed from the waist down. Dr. Susan Harkema, the head of neurological surgery at the Frazier Rehabilitation Institute, was the supervisor of Brielle’s internship. Brielle is majoring in biology and earning a minor in Spanish. She is a member of the Health Guild and will study abroad in Caceres, Spain, during her junior year.
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.
