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Muskingum College Annual Fall Research & Internship Forum October 3, 2007 BIOCHEMICAL EVIDENCE OF THE DYSTROGLYCAN COMPLEX IN EPIDERMIS Becky Schroeder and Dr. Amy Santas Department of Biology A patient friendly treatment for cancer has eluded us for decades. Studying wound healing in epidermis can provide insights on the processes that are uncontrolled in cancer. The dystroglycan complex appears to be down-regulated in wound healing and in some cancers (Jing, J. et al., 2004). Using murine skeletal muscle as a positive control, proteins of the dystroglycan complex are able to be identified in murine epidermis through western blot analysis. Alpha-dystrobrevin has been identified in murine epidermis and is likely associated with the dystroglycans. Future experiments will examine the presence of alpha-sarcoglycan in murine epidermis. Our long term goal will be to identify novel members of the epidermal dystroglycan complex. BIOCHEMICAL EVIDENCE OF THE DYSTROGLICAN COMPLEX IN EPIDERMIS Anya V. Belyaevskaya and Dr. Amy J. Santas Molecular Biology Program Skin can serve as an excellent foundation for studying general processes that occur in other organs due to easy accessibility. The long term goal of our research is to use wound healing in the skin to better understand aberrations that occur in cancer. However, before these processes can be studied, proteins that make up different complexes in the skin need to be better defined. This study uses affinity chromatography and western blot analysis to characterize the Epidermal Dystroglycan Complex. Biochemical evidence was obtained that Utrophin is one of the proteins that make up this complex due to its indirect binding of N-acetylglucosamine oligosaccharide containing proteins like alpha-Dystroglycan or betaDystroglycan. An antibody against Delta-Sarcoglycan was also optimized in western blotting of murine skeletalmuscle for further study of its presence in epidermis. Future work will be focused on identifying novel proteins of the Epidermal Dystroglycan Complex using nonbiased experimentation. FLOW CYTOMETRIC ANALYSIS OF RATIONALLY DESIGNED ANTI-BCRP HAMMERHEAD RIBOZYME ACTIVITIES IN VIVO Craig Miller Molecular Biology Program Breast cancer resistance protein (BCRP) is an ABC transporter that when overexpressed has been shown to present multidrug resistance in cancer cells. This has fueled interest in its elimination or downregulation in order to increase the effectiveness of chemotherapy treatments. One such approach that has been studied is the use of ribozymes. Because many sites on the same mRNA can be cleaved by a ribozyme, there are options of choosing between different ribozymes for knock-down studies. Also, ribozymes targeting the same mRNA at different sites can have various activities. Thus, being able to choose the most active ribozyme to down-regulate a protein would be of great importance. Previous work in the laboratory has already measured many rationally-designed antiBCRP hammerhead ribozyme activities in vitro and in vivo using RT-PCR analysis of mRNA levels. These were done to compare in vitro and in vivo activities to computer models of activities to help improve the computer algorithms. In the present study, 10 of the ribozymes used previously in the laboratory were analyzed at the protein level using flow cytometry to determine activities in order to compare with mRNA cleavage activities and further enhance computer models. While no correlation was observed between activities and the probability of single-strandedness of mRNA target site, weak correlations were detected between ribozyme activity and mRNA disruption energy and between in vivo ribozyme activities measured at protein and mRNA levels. KINETIC STUDY OF THE PRODUCTION OF ZIRCONIUM TUNGSTATE HYDROXIDE HYDRATE Karen Witker and Dr. Cora Lind, Advisor; University of Toledo Department of Chemistry Thermal Expansion is a property unique to all materials and is measured by the thermal coefficient, alpha. Zirconium tungstate is a material that shrinks when heated, therefore it is a negative thermal expansion (NTE) material. Zirconium tungstate can be formed from a precursor, zirconium tungstate hydroxide hydrate, which was the focus of this study. The goal of this project was to optimize the formation of the precursor, zirconium tungstate hydroxide hydrate. Several different concentrations were investigated, and phase characterization was carried out using powder X-ray diffraction (XRD). GRASSLAND BIRD NEST SITE FIDELITY AND ADDITIONAL RESEARCH OPPORTUNITIES AT THE WILDS Katlin Oress Environmental Science Program From early May through early July I assisted in with two major research projects at the Wilds: grassland bird site fidelity and giraffe foraging behavior. I assisted in capturing and color-banding over 80 grassland birds (grasshopper, savannah, and Henslow's sparrows and bobolinks) on mowed and unmowed plots. I also helped located returning birds banded during previous years (18 individuals). Finally, I assisted two senior conservation science students with their giraffe foraging project. I spent over 20 hours observing giraffes and collecting foraging data. ENVIRONMENTAL EDUCATION INTERNSHIP AT THE DAWES ARBORETUM Julie Travaglini Department of Biology “In the end we will conserve only what we love. We will love only what we understand. We will understand only what we are taught.” This quote by Baba Dioum illustrates the importance of conservation and environmental education to the future. During this internship, children were provided with the tools and knowledge to being appreciating and conserving the natural world. Educational programs that included topics such as: birds, mammals, reptiles, swamps, plants, bugs, pond studies, bugs and recycling, were provided. A Discovery Center was updated with games, crafts, live animals and educational worksheets for children. Informational exhibits and kiosks for adults were also designed. Off site educational programs for adults were also provided. THE DEVELOPMENT OF SERVER SOFTWARE TRACING & TESTING COLOR IMAGE COMPRESSION Holly Soper Department of Mathematics and Computer Science InfoPrint Solutions Company, a joint venture between Ricoh and IBM, wished to improve the server software tracing capabilities of their webbased application product known as InfoPrint ProcessDirector (IPPD), in response to customer and developer demands. A software package was developed that offered users the ability to trace or log particular events during IPPD's execution. Software performance was improved with respect to runtime, software organization, and user interface using Java development tools. A second project was undertaken, again with InfoPrint Solutions Company, to ensure the image transformation quality from software to hardware and vice versa. Color image compression outcomes were tested against an ideal base pattern by writing a bounding box algorithm and a peak signal-to-noise ratio (PSNR) algorithm. The algorithms' results were compared for color integrity and image distortion. FAMILY MEDICINE INTERNSHIP WITH JEFFERY BURRIER M.D. & BURRIER FAMILY PRACTICE INC. David Shahbodaghi Department of Biology EXPLICIT VAPOR PRESSURE PREDICTION FROM THE PRSV EQUATION OF STATE Amy Miller and Dr. Misovich, Hope College Department of Engineering Family practice is a specialty within primary care medicine. Family practice physicians treat infants to the elderly and a broad range of injuries and ailments from routine follow ups to traumatic injuries. This internship encompassed 160 hours of time spent observing as well as assisting Dr. Jeffrey Burrier in his small town practice. Many facets of the job were observed outside of direct patient care including paperwork, billing and working with pharmaceutical reps. Patient observations and interactions varied from common illnesses to a once in a lifetime case of primary pulmonary hypertension. The PRSV equation is a cubic equation of state that can be used to accurately estimate the vapor pressure of a substance by an iterative algorithm. When vapor pressure and phase densities are expressed as power series expansions about the critical point, they can be written as explicit functions of temperature, a more convenient computational strategy. Previous research successfully applied this strategy to the Peng-Robinson (PR) equation but a major hurdle in adapting this work for PRSV was the presence of an additional parameter, κ1, in the equation. Hence, the PRSV series coefficients contained two parameters instead of the single parameter present in the PR series. An improved method for evaluating the partial derivative expressions used in finding the series coefficients was developed and programmed in Maple® 10 mathematical software. This allowed the series coefficients to be evaluated principally in terms of polynomials in the two parameters. Quantification of truncation error from the series is ongoing. CINCINNATI ZOO EDUCATION INTERNSHIP Jessica Lade Conservation Science Program I had an education intership at the Cincinnati Zoo and Botanical Garden during the summer. As an intern I led summer camps and educational classes for ages three to adult and was trained in interpretation. Duties also included daily animal enrichment, workshops, and discussions. This internship allowed for greater understanding of the zoo and education based on environmental and conservation awareness. GIRAFFE RUMINATION STUDY AT THE WILDS Jessica Teaff and John Grennell Conservation Science Program We observed the behaviors of the Giraffe at the Wilds over the summer of 2007. Our main focus was to determine the health of the rumen by counting numbers of ruminations. From this experience we were able to get a better understanding of how to conduct a behavioral study. PIPING PLOVER AND LEAST TERN REPRODUCTION STUDY ON LONGISLAND NY Ashley Campbell Conservation Science Program In conjunction with the Army Corps of Engineers a survey of piping plover (Charadrius melodus) nest and fledge success was conducted over a five month period. Pair bonds were tracked, territories identified, and clutch size in proportion to hatchling and fledging success were monitored. Least tern (Sterna antillarum) colony estimates were also made throughout the shore bird nexting season. Similarly, all migrating ocean and shore birds were tracked. The surveys this year showed increasing predation of plover chicks by ferrel cats and of tern chicks by gull species. The excessive predation led to a fledge rate of 1-1.5 chicks per nest for plovers and several hundered plus colony abandonments for terns. IN THE ABSENCE OF GHRELIN RECEPTOR, HEART IS MORE PRONE TO CARDIAC ISCHEMIA Melissa Kollman and Anne Kwitek, Ph. D., Allison Beaty, MCW SPUR Program Department of Biology Ghrelin is an endogenous peptide hormone that interacts with GHSR, growth hormone secretagogue receptor, as a growth hormone releaser. Ghrelin plays a substantial role in energy homeostasis by stimulating appetite and weight gain. Studies involving ghrelin have shown that it is also active in the cardiovascular system, in particular protection from ischemic injury. In human-based studies, GHSR has been associated with obesity, left ventricular hypertrophy and myocardial infarctions. Finding an appropriate animal model for this study would lead to better understanding of the role ghrelin plays in cardiac function. To gain a better perspective of the protective role of ghrelin in the rat heart we studied an ENU rat knockout, FHH-Ghsrm1Mcwi, a nonsense mutation that results in deletion of the last 29 amino acids. In this experiment, we investigate the effect of a non-functional ghrelin receptor after global ischemia followed by reperfusion. We hypothesize there will be a significant difference in left ventricle damage between the FHH-Ghsrm1Mcwi and its FHH control. To characterize this experiment we performed Langendorff on the hearts and a rat acylated ghrelin enzyme immunoassay. We also measured plasma insulin, triglyceride, and cholesterol levels and performed real-time PCR for the GHSR mRNA in liver and pancreatic tissues. We concluded from the experiment that in the absence of the ghrelin receptor, GHSR, the heart is more prone to cardiac ischemia. Furthermore we found no differences in circulating plasma ghrelin levels, indicating the mutation does not effect circulating ghrelin and may play a tissue specific role in the heart. DATABASE DESIGN AND MANAGEMENT AT LMI CUSTOM MIXING, LLC Bryan Bates Department of Mathematics and Computer Science Throughout many industries in the world today, one will find the use of databases as the heart of small and large business facilities, especially in the field of manufacturing. LMI Custom Mixing, LLC is one of these manufacturing facilities that utilizes and takes advantage of having a database infrastructure that controls almost all operating functions throughout the plant. The brain of the plant lies within the utilization of a MS SQL Server that is comprised of Mesabi databases (Mesabi Control Engineering is the company that created the databases) to manage the operation of machines as well as collect data back from those machines. The server is responsible for directing and sending database commands to specific control units. The basis of the internship was to make use of the data received back from the control units around the plant to generate custom reports by designing and managing databases that work with the Mesabi databases. The internship also focused on designing databases for data entry in the Maintenance department to handle ordering and inventory and for the Quality Control department to handle rejections and repairs. GEOLOGY IN THE SUN Ashley Burkett Department of Geology This experiment involves the study of 12 soft sediment cores and associated airlift samples taken in varied environments in the U.S. Virgin Islands of St. Croix. By studying the taphonomic characteristics of airlift samples from different environments in the St. Croix reef system one is able to determine a taphonomic signature for each area. This project involves utilizing the taphonomic signatures determined at the surface of each to compare down the cores to determine whether these derived signatures are effective or obsolete subsurface. Should this signature prove to be effective subsurface a new tool for determining environment at the time of deposition will have been identified. SUMMER INTERNSHIP AT THE OHIO DEPARTMENT OF NATURAL RESOURCES (ODNR): A FIRST-HAND VIEW OF CORING, DRILLING, RECLAMATION EFFORTS, AND GIS APPLICATIONS Scott Madison and Anthony Carson Department of Geology This summer we interned at the Cambridge Field Office of the Ohio Department of Natural Resources (ODNR), which is responsible for the reclamation, supervising, and permitting of coal extraction. During our time at the ODNR, we were involved in a number of projects and worked closely with other geologists, drillers, and inspectors of coal, oil and gas, and abandoned mines. Projects included such things as: (1) coring and drilling related to mine subsidence and depositional processes of modern stream systems, (2) inputting coal data into spreadsheets for future GIS applications, (3) scanning Regulatory and AML files for data pertinent to GIS applications, (4) observing coal mining operations, and (5) providing upkeep for reforestation programs. Throughout all of these projects, we were able to do field work with other geologists and hydrologists conducting research at reclamation sites. The most rewarding aspect of this internship was the ability to first-hand conduct field work at coal mines, witnessing blasting operations, mining impacts, and reclamation efforts in the southeast portion of the state. SUMMER INTERNSHIP AT BIG OAKS NATIONAL WILDLIFE REFUGE Andrew Houze Conservation Science Program This summer I had an internship at the Big Oaks National Wildlife Refuge in Madison, IN. This internship was a great learning experience in a variety of different biological fields. I participated in multiple research projects and got my wildland firefighter type two training. This training allowed me to go out west for two weeks and fight fires. Working for the Fish and Wildlife Service opened my eyes to several job possibilities for me to shoot for after I graduate. EFFECTS OF FLUPHENAZINE DECANOATE ON CORTISOL LEVELS IN CENTRAL CHINESE GORAL (NAEMORRHAEDUS GORAL) Jessica B. Turner, Barbara A. Wolfe, DVM, PhD, DACZM, Rachael B. Weiss, DVM, Michael D. Whitacre, DVM, DACT, and Linda M. Penfold, PhD Conservation Science Program In management of ungulate species, long-acting neuroleptics (LANs), such as fluphenazine decanoate, are widely used in the zoo community. Fluphenazine decanoate can reduce stress and aggression amongst these animals and lead to positive husbandry situation when there is high interaction between human and animal. Stress, measured by cortisol expression, is strongly related to reproduction, for it can possibly aid in reproductive success. However, LANs can affect the neurotransmitter dopamine, which alters the release of prolactin and gonadotropin. The broad aspects of this study calculates the results of fluphenazine decanoate on ovulation of the central Chinese goral (Naemorrhaedus goral), but my focus was on the affects of fluphenazine on cortisol expression. Through Enzyme Immuno Assays, the amount of cortisol was compared between seven goral, four subjected to fluphenazine decanoate and three given a saline solution. Serum and fecal samples were analyzed. The results show there was a difference between the two test groups. AUDUBON CENTER FOR RESEARCH OF ENDANGERED SPECIES Kylie Johnson Conservation Science Program A POPULATION ESTIMATION OF WHITE-TAILED DEER (Odocoileus virginianus) AT THE WILDS Greg Leasure Conservation Science Program Two components of the Audubon Nature Institute in New Orleans, Louisiana include the Audubon Center for Research of Endangered Species (ACRES) and the Freeport-McMoRan Audubon Species Survival Center. Together, these divisions strive to protect wildlife through care of endangered animals and innovative reproductive techniques and breeding programs. As an intern in the crane facility, the focus is primarily placed on chick-rearing for the highly endangered Mississippi sandhill crane (MSC), of which only approximately 100 remain in the wild. As a crane intern, duties involve general husbandry for chicks and adult cranes, of which there are approximately 30 MSC and 8 whooping crane adults on site. In addition to husbandry, interns are given the unique opportunity to assist in artificial insemination, egg collection, chick socialization, as well as projects and other tasks. Another aspect of this internship is working in the Species Survival Center with exotic cats, Eland, Bongo, and Storks. Interns also have an opportunity to rotate through the ACRES facility and watch veterinary procedures, as well as embryo transfers, and nuclear transfers (cloning). It has been suggested that there may be an overabundance of deer at the Wilds, but there has been no substantial evidence to support this claim. I conducted a census of the white-tailed deer population at the wilds for the purpose of determining an accurate population estimate and density estimate of white-tailed deer within the Wilds. I conducted my census on six individual pre-determined transects within the Wilds, International road, Admin, Dip, NS Hall, Doc lane, and Scott road. Before starting each transect, I reset the odometer on my vehicle. Upon approaching a deer or group of deer, I recorded how far along the transect they were located, how many of them there were, and how far they were from the transect using a laser rangefinder. Determining accurate population estimates at the Wilds may play an important role in the future in solving problems such as over-browsing and disease that comes from an over population of deer. FINDING HEINRICH EVENTS AND STUDYING ANCIENT CLIMATE CHANGE USING ICE-RAFTED DEBRIS (IRD). Jason Tarbert Department of Geology This summer as part of my Muskie Fellow, I worked processing deep ocean sediment samples taken from Integrated Ocean Drilling Program Expedition 306 to the North Atlantic Ocean. Individual core samples were washed and sieved to obtain IRD, or ice-rafted debris. The amount of IRD extracted from the core samples helps to determine when Heinrich Events, or periods of glaciation, took place throughout Earth history. There have been seven distinct Heinrich Events (H0 through H6) in the geologic past when there has been heavy continental glaciation of Greenland and Canada. As a result, large numbers of icebergs break off from the continents and float off to sea carrying large amounts of continental sediments (IRD) with them. The most important result of this research from cores in the North Atlantic is the identification of four distinct Heinrich Events (H1, H3, H4, and H5). EFFECTS OF TASNIKS AND YxCxxxF MOTIFS FROM VARIANT-CODE CILIATED PROTOZOAN OXYTRICHA TRIFALLAX ON TRANSLATION TERMINATION IN SACCHAROMYCES CEREVISIAE Mai Dang, Jessica Buckley, and Dr. David Bedwell Summer Internship in Genetics Program, Department of Genetics, University of Alabama at Birmingham Department of Chemistry The reassignment of stop codons is found to be common among many ciliated protozoa. Previous studies have shown that the class 1 polypeptide release factor eRF1, which binds to stop codons during translational termination, facilitates stop codon recognition in eukaryotes. There are two highly conserved motifs on eRF1’s domain 1, which are thought to directly associate with the stop codon in all eukaryotic species, the TASNIKS and the YxCxxxF motifs. In this study, we introduced the TASNIKS and YxCxxxF motifs from Oxytricha trifallax, a variant-code ciliate, into the baker’s yeast Saccharomyces cerevisiae. The expressions of these mutated eRF1’s were measured using Luciferase assay. While TASNIKS and YxCxxxF might involve in the process of recognizing stop codons, the results suggested that YxCxxxF should play a higher role in stop codon specificity.