biology

Lamprey Research Unlocks Secrets of Vertebrate Evolution

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The work of biology professor James Langeland, as part of a large international consortium, was published in the journal Nature Genetics, one of the top 10 science journals worldwide.

Langeland has been part of the consortium working on sequencing and elucidating the genome of the sea lamprey (the simplest of living vertebrates and a species on which Langeland has worked for 16 years).

The title of the article is “Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution.” The paper is the first presentation of lamprey whole-genome sequence and assembly. Lampreys represent an ancient vertebrate lineage that diverged from our own some 500 millions year ago. Scientists have studied the sea lamprey genome to gain insights into the ancestry of vertebrate genomes, the underlying principles of vertebrate biology, and evolutionary events that have shaped the genomes of existing organisms.

Langeland is the Upjohn Professor of Life Sciences at Kalamazoo College.

K alumna is both medical student and medical detective

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Medical student Sarah Allexan
Medical student and sleuth, Sarah Allexan ’11

Sarah Allexan ’11 is the lead author of a research paper published in the Journal of the American Academy of Pediatrics that looks into the cause of blindness in Mary Ingalls, older sister of Laura Ingalls Wilder, author of the popular “Little House” book series.

Ingalls Wilder wrote that Scarlet Fever caused her sister to lose her eyesight. Allexan and her research team determined otherwise. Their findings have attracted a lot of news media attention, including an article in USA Today and an article in the New York Times. Sarah also participated in an interview with WMUK radio (102.1 FM), the NPR affiliate at Western Michigan University.

Originally from Englewood, Colo., while at K, Sarah majored in biology, studied abroad in Ecuador, ran on the Hornet cross country team, and sang in the Limelights student a cappella group. She also served as a bi-lingual tutor for first-graders at a Kalamazoo Public School, and completed both an internship at the Seattle Aquarium and an externship at Vanderbilt Children’s Hospital.

Shortly after her K commencement, she took a job as a research assistant at University of Michigan in Ann Arbor. While there, she became involved in the Ingalls research project.

“It was fun tracing Laura’s journey and playing medical detective,” Sarah said. “This was my first real exposure to lineal reasoning and prepared me well for medical school.”

Sarah is now enrolled at University of Colorado School of Medicine. “But I bleed ‘Orange and Black!’” she said.

 

Charles Holmes, MD ’93 Leads Effort to Combat Infectious Disease in Zambia

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Kalamazoo College alumnus Charles Homes speaking at a lecturn
Charles Holmes, MD ’93 has “a legacy of listening to, and using science, say long-time Washington workers in the AIDS response.”

Charles Holmes ’93 was completing his medical education when he lived and worked for three months in Malawi in 1999. The AIDS epidemic there, uncontrolled, was peaking. Desperately sick people lay three to a bed in the Lilongwe hospital where Holmes worked, and where the best medicine on hand could only alleviate their agony until they died.

“Deaths were an hourly occurrence,” he said later. “It was an important and formative experience for me to be a firsthand witness to that tragedy.”

It has shaped his work and interests ever since, he added.

This month, he packed his bags for Africa again, to lead the Centre for Infectious Disease Research in Zambia, widely considered one of the most effective in-country programs to improve health care capacities in a resource-poor country.

Read more about this Kalamazoo College graduate’s work in Science Speaks: HIV and TB News, a project of the Center for Global Health Policy.

K Alumna Wins Prize for Science Journalism

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Kirsten Weir ’99 is the winner of the 2012 AAAS Kavli Science Journalism Award in the children’s science news category. The awards are administered by the American Association for the Advancement of Science (AAAS) for professional journalists to honor distinguished reporting for a general audience. Weir received the award for her article “Uninvited Guests,” which appeared in the April/May 2012 issue of Current Health Kids. In a way that appeals to children and adults the article describes the parasites and microbes that live in and on our bodies. Said Weir: “Kids often seem to think that science is something that happens in a laboratory or a faraway place. I loved that this story underscored how much is still unknown about the organisms living right under our noses (not to mention the rest of our bodies).”

K Science Majors Present at Undergraduate Research Conference

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Six students who presented at the West Michigan Regional Undergraduate Science Research Conference
Scientific presenters at the West Michigan Regional Undergraduate Science Research Conference included (l-r): Carline Dugue, Josh Abbott, Amanda Bolles, Mara Livezey, Kelly Bresnahan, and Chelsea Wallace. Not pictured are Erran Briggs, Michael Hicks, Nicolas Sweda, and Associate Professors of Chemistry Laura Lowe Furge and Regina Stevens-Truss.

Nine Kalamazoo College science majors and two chemistry department faculty members (Regina Stevens-Truss and Laura Lowe Furge) attended the recent West Michigan Regional Undergraduate Science Research Conference in Grand Rapids. The students were Carline Dugue ’12, Chelsea Wallace ’13, Nicholas Sweda ’12, Mara Livezey ’13, Michael Hicks ’12, Kelly Bresnahan ’12, Josh Abbott ’12, Amanda Bolles ’14, and Erran Briggs ’14. Hicks and Wallace are biology majors; the others are majoring in chemistry. They presented results of their summer and academic year research experiences, including Senior Individualized Project work for Dugue, Bresnahan, Sweda, and Abbott. More than 170 posters from colleges across West Michigan were part of the conference’s poster session, and some 400 people participated in the conference. Dugue’s research focused on semiconductor quantum dots and charge transfer; she worked with Western Michigan University professor Sherine Obare. Abbott’s work focused on the role of a specific liver enzyme (CYP2B6) in the way the body processes the cancer drug cyclophosphamide. He did this work in the lab of Professor Paul Hollenberg at the University of Michigan. Bresnahan completed her SIP at the University of Michigan laboratory of Professor James Woods. She worked on animal models for testing of molecules called cholinergic receptor agonists for aid in smoking cessation studies. The other six posters described research done at Kalamazoo College. Sweda presented ongoing studies from Professor Stevens-Truss’s lab on suramin selective inhibition of nitric oxide synthases, part of a chain of events that affects production of nitric oxide in the human body. An excess of nitric oxide is associated with conditions such as Parkinson’s disease and Alzheimer’s disease. This work is the basis of a manuscript in preparation with Sweda and Alyssa McNamara ’11 as co-authors. Wallace’s research (with Associate Professor of Biology Blaine Moore) showed that BCL-2 is able to rescue neuroblastoma cells from ethanol toxicity. Livezey, Hicks, Bolles, and Briggs each presented individual posters with results of three projects from Professor Furge’s lab on the interactions of inhibitors with human cytochrome P450 enzymes. These enzymes metabolize compounds, including medicines, in the liver, and the inhibition of those enzymes may influence the effectiveness of current and new medicines. The work presented by Bolles and Briggs is currently being prepared in a manuscript for publication with both students as co-authors along with Livezey. The posters presented by Hicks and Livezey are the basis of a current NIH grant renewal to support ongoing opportunities for student research in the Furge lab. In addition to the poster sessions, students attended several lectures and were able to meet with graduate school recruiters.

K Grad Studies Desert Fish With a Far Eye Cast to Cancer

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Claire Riggs ’11 received a pre-doctoral fellowship from the National Science Foundation, a prestigious award that allows her to continue research on killifish embryos as she works on her doctorate at Portland State University. Her research was the subject of an article (“Life in the Extreme”) by Maya Seaman that appeared in the publication, Vanguard. Killifish embryos can survive pretty tough conditions–in extreme heat, without water, and, believe it or not, without oxygen. Riggs studies the role of the fish embryos’ microDNA in their ability to go dormant and survive in anoxic environments. For killifish embryos, such dormancy is characterized by a reduction of metabolism, inhibition of cell development, and stoppage of the heart beat … up to 90 days … without harm! Clues to how this process works, should it ever prove applicable to humans, could eventually have important potential for cancer therapy and treatment of heart attack and stroke.

“I Went to Kalamazoo College!”

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Dan Blustein, Joel Haas, and Tess Killpack have a great deal in common. They’re classmates (2006); they’re working on their doctorates; and they’re finalists in a video contest! “Dan entered us in an NSF fellows video contest (of course he did…),” wrote Tess to Professor of Biology Paul Sotherland, “and we made it to the finals.” The contest celebrates the 60th anniversary of the National Science Foundation’s Graduate Research Fellowship Program. Dan, Joel, and Tess share that too; each is an NSF GRF. The title of their video is “Sharing Our NSF GRF Skills With the World.” “We took a little different approach from most of the other entries and did a collaborative entry filming on our own and working over the Internet,” said Dan. “Judges pick winners, and there is one People’s Choice award determined by online votes.” There’s great variety in their research work and geographic dispersion—robot lobsters, cellular energy balance, and avian immune system development, in Boston, San Francisco, and Madison (Wis.) for Dan, Joel, and Tess, respectively. In true K fashion, they do much more than their research. Each works on issues important to science and society, including effective teaching, diversity in the sciences, and scientific policy. Congratulations, Dan, Joel, and Tess. And good luck in the finals.

K Professor and Students Publish Encouraging Science on the Search for a Useful Bio-Indicator

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Maintaining good human health depends in part on reliable markers. Think blood pressure in cardiovascular medicine or blood sugar and triglyceride levels in determining the effects of diet on metabolic disorders. Reliable markers are important for ecological health as well, which is why science seeks them. Associate Professor of Biology Ann Fraser and five Kalamazoo College undergraduates recently published peer-reviewed science (“Evaluating Multiple Arthropod Taxa as Indicators of Invertebrate Diversity in Old Fields,” The Great Lakes Entomologist, Vol. 45, Nos. 1 – 2) that advances efforts to find a manageable indicator of the effect invasive species have on biodiversity.

Like most good science, the journey was both years long and collaborative—as well as a great example of the kind of professor-student partnerships that make science education at K great—a matter of “more in four years.” The idea for the project began with some preliminary data gathered during a lab exercise in Fraser’s Organism Diversity class. That field work took place at the College’s Lillian Anderson Arboretum, where the class sought to test whether the invasive plant species known as spotted knapweed was affecting ground-dwelling invertebrates (mainly insects). Joe Waller ’06 followed up on the preliminary class data with a more in-depth study for his Senior Individualized Project. He used pitfall traps to collect invertebrates in areas with varying densities of knapweed but was soon overwhelmed with huge numbers and types of insects to sort through. He shifted the focus of his SIP to determine whether a certain insect or other arthropod species, such as spiders, might be a proxy or reliable marker for general invertebrate diversity. He spent most of his summer sorting through and classifying thousands of specimens. In late summer a second round of pitfall sampling was conducted and the project’s torch was passed to other undergraduates.

The sorting, identification, and matching of this second sample with the first sample were conducted by Alyssa Bradshaw ’08, David Hyman ’08, Michael Johnson ’06, and Rob Morrison ’06. “We were able to identify several insect groups as promising indicators of larger invertebrate diversity in old field habitat,” said Fraser. “More work across a greater number of field sites is needed to confirm their usefulness as bio-indicators, but this is an encouraging first step in finding manageable ways to assess the impact of invasive plant species on invertebrate diversity.”

Fraser cited the pivotal role of Morrison in bringing the project to completion and publication, earning him first author on the paper. Such studies are time-consuming but well suited to undergraduate research projects. The K grads continue their science education in various ways. “Rob Morrison is conducting his Ph.D. in applied entomology at Michigan State,” said Fraser. “Joe Waller, I believe, is in a physician assistant program at Michigan or MSU. Alyssa Brayshaw has been working as a research assistant in wildlife biology and is applying to graduate programs in that subject; David Hyman is in medical school at Loyola University in Chicago, and Michael Johnson will begin his Ph.D. in paleontology at the University of Wisconsin this fall. It’s very satisfying to see this collaborative project come to fruition with a peer reviewed publication.”

Alum Keith Crandall Hired to Direct Computational Biology Institute at George Washington University

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Keith Crandall ’87 has been hired by George Washington University to direct its new Computational Biology Institute.

Computational biology combines elements of computer science and biology, and its practitioners develop tools to analyze data generated in researching genetics and genomics, including genetic mapping and DNA sequencing.

Crandall’s research interests have included crustacean biology, biodiversity, and infectious diseases. His B.A. from Kalamazoo College is in biology. At Washington University in St. Louis he earned a Ph.D.in population and evolutionary biology and a master’s degree in statistics. His work at CBI will include an investigation of the impact of the BP oil spill in the Gulf of Mexico, using gene expression to identify how oil pollutants affect deep sea crustaceans.

The Magnificent Five

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Five women representing Kalamazoo College
(Left to right) Regina Stevens-Truss, Lindsey Gaston, Sandrine Zilikana, Laura Lowe Furge, and Mara Livezey

Majors Sandrine Zilikana ’12 and Mara Livezey ’13 and biology major Lindsey Gaston ’12  joined chemistry department faculty members Regina Stevens-Truss and Laura Lowe Furge at the American Society for Biochemistry and Molecular Biology Meeting in San Diego in late April. The students presented results of their summer research experiences (part of the Senior Individualized Projects for Sandrine and Lindsey) as part of both the Annual Undergraduate Poster Competition and the regular scientific sessions of the meeting.

More than 200 students from schools across the country were part of the undergraduate poster competition.  Zilikana’s research measured differences in reducing the potential of cancer cell types to affect drug delivery. She conducted this scientific work at the University of Michigan with Professor Kyung-Dall Lee.  Gaston’s showed that a specific hormone prevented nerve cell death after brain injury. Her research, conducted with Professor Vishal Bansal at the University of California-San Diego, will be included in a manuscript just accepted to the Journal of Neuropathology and Experimental Neurology. Livezey presented the results of a study she has worked on for the past two years in Furge’s lab modeling the interactions of inhibitors with human cytochrome P450 enzymes. That study was recently published in Drug Metabolism Letters. While in San Diego, Stevens-Truss directed a teaching workshop for middle school and high school science teachers in the San Diego area. Her innovation in development of the workshop has drawn increasing numbers of teachers to the workshop and provided a new platform for scientists to collaborate with and mentor the nation’s secondary school science teachers.

The workshop was funded by a grant from the National Science Foundation. Next year’s meeting will be in Boston, and Stevens-Truss and Furge plan to attend with another group of students. Stevens-Truss will also lead another teaching workshop there.