January 2013 Volume 11, Issue 4 |
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ContentsBio 385 Class Visits University of Minnesota Neuroscience Labs On Caulobacter and Waiting: an Interim of Researching, Patience |
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News and AnnoucementsProfessor Emeritus James Zischke, known affectionately as "Dr. Z", passed away in December. He is remembered fondly for his enthusiasm for biology, particularly invertebrates, his highly sought after marine biology class in Pigeon Key Research Station, Florida, and for providing many research experiences and mentoring many St. Olaf students. Biology faculty member Lisa Lenertz ran the Zum Yah Yah marathon in January! Now that is a feat! St. Olaf College was recently awarded a grant from the Arnold and Mabel Beckman Foundation to support students doing undergraduate research in biology and chemistry. To learn about criteria and applying, click here. |
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Bio 385 Class Visits University of Minnesota Neuroscience Labs |
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By Evan Anderson '13 On the morning of January 17, while most students were bundling up to go to class, 13 students taking this interim’s Biology Seminar in Neuroscience, Bio 385, were loading into a van for a field trip to the University of Minnesota. Two weeks prior to the trip, we had been learning fundamentals of the molecular biology of the neuron. A visit to the University of Minnesota provided the opportunity to see the labs where the boundaries of modern neuroscience are pushed. For some who had had relatively little research experience it was an eye-opening day -- ”it was a completely different experience actually seeing the lab in person. I was shocked at the technology they use! I’ve never seen machinery quite like I did today.” The morning started in Dr. Eric Newman’s lab, which studies the cellular regulation of blood vessels in the retina among other retinal studies. After a 30-minute crash course on the lab’s current areas of research, he showed off the high-tech instruments in his lab. One of his multiple microscopes features a specialized stage and set-up for anesthetizing, ventilating, and sticking electrodes into a live mouse retina! “It looked like the mouse was about to undergo open heart surgery, judging by the array of instruments that surrounded the microscope.....just so they can study changes in blood flow and only blood flow, so they anesthetize the rat or mouse, put it on a breathing machine, and keep its temperature constant. Oh, and the rat was hooked up to a pulse oximeter and its CO2 exhalation was measured as well.” We next visited Dr. Mark Masino’s lab, which works to identify the neurocircuits responsible for locomotion in zebrafish. A handful of graduate students and postdoctoral fellows showed us the techniques used to approach this research at three different levels: behavioral, physiological, and molecular. Similarly, this lab was also filled with microscopes: some looked at fish motion in groups using super fancy software while others focused on fluorescence on the cellular level. It was fun to be challenged with new ideas such as learning that the “swimming of zebra fish and bipedal walking of humans” are parallel phenomena. The lab visit provided better understanding of the research techniques behind the stacks of primary literature we had been exploring this interim. We also really appreciated seeing the grad students and post docs at work. To top off the field trip, we grabbed lunch at The U’s student union before heading back to campus. |
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Q & A with Tom Giarla |
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Tom Giarla will join the biology department faculty for 2nd semester. He will be teaching Bio 126, Evolution and Diversity. How would you describe yourself? |
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Dealing with Deer |
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By Emma Cornwell '13 If you’ve ever been out in the St. Olaf Natural Lands around dawn or dusk, chances are you’ve come across a deer. Deer always seem so gentle and harmless, conjuring up images of Bambi and the friendly forest animals in Snow White. It’s hard to believe they are actually a major threat to forest restoration efforts on campus. White-tailed deer are native to Minnesota’s prairies and forests, but their population is much higher than these ecosystems can support, largely because their growth is unchecked by natural predators. Human interference has all but eliminated the wolves, bears and bobcats that traditionally fed on deer. In the absence of these natural predators, deer hunting is one way to manage the population, but overpopulation remains a persistent problem. Deer overpopulation is a nuisance to people and the environment. According to the Minnesota DNR, these herbivorous animals have a wide range of food choices, including acorns, mushrooms, grasses, apples, tree leaves and buds. They’ve also expanded their diet to include agricultural corn and soybeans, which causes economic losses for farmers. Intensive grazing by large populations decimates the forest understory, negatively impacting birds and small mammals that use the understory for food and hiding places. The deer’s preferred plant foods often become locally extinct, and biodiversity in the forest as a whole declines.
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On Caulobacter and Waiting: an Interim of Researching, Patience |
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By Lynna Long '13 Thaw competent E. coli on ice for 30 minutes. Of my many character flaws, lack of patience is pretty high ranking which is a great misfortune considering that waiting constitutes a large majority of the research I’ve been working on lately. In some cases, the waiting is a long enough period that a lunch or dinner break fills in the void. In other circumstances, time is the enemy, testing your patience at 11 p.m. because the digest you are running takes 1 hour at 37° C, and you can’t remember if you have 5 minutes left or if you are 5 minutes over. However, the tedious hours and minutes between executing various procedures does lead to laboratory insights. Why isn’t parafilm used in domestic kitchens when it’s clearly superior to saran wrap? Why do we use tupperware for ethidium bromide staining- aren’t those for sandwiches? Agarose gel looks like more science-y, less delicious jello... Aside from the various thoughts on homemaking and food that have flooded my mind in the late hours of the night while working in the biomolecular science research lab, I have actually been quite engrossed by my work in Bio 396: Bacteria Cell Cycles. Taught by recent St. Olaf hire Lisa Bowers, this directed undergraduate research (DUR) class has granted me and 7 other classmates the opportunity to individually investigate a transcription factor gene in Caulobacter crescentus. Our studies are based on Professor Bowers' previous work where she used molecular, genetic, and biochemistry techniques to figure out the role of known proteins that regulate cell cycle and looked for new genes not previously studied that are also involved. As a class, we are expanding on the latter, each of us being responsible for producing a gene-knockout and subsequently describing the mutants' morphology. Similar to graduate-level research, we predominantly work individually but meet frequently during the week to discuss progress and troubleshooting, and for journal club. Having only four short weeks to work on our projects, this Interim experience has been condensed into a tight ball of emotions ranging from bewildered excitement that your PCR product yielded the correct size of DNA the first round to deep disappointment when you realize that you have lost all of your viable ligation product from running an unnecessary gel. My classmate Lauren Carlson '13 says that while in the past the end of Interim signaled for her a transition to a less monotonous schedule, she feels “that [she is] just mastering these biomolecular techniques and becoming attached to [her] own plasmid, when all of a sudden this course will be finished.” Despite having only a brief time to execute our research, the variety in daily tasks and real world research experience is what attracted students, including Kelly Hennessey '13 who agrees that “[DUR is] so different from what goes on in weekly biology labs for class”. And in the same way that this class has taught me a lesson in waiting, Hennessey found that the class has unexpectedly showed her the merit in troubleshooting. She elaborates, “Even when you think you have a system down, out of the blue it will fail and you have to rethink the process. It keeps you on your toes.” Despite the frustrations I face trying to be unperturbed by the slow tick-tock of Caulobacter growing at a three-day incubation rate, this research experience has proved enriching to technical lab skill, analytical thought, troubleshooting, waiting, and having a good attitude at the end of it all. In the words of fellow researcher Katie Hamel '13, "participating in a DUR is a great opportunity for any Ole who wants to see what doing scientific research is like. It's not a typical lecture setting so you don't learn from a textbook, you learn from experience.... you get a lot more out of this class than you ever would from a textbook.” |
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| Summer Research Projects in Biology | |
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Anne Walter and Rebecca VanDiver |
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Diane Angell - Bumble Biodiversity The goal of this research is to determine the species diversity of Bombus in and around Northfield and to understand their habitat use. Despite being important pollinators, a number of Bombus species have not been seen in the area for a number of years (Bombus terricola, Bombus affinus). As stated in the student description above bumblebees (Bombus spp.) play a valuable role in ecosystems, pollinating flowers and crops (Grixti et al., 2009; Goulson et al., 2008). A reduction in such pollination services can reduce plant species richness (Goulson et al., 2008). Bumblebees are also economically important; without these native pollinators farmers would have to rely on, and pay, for domestic bees to do the work of these missing native species (Spivak and Mader, 2010). Recently, bumblebee populations have declined substantially in North America (Cameron et al., 2010; Grixti et al., 2009; Goulson et al., 2008). Researchers have highlighted the expansion of agricultural and urban settings, the overuse of chemicals for weed control and agriculture and pathogen spillover from domestic bees as reasons for the decline in Bombus populations (Grixti et al., 2009). Our surveys will help inform efforts by various agencies and institutions as they enact incentives to create Bombus habitat in Minnesota. Surveys will take place at locations including St. Olaf’s natural lands, Carleton College’s Arboretum, Carleton College’s McKnight Prairie along with a number of privately owned remnant prairies in the area. Surveys typically occur on sunny days with temperatures between 70-90 °F and wind speed between 1-7 mph. Plot size of 100m x 100m have been used in the past. For 1 hour, collectors used insect nets to capture all bees found within the perimeter and individuals are held in insect cages in the field as collected. The types of plant species being foraged upon will also be noted. Specimens are then identified in the field where possible and taken back to the lab for identification if field identification is impossible. Sample specimens are reserved for pinning and will be a part of St. Olaf’s collection. Out of the approximately 19 Bombus species in Minnesota we caught 8 in 2011 but only 5 species in 2012. Most of the species caught were relatively common and locations surveyed do not seem to have either of the two species known to be declining in Minnesota. Interestingly, one declining species found by Dickinson and McKone (1992) at Carleton in the 1990’s was not located. B. bimaculatus, and B. griseocollis, species with stable populations over the years, were the most commonly found. We did find a single B. pennsylvanicus which is also a species known to be declining. The most common species in each prairie differed, with B. bimaculatus being most common in restored prairies and B. griseocollis being most common in remnant prairies. Students in the past have contributed posters to sessions such as the Minnesota Academy of Sciences and the National Council on Undergraduate Research. Results will be shared with Carleton College and we have also interacted with researchers at the University of Minnesota’s bee lab. Results from last summer concerning the lack of bumblebees using local farms initiated a collaboration with the SEEDS farm, Tony Seidl’s 4th grade class at Greenvale and several St. Olaf students. Two students wrote grants to fund a native prairie planting planted by the 4th grade class with local seed contributed by Carleton College. We look forward to such community collaborations with local sustainable farms in the future. Lisa Bowers - Regulation of development in Caulobacter crescentus Caulobacter crescentus is a model bacterium for the study of bacterial development. During every cell cycle, a swarmer cell, which is motile but unable to replicate its chromosome, undergoes a complicated series of steps to differentiate into a stalked cell, which is non-motile but fully capable of replicating its chromosome. This project will investigate a set of genes predicted to be involved stalk development in Caulobacter. In a recent paper, a Caulobacter protein called BamE was shown to function in the assembly of proteins in its outer membrane. Not surprisingly, a mutant with a deletion of the bamE gene was missing several proteins in the outer membrane. Curiously, this mutant was also defective in stalk formation. Three of the proteins missing from the outer membrane were “TonB dependent receptors”. TonB dependent receptors are largely unstudied in Caulobacter but are known in other bacteria to transport specific molecules from the extracellular space to the inside of the cell in an energy-dependent manner. Based on its genome sequence, Caulobacter is predicted to have 65 different TonB dependent receptors, more than any other known bacterium. This unusually high number is likely an adaptation that helps cells import nutrients in a nutrient-poor environment. To date, only one of the 65 TonB dependent receptors in Caulobacter has been studied and it was found to transport maltose. What molecules are the other TonB dependent receptors transporting? Could one or more of the TonB dependent receptors that are missing in the stalk-less ΔbamE deletion mutant be involved in the initiation of stalk formation? Student projects: Students interested in this project will delete the genes encoding the three TonB dependent receptors that were missing in the stalk-less ΔbamE deletion mutant of Caulobacter. They will then design and carry out experiments to characterize the deletion mutants, paying special attention to stalk formation, nutrient uptake, and membrane stability. Possible assays include DIC microscopy, growth curves, chemical sensitivity tests, cell culture synchronies and western blots. Students will have the opportunity to present their results in poster or oral format at a number of scientific meetings, including the American Society for Microbiology Midwest Branch meeting in Fall 2013 (location and date TBA) and the National Conference on Undergraduate Research Spring 2014. Kevin Crisp - Development of Wireless Implantable Devices for Sensing and Stimulating Nerves Several objectives will be worked toward in parallel: Jay Demas (Biology and Physics) - Visual input onto non-visual photoreceptors Most organisms organize their behavior on a daily schedule. For example, nocturnal species, such as mice, are relatively active at night (foraging for food, mating, etc.) and are relatively quiescent during the day. An internal clock in the brain, the suprachiasmatic nucleus (SCN) regulates the timing of these daily behaviors. The roughly 24 hour periodicity of the clock is intrinsic. However, to be useful this clock must be synchronized with the outside world. A subpopulation of retinal neurons that expresses the light sensing protein melanopsin reports light levels directly to the SCN in order to indicate whether it is currently daytime or nighttime. Melanopsin’s presence in these cells, and only these cells, gives them the cells the ability to “see” without input from any other cell in the retina. Laura Listenberger (Biology and Chemistry) - Cellular mechanisms of lipid storage Excess lipid is stored inside cells in structures known as lipid droplets. Despite their importance in obesity-related disorders, the mechanisms that cause lipid droplets to be formed or broken down inside cells are not understood. It is known that these processes require specific proteins to interact with the lipid droplet surface. The number and type of proteins of the lipid droplet surface determine the fate of the stored lipid. Therefore, our research aims to understand the mechanisms that target proteins to the surface of lipid droplets. Anne Walter and Rebecca VanDiver - Putting the math into biology and the biology into the math Seeking students to be part of a team to upgrade Animal Physiology (Bio 247) labs/course by integrating appropriate mathematical analysis and create a set of labs for Mathematics of Biology (Math 236) tied to the course content. The research will include finding and testing appropriate exercises and supporting primary literature as well as preparing the lab manual text and figures. We would like to plan an assessment of the learning effectiveness of these new exercises as well. Applicants must have interest in engaging in both the biological and the mathematical parts of the projects. John Schade (Biology and Environmental Studies) - The Polaris Project: assessing the impacts of climate change in Minnesota and Siberia The Polaris Project is a multifaceted effort that includes a summer field course and research experience for undergraduate students that will take place in Minnesota in June and in the Siberian Arctic in July of 2013. The unifying scientific theme of the Polaris Project is the study of the potential effects of climate change on the cycling of carbon, nitrogen, and phosphorus in terrestrial and aquatic ecosystems. I am requesting funding for two St. Olaf students to work with me to develop a project on campus in the month of June studying agricultural lands, restored prairies and small streams on and around campus, which will be part of a comparative project also conducted in a permafrost-dominated watershed in the East Siberian Arctic in the month of July. The overarching research question is what factors influence the movement of carbon, nitrogen and phosphorus along hydrologic flowpaths from terrestrial to aquatic ecosystems, and what are the implications for the export of these materials from agricultural and permafrost-dominated watersheds? We are particularly interested in comparing the impacts of climate change on different types of watersheds to improve our ability to assess feedbacks between climate change and processes occurring within these watersheds. The students selected are also required to have separately applied and been accepted to the Polaris Project (see www.thepolarisproject.org for more information), which comprises an international team of scientists and students traveling to Russia together. This funding, when added to the funding already supplied by the Polaris Project, will allow these students to complete a 10 week summer research experience and give the three of us the opportunity to collaborate on a comparative research project in Minnesota and Siberia. It will also allow them to return to campus after traveling to Siberia to complete analyses and present their results to the St. Olaf community during the end of summer research symposium. As in past years, we also plan to travel to the American Geophysical Union meeting in San Francisco in December to present our research results. This funding request includes full stipends for both students and on-campus housing for the month of June. Research expenses and travel and to Russia are covered by separate funding from the National Science Foundation. Kathy Shea (Biology and Environmental Studies) - Ecology of the St. Olaf Natural and Agricultural Lands 1. Analysis of tree growth patterns in restored and mature maple basswood forests. 2. Effects of variation in fertilizer and farming methods on agricultural yields. 3. Management of invasive and rare species 4. Prairie biodiversity and biomass production in response to burn patterns 5. Additional research questions Students working during the summer will be encouraged to use some of this research as the basis for an independent research project during the academic year. Mike Swift (Biology and Environmental Studies) - Environmental Contaminants in Mussels from the Cannon River The purpose of this project is to measure environmental contamination in long-lived animals from the Cannon River. The freshwater mussels, Potamilus alatus (pink heelsplitter) and Lasmigona complanata (white heelsplitter) are long-lived, abundant members of the benthic community in the Cannon River. We are interested in what environmental contaminants they have accumulated and how they are utilizing nitrogen and phosphorus from agricultural runoff. By estimating the age of the mussels we sample we will be able to determine contaminant load as a function of their length of exposure. We will collect mussels from throughout the Cannon River basin with a focus on sites that our database investigations indicate as possible historical and recent sources of contamination. Shells will be sectioned so that age can be determined by counting growth rings and contaminants can be isolated from each growth ring. Contaminants will be extracted from tissue and shell samples for analysis using atomic absorption spectroscopy, atomic emission, and GC/MS techniques. Utilization of agricultural nutrients will be analyzed using stable isotope analysis methods. Results from this study will be presented at the end-of-summer CURI research symposium and at appropriate national scientific meetings. We anticipate that our results will be appropriate for the Annual Meetings of the Society for Freshwater Science, the Society for Environmental Toxicology and Chemistry, the Ecological Society of America, and the American Chemical Society. Charles Umbanhowar (Biology and Environmental Studies) - Reconstructing Changes in Lake Level Using Historical Aerial Photos Lake level responses to drought may vary considerably depending on the relative importance of surface flow vs groundwater. This project will be focused on documenting lake level variability in Minnesota in response to the 1930s drought. |
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In St. Olaf’s Natural Lands, deer overpopulation interferes with restoration efforts. Over 90 acres of St. Olaf land, previously used for agriculture, has been planted with native trees. As these forest plots get established, the young trees are vulnerable to grazing by deer. The buds of oak trees are an especially tasty treat for them, particularly in the winter when other foods like grasses and fruits are scarce. Until the oak trees grow tall enough that the buds are out of reach of the hungry deer, we take measures to protect them. Natural lands workers coat oak buds with a non-toxic bitter-tasting liquid that tastes bad enough to deter deer from munching away. This gives the trees a fighting chance, and aids in our efforts to restore the native Big Woods forest ecosystem.