Diane DeZwaan ’05 is conducting cancer research in the Department of Anatomy and Cell Biology at the University of Iowa Carver College of Medicine. She is one of the authors of a research article whose impact of has been much larger than expected. The article, which appears in the journal PLOS/Genetics, is titled “The Stress-Regulated Transcription Factor CHOP Promotes Hepatic Inflammatory Gene Expression, Fibrosis, and Oncogenesis.” Her research provides evidence of a chain of events that leads to the formation of liver cancer (hepatocellular carcinoma, or HCC), the third most common cause of cancer death worldwide. Liver cancer is most commonly caused by viral hepatitis, alcoholism, or obesity, all of which activate cell stress in the liver. DeZwaan’s research may be the first that links elements of this stress response–specifically the expression of a stress-regulated transcription factor called CHOP–to the appearance of cancerous tumors in the liver. The research also showed that exposure (in mice) to a tumor-causing agent when CHOP is absent results in fewer tumors and less cell death. The findings of the research establish CHOP as a biological marker for liver cancer and showed its importance in promoting liver tumor formation. It’s possible that the genesis of tumors by CHOP is a common feature of liver cancer. The research raises intriguing questions that require additional research, which may lead to important new insights into the development of liver cancer. The editors of the magazine were so taken by the potential of the work that they contributed a perspectives article (“The Integrated Stress Response in HCC: Not Just CHOPped Liver”) on it. Television and print media outlets in Iowa have published stories on DeZwaan’s research. As an undergraduate at K DeZwaan majored in biology, studied abroad in Australia, and played on the Hornet basketball team.
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Headline and Lead Combine “Data,” “Value,” and Kalamazoo College
A Wall Street Journal article (“College Uses Test Data to Show Value,” by Douglas Belkin, February 20, 2014) describes K’s efforts to measure (and market) the gains its students experience in critical thinking and problem solving skills because of the K undergraduate learning experience.
The article notes that K leads a growing trend of colleges and universities becoming more transparent about sharing test data and other metrics to show the learning outcomes of a higher education. For his story Belkin interviewed Dean of Admission Eric Staab and Associate Provost Paul Sotherland as well students and their parents for his article. The piece notes that K (Sotherland) shares data that documents the effect and value of a K education with parents and prospective students during campus visits.
Much of that data originates from the Collegiate Learning Assessment, currently the most reliable direct measure of students’ gains in critical thinking, analytical reasoning, writing, and problem solving as a result of particular undergraduate learning experiences. What distinguishes the CLA from other assessments is its focus on direct measures of learning rather than an aggregate of surrogate markers that include, for example (in some rankings), the size of an institution’s endowment or the number of alumni that provide annual gifts.
Sound Affects DOOM
Sound off or sound on?
Turns out that music makes better DOOM–or, more precisely, players of that first-person video shooter game score a lot higher with the sound (music and effects) on … at least according to one study.
Associate Professor of Psychology Siu-Lan Tan joined renowned video game composer Sascha Dikiciyan (Sonic Mayhem) to give an interview on the psychological effects of video game music. The interview occurred on the blog Consequence of Sound, a.k.a. CoS. That interview went live a couple days ago and is nearing 1,500 views on YouTube.
In order to tell the rest of the science behind the story, Professor Tan used her Psychology Today blog to post a related piece: “Video Games: Do you play better with sound on or off?”
Turns out the science is complicated. The results of the aforementioned DOOM study were seemingly contradicted by a study of Ridge Racer V, which found that gamers with the fastest lap times had the music off.
And it gets more complicated than that. Professor Tan’s K research (a collaboration with her SIP student John Baxa ’09) studied gamers playing Twilight Princess-Legend of Zelda (ya gotta love these names!). In the Twilight study, the worst performers played with both music and sound effects off. And the study found that the more the game’s audio was incrementally added, the more performance improved. And yet (in another wrinkle) the best performances occurred to background music UNRELATED TO THE GAME (!) … think boom box across the room. A closer examination suggested more nuances based on game familiarity and gaming skill. Turns out that average skill level newbies tune out the audio to focus exclusively on visual cues when first navigating the game. Not so for high skill level players, new to the game or not. These players are skilled, in part, because they pay attention–and effectively integrate–auditory and visual cues, both of which provide feedback for the best moves.
Tan writes: “I’m also reminded of what a participant in our study expressed so well: ’There’s more to a game than just high scores. It’s also about being transported and immersed in another world, and music and sound effects are what bring you there.’”
Indeed, writes Tan, “When you have a great soundtrack, music can be the soul of a game.” NOTE: Tan and Baxa (along with Matt Sprackman) published their music/video game research in 2010 and 2012. Baxa said it aided his entrance to graduate school for study on video games. He is currently a Ph.D. student at Carnegie Mellon University.
Of Bears and Babies
Associate Professor of Psychology Siu-Lan Tan writes a blog for the magazine Psychology Today under the topic heading “What Shapes Film? Elements of the Cinematic Experience.” That assignment keeps her eye on YouTube videos that go viral. For example, recently, some 4 million viewers have had the “cinematic experience” of watching a three-month old polar bear take his first wobbly steps at the Toronto Zoo. Where most of us may see a bear only, Tan sees human beings as well. Her recent blog post notes that both share a phenomenon of physical development known as the cephalocaudal principle, which means that bear and baby’s first movements tend to be in reverse. The blog is a fun, informative read with some pretty cute video illustrations. Part of the fun derives from the fact that both species are subject to a lot of individual variation when it comes to learning self-locomotion. Crawlers, rollers, and scooters, oh my!
Tan is a popular blogger on other academic topics. One of her posts on singing and emotional contagion was named #4 of Oxford University Press Blog’s Top 10 Posts of the Year 2013. That post was also selected as #22 of Psychology Today’s Top 25 Posts of the Year 2013, out of a total of about 14,000 annual posts.
In other news, Tan’s article titled “Visual Representations of Music in Three Cultures: UK, Japan, and Papua New Guinea” was published in December in the Empirical Musicology Review. Her blog is also posted at Oxford University Press.
Research Published on Alzheimer’s Molecules
Biology professors Jim Langeland ’86 and Blaine Moore join one K student and three K alumni as authors of an important paper that will soon be published in the journal Molecular Biology and Evolution. The co-authors are Nathalie Botezatu ’14, Maddie Gillentine ’13, Ashley (Boehmke) Benson ’08, and Kyle Wilson ’08. All were (or are) biology majors at K, and in the case of some, the scientific work—which describes the evolution of key molecules involved in Alzheimer’s disease—was part of a Senior Individualized Project (SIP). The work is groundbreaking in at least two ways. First, it approaches Alzheimer’s disease from an evolutionary perspective. And second, it illustrates a particular niche approach to research that the scientific environment at K is well positioned to pull off.
“The experiments that culminated in this paper began in 2007 with the SIP work of Benson and Wilson,” says Langeland. “The six-year duration shows that science can take a long time to come to fruition.” That duration derives, in part, from the complementary expertise of the two collaborating labs—Langeland’s expertise in gene evolution and Moore’s background in Alzheimer’s disease research and experience with cellular expression of proteins. According to Langeland, for most of the larger labs the exigency of understanding Alzheimer’s in order to development treatments for it may not favor such an extended timeline or evolutionary approach. Indeed, Moore says, “Most researchers in the Alzheimer’s field are exclusively focused on inhibiting the production of protein fragments that have been linked to the progression of the disease. One of the exciting aspects of this project was the chance to take a broader view of the proteins involved in the disease process.”
A broader view allows for unique approaches (suggesting that time and creativity are the two pillars of the particular niche approach to research for which K is so well-equipped). Six years ago Langeland decided to investigate the evolution of two molecules associated with Alzheimer’s—APP and BACE. BACE acts like a scissors to cut (or cleave) APP. The excess accumulation of one of the “cut pieces” (a.k.a. products or substrates, this particular one known as A-Beta) is linked to the development of the disease. Benson and Wilson sought answers to how far back on the evolutionary tree of life these molecules could be found. Turns out that APP is nearly a billion years old. BACE (and its cleavage effect) is much younger, about 500 million years old. Just down the hall, Moore’s lab had been studying the regulation of enzymes that produce A-Beta, and had well-developed systems for expressing Alzheimer’s proteins and analyzing cleavage products. Put the two together and you have a unique project that would have been unlikely at a larger institution or medical school.
The principle of natural selection suggests that BACE’s action on APP is vital to life in ways we don’t yet understand, according to Langeland. The A-Beta substrate may be some kind of mistake that natural selection is unable to “correct” because Alzheimer’s expresses so late in human lifetimes, usually long after reproductive success has been achieved. Moore says, “It’s essentially a wrong place, wrong time phenomenon. The APP substrate evolves the A-Beta motif, then comes in cellular contact with preexisting BACE. The result is a devastating disease process that is most likely an accidental by-product of some normal, as yet unknown, cellular process.”
Moore and his lab (including Gillentine and Botezatu) conducted an elegant experiment to confirm the importance of the BACE molecule. They expressed the BACE molecule from an organism—in this case a primitive marine dweller called amphioxus—that diverged from the human evolutionary branch some 750 million years ago. Amphioxus has no A-Beta. Then, Moore’s group discovered that amphioxus BACE nevertheless acts as a scissors to the human APP molecule. The result adds evidence to the biological importance (albeit unknown) of BACE’s cleaving action.
According to Langeland, an evolutionary approach to diseases may suggest molecular targets for treatment intervention, and, just as important, the limitation of a non-nuanced approach to potential targets.
The paper is titled “Asynchronous Evolutionary Origins of A-Beta and BACE-1.” The work was supported, in part, by a Great Lakes Colleges Association (GLCA) New Directions Initiative Grant, a program that supports professional growth of mid-career liberal arts faculty, with particular emphasis on projects outside traditional boundaries.
Face Time
We love faces; our lives depend on it from an early age. And a close-up on a face is one of the most notable differences between the experience of a movie and the experience of live theater. When we choose to see a film instead of a play it may be, in part, because were drawn to the human face. In her latest installment of her Psychology Today blog (What Shapes Film?) Associate Professor of Psychology Siu-Lan Tan explores what attracts us to cinematic face time. Her article is aptly titled “3 Reasons Why We’re Drawn to Faces in Film.” Maybe it should be four reasons, because music plays a big role as well. It’s a fascinating read, and Tan demonstrates her points with faces from some pretty famous films, including Amelie, It’s a Wonderful Life, Saving Private Ryan, and Toy Story 2, among others. Of particular interest is how facial close-ups make us, the audience, both mirror and blank-canvas-and-painter, depending on a face’s intensity or nuance, respectively.
Hands-On HOPES
Regina Stevens-Truss, the Kurt D. Kaufman Associate Professor of Chemistry has written an article updating an idea of hers and the American Society of Biochemistry and Molecular Biology: the HOPES Initiative. HOPES pairs teachers with working scientists so that together they could provide hands-on opportunities to students. “We didn’t anticipate the sweeping impact the program would have across the nation,” wrote Stevens-Truss in the update. The HOPES initiative has resulted in 27 partnerships in 22 cities across the U.S. and has affected the education of more than 3,600 fourth- through 12th-graders.
Seniors Present Chemistry Research
Three Kalamazoo College seniors presented their Senior Individualized Project (SIP) research at the Midwest Symposium on Undergraduate Research. The event took place at Michigan State University on Saturday, October 5. The students, their presentation titles, and where they did their SIP:
Sara Adelman’s poster (see photo) won the Outstanding Poster Award for Biochemistry. It was titled “Effects of Copper Bipyridine Catalysed Alkaline Hydrogen Peroxide Pretreatment on Lignocellulostic Biomass in the Ethanol Production Process.” Adelman did her research with Professor Eric Hegg ’91 at Michigan State University.
Geneci Marroquin presented a poster titled “Reactions of Cobalt(II) and Nickel(II) Complexes Containing Binucleating Macrocyclic and Pyridine Ligands with Carboxylic Acids: Formation of Binuclear Co(II), Co(II)Co(III), and Ni(II) and Tetranuclear Co(II) and Ni(II) Complexes.” Her research was done in the laboratory of Professor Thomas J. Smith at Kalamazoo College.
Kendrith Rowland conducted his research in the laboratory of Professor Catherine Murphy at the University of Illinois at Urbana-Champaign. Rowland’s poster was titled “High Sensitivity Surface Enhanced Raman Spectroscopy (SERS) Nanoplatform Based on Gold Nanoparticle Aggregates.”
Kalamazoo College Professor of Chemistry Jeffrey Bartz gave an invited talk at the symposium. That talk, “Detecting Cartwheels and Propellers by Velocity-Mapped Ion Imaging,” highlighted the SIP work of Ryan Kieda ’09, Masroor Hossain ’12, and Nic West ’12, as well as the research of Amber Peden ’11, Aidan Klobuchar ’12, Kelly Usakoski ’14, Braeden Rodriguez ’16, and Myles Truss ’17.
Transition Fan
Professor of Physics Jan Tobochnik is a self-described “big fan” of phase transitions–solids to liquids; liquids to gas; magnetic to non-magnetic; the fall of the Soviet Union. Just a few examples of spectacular phase transitions, and phase transitions are “always interesting,” says Tobochnik. Also, some systems act like they are at a phase transition, such as perhaps the neural firings of the brain. In particular, he’s intrigued by the physics associated with the very moment of change–a period of “criticality” at which all scales of behavior are important.
So it’s no surprise that for the next three years his research (supported by a grant from the Petroleum Research Fund) will involve reproducing experimental data and generation of new data through computer models of melting. Wait…melting? Surely a phenomenon as long observed as this (just set an ice cube on the counter) is thoroughly known to science. Not so, says Tobochnik. “Science has no comprehensive theory for three-dimensional melting,” he says. “Consider that ice cube on the counter–we know it melts from the outside in, but we only know the mechanisms for melting related to surfaces or defects. Absent a surface or a defect, we don’t know how a material melts. We have no general theory, which, in the case of new materials, makes the prediction of melting points and other properties unreliable.”
Two very recent–and painstaking–experiments (one at Harvard, the other in China) managed to explore the phenomenon of melting when there are no surfaces or defects by using colloidal spheres suspended in a fluid. The result was some fascinating new data. But the experiment is extremely difficult to set up, making replication, confirmation, and extension of the data a problem. Tobochnik’s grant will enable his lab to work with the Harvard group to set up a computer modeling simulation of the experiment. That modeling will confirm and, hopefully, provide new knowledge of melting in three dimensional substances.
The grant will fund two students in Tobochnik’s lab for three consecutive summers. They may, or MAY NOT, be physics majors doing SIP work. “Many times I prefer to provide significant research experiences to younger students, including first-years,” Tobochnik says.
Healthy Body May Mean Healthy Bacteria
Rob Dunn ’97 is extensively quoted (and his best-selling book cited, The Wild Life of Our Bodies: Predators, Parasites, and Partners That Shape Who We Are Today) in an article by Nancy Churnin that appeared in the Dallas Morning News’ “Dallas News Life.” The article, “Be nice to your bacteria and they’ll be nice to you, doctors say,” notes a growing belief among experts that good health is strongly influenced by the ecology of the multitudes of bacteria that reside in our bodies and in our natural environment. It cites examples of probiotic treatment, or the introduction of bacteria as a therapeutic measure to restore the balance of bacterial populations in the body. It is a fascinating read, and Dunn is at his curious K best, equating excitement with the new found extent of all we don’t know. Dunn is a scientist and professor at North Carolina State.