2014 Summer Research Projects
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2014 Summer Research Projects Prof Department Funded by Student Bebej, Ryan Biology The William Josiah Valk H. and Celia I. Dornbush DeVries Family Student Research Fellowship Project Title and Abstract Interpretation of tail function in fossil cetaceans through multivariate analyses of caudal vertebrae in modern mammals The evolution of modern whales from terrestrial ancestors required many drastic anatomical, physiological, and behavioral changes. The development of an efficient swimming mode in the earliest cetaceans is one key to understanding this remarkable transition. This behavioral change from a limb-dominated form of swimming to a tail-dominated form can be inferred from the anatomies of fossil whales, but it requires careful comparison with the anatomies of modern mammals, whose behaviors can be directly observed and correlated with their anatomies. This project seeks to develop a quantitative framework from the anatomies of modern mammals in order to infer the behavioral capabilities of early fossil whales. It will involve working with a wealth of previously collected data, in order to discern patterns that will provide insight into the evolution of tail function in early cetaceans. Analytical techniques will center on multivariate statistical analyses, but student-initiated approaches to analyzing the data will be encouraged. This project may also involve day trips to the Museums of Zoology and Paleontology at the University of Michigan to collect additional data as needed. DeJong, Randall Exploring Bacteriophages in Microbe-Host Symbiotic Systems There are estimated to be 1031 bacteriophages (viruses that infect bacteria) on the planet, making them the most abundant “life-form” on earth. As such, they have the possibility to impact their local ecosystem in a myriad of ways. Though they are ubiquitous, relatively few studies have investigated the interaction of bacteriophages within microbe-host symbiotic systems. In these systems, the host animal is partially or completely dependent upon the bacterial symbionts for survival. Hence, these systems must contain mechanisms to prevent microbe disruption by bacteriophages, which may be dependent or independent from the bacteriophages themselves. Two such animal systems, the guts of snails and termites, are ones in which the roles of bacteriophages are completely unknown. This project seeks to build on genomic information obtained from bacteriophages recently isolated from these two systems to (i) assess the abundance of particular bacteriophages within these systems (ii) analyze the genomes for horizontal gene transfer events (iii) identify genes likely to be relevant to the stability of the system (e.g. genes known to protect bacteria from infection by other, similar phages) and (iv) perform comparative genomics. Additionally, an assessment of bacteriophage diversity in these systems via metagenomic sequencing will be done. The student will use a variety of computational, molecular and microbiological techniques to accomplish this, including cultivation and purification of bacteria and bacteriophages, isolation of DNA, quantification of phages using digital PCR, metagenomic library preparation and DNA sequencing. Various bioinformatic tools will be used to analyze the genomes of existing phages and mine data from the metagenomic library to assess genomic diversity, probable gene function, and horizontal gene transfer events Biology Calvin College Abby Stapleton Biology Department Prof Grasman, Keith Koetje, David; Fynewever, Herb; Wilstermann, Amy Department Funded by Biology The Clarence (Bud) Star and Arlene Talen Star Student Research Fellowship, US Fish and Wildlife Service Biology National Science Foundation Student Stacy Hooker, Monica Langeland, Dorthea Leisman Project Title and Abstract Fish-Eating Birds as Sentinels for Pollution in Aquatic Ecosystems Fish-eating birds are important upper-level predators in aquatic ecosystems and as such are often vulnerable to environmental stressors including pollution. These species are effective “sentinel species” for measuring ecosystem health, which can be assessed and monitored through a variety of ecological, physiological, and cellular methods. Two related projects will investigate the effects of pollution on fish-eating birds such as gulls, terns, and loons in Michigan and New York. 1) Our previous studies have shown associations between pollutants and suppressed immune and hormonal functions in gulls, terns, and herons of the Great Lakes. The objective of the current study is to continue the assessment and monitoring of these health effects at contaminated sites around the Great Lakes. Specifically, this project is funded by the US Fish and Wildlife Service under the Great Lakes Restoration Initiative to measure the current health and population status of birds at specifically designated Areas of Concern. The data from this and other studies will help help the USFWS and other government agencies determine whether water quality at these sites has improved enough to remove them from the list of impaired sites, or whether they should remain designated as Areas of Concern. This project involves travel and boating for field work around the Great Lakes and follow-up laboratory work at Calvin. Students will have the opportunity to interact with USFWS scientists. 2) The deposition of airborne mercury into lakes in the northeastern US and Canada presents significant health risks to fisheating wildlife such as common loons. This mercury comes primarily from coal-fired power plants and cement kilns. In a previous laboratory study, dietary mercury exposure suppressed immune function in young loons. Field studies conducted during the past 4 years suggest significant immunological effects in young wild loons but minimal effects in adults. This study will continue investigations into immunological effects in wild loons living in New York's Adirondack Park (and possibly other locations in North America such as New Brunswick, Wisconsin, Maine, and Michigan, depending on funding). Loons will be captured at night by spotlighting and netting them from boats and canoes. White blood cells will be isolated from blood samples and cryopreserved for transport back to the laboratory at Calvin. Immunological functions of these white blood cells will be assessed using cell culture assays in the laboratory. Students will have the opportunity to work with biologists, rangers, and veterinarians from the New York Department of Environmental Conservation, the Bronx Zoo, and the BioDiversity Research Institute. Nate Buteyn, Ye In Oh Assessing the Effectiveness of Investigative Labs in Biology 224 and 225 Students will work to evaluate data gathered from three semesters of students in Biology 224 and 225. These courses have been revised with funding from the National Science Foundation to promote the development of students' interdisciplinary science competencies in ways that integrate with best educational practices. Our goal this summer is to assess the effectiveness of these laboratory learning modules, to prepare dissemination-ready drafts of our manuals, and to compose manuscripts for peer-reviewed publication in professional journals. Prof Proppe, Darren Department Funded by Student Biology The Andrew Leanna DeJong, Family Thuy-Nhi Foundation, Nguyen Calvin College Science Division Project Title and Abstract Conspecific attraction: Are birds attracted to their own species songs? Some species of songbirds will establish more readily in an area if songs from other males of their species (conspecifics) are played back on speakers during migration. However, this phenomenon has not been tested for many species of birds in Michigan. This summer I aim to work with Calvin students to test whether conspecific song playback increases establishment rates for five species of songbirds in Northern Michigan. The selected students will survey birds by sight and sound at 20-40 sites in Northern Michigan. Further, the students will monitor breeding cycles for least flycatchers and redbreasted nuthatches to develop baseline reproductive information for these species in this region. This work will lay the foundation for future research that will investigate whether conspecific playback can be used to draw birds successfully into noisy areas. Shen, Anding Biology National Institutes of Health Tran Nguyen, Abuoma Nwadike The roles of endothelial cells on HIV infection and latency formation in resting T helper cells In many patients with HIV-1 infection, highly active antiretroviral therapy (HAART) successfully suppresses viral loads and restores the immune system. However, a major latent reservoir identified in resting T helper cells (a type of white blood cells) poses a great barrier to viral eradication and ensures viral persistence in patients. A more complete understanding of the mechanisms contributing to the establishment of the reservoir will influence the strategies in battling viral persistence.Some recent studies demonstrated that endothelial cells increased the level of HIV infection in resting T helper cells and might play a significant role in latency formation in these cells. In this study, a replication incompetent pseudotyped virus system is used to investigate how endothelial cells interact with resting T helper cells to promote HIV infection and latency formation. Ubels, John Biology National Institutes of Health and Den Ouden Research Fellowship Peter Boersma, Courtney Glupker UVB-induced apoptosis in the corneal epithelium In this project we are studying the effect of UVB radiation on the corneal epithelium. Induction of apoptosis in response to UVB is investigated by measuring activation of caspase enzymes, DNA damage and loss of K+ from cells before and after siRNA knock down of of components of signaling pathways that mediate apoptosis. The experiments are conducted using cells in culture and intact pig corneas. The studies are part of a project testing the hypothesis that the relatively high concentration of K+ in the tears helps to protect the cornea from ambient UVB radiation. Prof Van Dragt, Randall Department Funded by Biology Cargill Foundation Grant, Eco System Preserve Bunker Endowment Student Jonathan Knott, David Postma Project Title and Abstract Forty years of forest development on the Calvin College Ecosystem Preserve In 1974 the Calvin College Biology Department began a long-term study to examine the successional changes in a small suburban woodlot on what is now the Ecosystem Preserve. Two hectares of the woodlot was divided into quadrats, and all the trees larger than two inches in diameter were measured and mapped. Since 1984 tree growth has been measured every 5 years, and recruitment to and losses from the woodlot's tree populations has been determined as well. This summer we will conduct the 40-year census of the forest populations which will involve 1) locating mapped trees and previously unmapped trees that now exceed the 2-inch diameter criterion, 2) measuring the size of all trees, 3) physically mapping all trees using a GPS instrument, and 4) beginning to process the 40 years of growth data we have obtained to help develop a picture of how the preserve's tree populations have changed over the past 40 years. In processing the growth and mortality data, we will be taking into account several rounds of disease that have happened in that period and the ongoing changes in climate that accompany global warming. Van Dragt, Randall Biology Calvin College Marissa Eco System Beversluis, Preserve Karl Boldenow Land Stewardship in the Ecosystem Preserve Each summer the Calvin College Ecosystem Preserve employs two or three students to work in the Ecosystem Preserve, maintaining trails and other infrastructure, managing preserve habitats and gathering data for long-term monitoring studies. These positions are different than other research positions since they combine various elements of land management practice to give students a broad exposure to land management. Maintenance and management include the upkeep of trails and other structures, control of invasive species, clearing vegetation to maintain open habitat, and planting native species. Monitoring projects involve a complete census of the birds breeding on the preserves, monitoring small mammal populations in target areas, surveying macroinvertebrates in the many small ponds on the preserve. Van Dragt, Randall Biology The Fritz and Cassidy Richard Carol Rottman Student Research Fellowship Impact of Fire on Insect communities at the Flat Iron Lake prairie Fire is necessary for maintaining the plant composition of prairie grasslands, but fire also changes the composition of other community elements which can only poorly evade fire. Insect communities, in particular, can be significantly modified by moderately hot prairie fires. At the restored prairie at Flat Iron Lake, we have shown that the dominance of certain soil insects, like springtails, can be reduced significantly by spring burns, and populations of these important soil modifiers take a year or more to recover. Our data so far do not allow us to rule out the effects of specific habitats; thus, the summer 2014 study will repeat the study conducted last summer (2013) but with reciprocal treatments: the fields freshly burned and one year out from a burn will be reversed. Insects will be trapped, identified, and enumerated to determine whether community-level effects seen last summer can be repeated this year. Since prairies provide valuable refuge to insects, data from studies like this help to determine the frequency of burning that will best sustain important insect populations. Prof Department Funded by Student Warners, Calvin College Kara Smit, Biology David, Biology Deanna Department, Geelhoed Gail Heffner Calvin College Science Division Project Title and Abstract Restoring Native Habitats In Urban Landscapes In this project, students will work in the greenhouse, nursery and at sites on and off campus investigating the reintroduction of native plants and native habitats into urban areas. Part of this work will involve controlled experiments to determine optimal germination and growing conditions for a group of particularly desirable native species. These students will also help with management and hopeful expansion of native habitat plantings on campus. If additional funding is secured the Calvin students will also spend some time working with a high school 'Green Team' of urban youth who will be receiving training in environmental restoration and green infrastructure skills. Warners, David Biology The Fritz and Caitlin Carol Rottman Strikwerda Student Research Fellowship Plant Responses to Climate Change at Flat Iron Lake Preserve This project will take place at Flat Iron Lake. This project is an ongoing flower phenology study, investigating the timing of flowering period for a variety of native prairie plants. Through this long term field study our objective is to document the variety of responses to climate change exhibited by the extensive diversity of plants at the Flat Iron Lake Preserve. Students will also evaluate a variety of planting strategies that were employed during a 2011 prairie restoration effort in a former feed plot located within the larger Flat Iron Lake prairie. Warners, David Biology Plaster Creek Stewards Andre Otte Assessment and Restoration of Plaster Creek This project will focus on the water quality and overall stream health of our local urban stream, Plaster Creek. The project will continue research that was done in 2012 and 2013, and will begin to assess data that are being collected from stationary level loggers that were installed in the stream in 2013. A primary focus will be to continue to assess bacterial levels over time and space, as well as sediment, nutrient loading, pH, conductivity, and discharge volume. These data will be organized, processed, and compared among the different sites, and between years. This work will help us identify the most problematic and dangerous sites in the stream, and in this way inform the prioritization of restoration plans. Wertz, John Biology The Harvey Rozema Student Research Fellowship Jonathan Lin Physiological Characterization and Naming of Novel Bacteria from the Guts of Cephalotes Ants Bacterial symbionts are considered to be key innovations behind the evolutionary success and ecological dominance of numerous animals and plants. Among the insects, ants number among the most well-studied. Of the immense diversity of ants, only the turtle ants (Cephalotes) have been the focus of studies investigating the diversity of bacteria harbored in their guts, and these studies have only recently began. DNA-based methods have demonstrated the turtle ants harbor a plethora of very unique bacteria, including members of the Verrucomicrobia and Proteobacteria. As these are only distantly related to other bacteria, are abundant within turtle ants collected from disparate geographical locations, and shift in abundance depending on the diet of the ant, they appear to be true mutualistic symbionts critical for the health and survival of the host. We have recently been successful in cultivating these bacteria in the laboratory. As with the discovery of any new organism, the organism needs to be well-characterized, named, and published in the scientific literature. Hence, this project will focus on deep characterization of these isolates, including substrates utilized and products produced, growth assays including temperature, oxygen, CO2, pH and NaCl optima, as well as experiments that will move us towards elucidating an ecophysiological role for these bacteria within the gut community (enzyme assays and RT-PCR). Prof Anderson, Carolyn Department Funded by Chemistry & Arnold and Biochemistry Mabel Beckman Scholars Program Student Project Title and Abstract Andrea Bootsma Exploration into Rotationally Restricted N-Alkyl Quinolines Organic synthesis is a powerful technique that allows access to a wide range of different structural motifs. Computational studies can be used to help us predict what specific target we are interested in pursuing. During an earlier project, we discovered that some N-alkyl quinolones experience slow rotation around their C-N bond due to steric factors. In this project, we would like to evaluate additional members of this class of compounds computationally in order to predict what type of substituents are likely to provide the greatest rotational restriction. After completing these studies, the student involved on this project will be charged with preparing the identified targets in the laboratory. Thus by coupling computational studies with synthesis, we hope to be able to quickly identify and prepare rotationally restricted Nalkyl quinolones. The student working on this project will gain experience with both computational and synthetic organic chemistry techniques, including: Gaussian, running reactions, purification, organic spectroscopy, and experimental design. Anderson, Carolyn Chemistry & National Biochemistry Science Foundation Brian Heidmann Microwave Assisted Gold-catalyzed Rearrangement of N-Propargyloxypyridines Organic synthesis is a powerful technique that allows access to a wide range of different structural motifs. In this project, we are working to advance a method for the synthesis of N-substituted pyridones; an interesting functional group found in a series of pharmacologically interesting compounds. To date, we have observed a new gold(I)-catalyzed method for accessing this motif by rearranging a related system. More recently we have discovered that this reaction is greatly accelerated under conditions of microwave heating. The student working in this area will be responsible for exploring and optimizing the gold(I)-catalyzed rearrangement. The student will gain experience with synthetic organic chemistry techniques, including: using the microwave reactor, running reactions, purification, organic spectroscopy, experimental design, and working in the inert atmosphere glove box. Anderson, Carolyn Chemistry & National Biochemistry Science Foundation Connor Reidy, Joy Christopher Synthesis of β- and γ-Amino Acids Containing N-Alkyl Pyridones Organic synthesis is a powerful technique that allows access to a wide range of different structural motifs. In this project, we are working to develop a method for the synthesis of β- and γ-amino acids containing N-alkyl pyridones, which are homologues of natural amino acids and contain an interesting functional group found in a series of pharmacologically active compounds. To date, we have discovered an important intermediate in route to these species and have begun to optimize its synthesis. The students working in this area will continue to seek conditions for the preparation of this intermediate and its conversion into the desired amino acids. The students will gain experience with synthetic organic chemistry techniques, including: running reactions, purification, organic spectroscopy, and experimental design. Prof Arnoys, Eric Department Funded by Student Chemistry & The Thedford Sam Schuiteman, Biochemistry P. Dirkse Aimee Vos Summer Research Fellowship, The Enno Wolthuis Summer Student Research Fellowship Project Title and Abstract Watching Proteins in Real Time We will characterize the behavior of several membrane-bound proteins in living cells with state-of-the-art techniques to examine their cellular localization, mobility, and interactions with other proteins. Protein targets have been tagged with fluorescent proteins so that they can be viewed in living systems. We will also examine what effect extracellular signals have on the proteins' behavior. Barbachyn, Michael Chemistry & The William Niecia Flikweert, Biochemistry H. and Celia I. Abbegail Bell Dornbush DeVries Family Student Research Fellowship, Brummel Chair Synthesis of functionalized 3-aryl and 3-heteroaryl-5-iodomethyl-2-oxazolidinones via an iodocyclocarbamation reaction The iodocyclocarbamation reaction of allylic and homoallylic carbamates is an effective means of constructing 5-membered oxazolidinone and 6-membered carbamate ring systems. The reaction has here-to-fore been exploited primarily as a means to stereoselectively assemble vicinal or 1,3-cis amino alcohol functional arrays, via a subsequent degradation of the cyclic carbamates. Interestingly, in all early accounts of the iodocyclocarbamation reaction of which we are aware, the substrate allylic carbamate's nitrogen (and hence the resultant oxazolidinone's 3 position) is found substituted with only alkyl, benzyl, or carbobenzyloxy moieties. We are interested in exploring the iodocyclocarbamation reaction as an efficient means to prepare racemic 5(iodomethyl)oxazolidinones having more complex functional arrays at the oxazolidinone's N-3 position, especially aromatic and heteroaromatic ring systems. Such oxazolidinone derivatives will have synthetic utility in preparing racemic versions of marketed and emerging antibacterial and anti-inflammatory agents. Benson, David Chemistry & Arnold and Biochemistry Mabel Beckman Scholars Program, National Science Foundation Susan Hromada, Proteins as antioxidants Most antioxidants are low molecular weight molecules that are sacrificially oxidized in Matt Hollowell, the presence of oxidants produced by the immune system. The Benson laboratory has found that a covalent cross Taylor Hegg link between a tyrosine side chain and cysteine side chain of proteins can also be oxidized in the presence of hydrogen peroxide, and other oxidants, while still attached to the protein backbone. While we do not expect such covalent side chain cross links to replace antioxidants, such as ascorbic acid, we do expect these cross links to minimize damage inflicted on proteins by oxidants from the immune system. This research is currently performed at the protein-level meaning that purified proteins are produced and purified for our experiments. We perform a variety of biophysical (NMR, DSC, etc) and biochemical (UV absorbance, fluorescence, etc.) experiments to determine whether and when the cross link has formed, the oxidation state of the cross link, and the oxidations state of other amino acids in the protein. Prof DeKock, Roger Department Funded by Student Chemistry & The Rollin M. Jared Weidman Biochemistry Gerstacker Foundation Student Research Fellowship Looyenga, Brendan Chemistry & The Enno Biochemistry Wolthuis Summer Student Research Fellowship, Chemistry Pfizer Fellowship Louters, Larry Chemistry & The Dr. Daniel Kathryn Wrobel, Biochemistry J. Visser Evans Lodge Student Research Fellowship in the Medical Sciences, National Health Institutes, Calvin College Chemistry Department Project Title and Abstract Trends in the Electronic Structure of Atoms For several years we have performed theoretical studies in order to obtain insight into the electronic structure of atoms. Specifically we aim to provide: 1) a theoretical underpinning as to why the experimental sequential ionization energies of atoms roughly follow an arithmetic progression, and 2) a theoretical understanding of the trends observed in the experimental K(alpha) X-ray emission energies as initially observed by Moseley more than 100 years ago. We employ the GAMESS software, and the Constrained Unrestricted Hartree Fock (CUHF) model within GAMESS (General Atomic and Molecular Electronic Structure System). Miriam Rienstra, Cell Signaling and Endocytosis in Kidney Cancer Recent work in the field of cancer research has demonstrated Calvin that functional alterations of the cellular trafficking machinery that regulates important cell signaling proteins is VanOpstall involved in cellular transformation, which is the process whereby normal cells become cancerous. Identifying and understanding these cellular alterations is critically important, as the molecules involved may provide good targets for cancer therapy. During my postdoctoral fellowship, I identified a unique genetic mechanism in which two proteins-- leucine-rich repeat kinase 2 (LRRK2) and MET-- function coordinately to transformation normal kidney cells into papillary renal carcinoma cells. My ongoing research suggests that LRRK2 is a critical regulator of endosomal trafficking in various cell types, including the proximal renal tubule epithelia from which papillary renal cancers arise. We hypothesize that increased LRRK2 activity, due to its genomic amplification or mutation, modifies trafficking of activated MET proteins, resulting in increased endosomal retention and prolonged activation. This prolonged signaling instructs cells to continue to survive and proliferate in situations where there growth should have stopped, and can thus potentially lead to formation of tumors in the kidney. Relationship of the activity of GLUT1 to its tethering to the cytoskeleton GLUT1, like many membrane proteins, can be tethered to the cell cytoskeleton by connector proteins. Typically this tethering is involve in the recycling of the protein to and from the membrane surface. We will measure the fraction of GLUT1 tethered to the cytoskeleton and determine if that fraction changes when GLUT1 is activated. Prof Louters, Larry Department Funded by Chemistry & the Luke and Biochemistry Pauline Schaap Summer Research Fellowship Student Jedidiah Bell Project Title and Abstract Effects of selected nutrichemicals on glucose uptake Curcumin, an ingredient in the Indian spice, tumeric, has a molecular structure that is reactive with thiols. GLUT1, the glucose transporter in L929 cells and HCLE cells, is thought to be activated by the formation of a disulfide bond. Epicatechin, found in green tea, has been suggested to have hypoglycemic effects. Therefore, we will determine if these two nutrichemicals will alter the glucose transport activity of GLUT1 in L929 and HCLE cells. Muyskens, Mark Chemistry & The Jack and Biochemistry Lois Kuipers Applied Mathematics Endowment Kyle Disselkoen Photochemistry: Photoelimination in Acetylacetone The project will involve primarily using computational tools to model the kinetic and molecular structural details of a gas-phase photochemical reaction. The central idea is a simple collisional model that predict an mathematical form to which the data is fitted. My research has experimental results from the ultraviolet laser photoelimination of hydrogen fluoride from fluorine containing acetylacetone in the gas phase. The work will be greatly assisted by developing models related to the data. Some experimental work on gas phase IR absorption is possible. Sinniah, Kumar Chemistry & National Biochemistry Science Foundation Abby Leistra, Kayla Scholten Characterizing Riboflavin Conjugated Nanoparticles for Targeted Drug Delivery in Chemotherapeutics Our group is interested in developing methods for delivering chemotherapeutics to cancer cells while limiting damage to healthy cells. The approach we take to target cells is based on the overexpression of cell markers. One such example is riboflavin (RF) receptors, which are over-expressed in prostate and breast cancer cells. RF receptors can be targeted for selective delivery of anticancer drug molecules. Our group has characterized RF conjugated dendrimer nanoparticles for targeting the RF receptor. This summer we hope to extend this work to study multivalent interactions between RF and the riboflavin receptor using single molecule methods. Sinniah, Kumar Chemistry & National Biochemistry Science Foundation Lydia DeJonge, Maggie Van Winkle Investigating the Binding Interaction of Insulin with G-Quadruplex DNA G-quadruplexes (G4s) are noncanonical DNA structures formed from guanine-rich DNA sequences. Over 376,000 sequences of human DNA have been identified that have potential to form G4s, including many sequences in telomeres and gene promoter regions. These findings suggest that G4s may influence gene stability and therefore potentially impact transcription and other biological processes. Our group is currently studying the interactions between insulin and the various sequences of G-quadruplex DNA found in the insulin linked polymorphic region (ILPR). Our results indicate the studies done thus far involved the binding of ILPR DNA with a dimeric form of insulin. Since insulin is found in the hexameric form in the human body, this summer we plan to investigate the binding of the ILPR DNA with the hexameric form of insulin. Vander Griend, Douglas Chemistry & The DeKock Biochemistry Chemistry Summer Research Fellowship, National Science SeongEun Kim, Anna Michmerhuizen, Zac Drees Nanomolecular Building Projects Understanding and controlling the synthesis of supramolecules is a key goal of nanotechnology. The students working on this project will use UV-vis spectroscopy and mass spectrometry to investigate the solution chemistry of various types of molecules that interact with each other. Different building blocks can be used for nanocontainers, nanomachines, and biochemical solutions. A significant element of the research involves collaboration with a graduate labs at Indiana and Western Michigan University. Prof Department Funded by Adams, Joel Computer National Science Science Foundation Student Patrick Crain, Mark Vander Stel Project Title and Abstract Computing in Parallel Nearly all modern computers contain parallel processors, meaning they can perform multiple actions simultaneously in real time. The two students selected for this project will learn about and practice software development that leverages these parallel systems, including Calvin's supercomputer. The students will work with Prof. Adams on his NSF-funded project, immersing themselves in cutting-edge technologies like Google's MapReduce (Hadoop), accelerated computing using graphics processing units (GPUs) and co-processors, supercomputing using the message passing interface (MPI), and multicore computing using open multiprocessing (OpenMP). The students may also have the opportunity to travel to and present their work at the Supercomputing 2014 (SC'14) conference in New Orleans, LA in November 2014. Kim, Yoon Engineering Program for Carl Cooper Sustainability Engineering Kim, Yoon Engineering Program for Nathan Terschak Development of Solar Simulator Modules Based on High-Power LEDs Sustainability Engineering Development of Wireless Energy Monitoring Systems and Smartphone Apps Prof Si, April Department Funded by Student Engineering The Jansma Ayooluwa Family Ayoola, Research Fund Hezkiel Nanda in the Sciences and Business Project Title and Abstract Electric and Magnetic Focusing and Navigation for Ingtranasal Target Drug Delivery The need of developing a simple, safe, and effective way of delivering drugs for the treatment of CNS disorders is urgent.The olfactory region is the only site in human body where CNS is in direct contact with the outer environment. If drug could be directly sent to this region through nose, it can diffuse across this film and reach to CNS within a short time. Direct nose-to-brain drug delivery circumvents the blood-brain-barrier and has multiple advantages over conventional intravenous delivery. It is critical to search for more effective drug-delivery strategies that can directly deliver drugs to the olfactory region. A new delivery method that utilizes the electrophoretic force to focus and guide drug particles to the olfactory region was proposed and studied during last year. In order to develop and design the electric drug delivery device, computational simulation is the first step, which has been done last year. The second step is to test it in vitro experiments. The first objective of the proposed study in this summer is to find the essential elements and parameters such as the flow rate, aerosol size, aerosol charge level, size of the electrodes, the lay-out of the electrodes around the nose, which are necessary for designing the electric nasal drug delivery device. The second objective of this proposed study is to study the feasibility of using magnetic force to enhance nasal drug delivery efficiency through computational simulation in a 2-D nasal passage model. The simulation results will help us to determine (1) if magnetic force guided drug delivery is applicable, (2) how effective this delivery method will be compared to conventional methods, (3) what’s the range of the required magnetic strength, and (4) how to arrange the magnets around human head. All those parameters are important factors for the design of an effective magnetic olfactory drug delivery device. Wunder, David Engineering The Jansma Jeremiah Rocha Family Research Fund in the Sciences and Business Fate and Impact of Antibiotics in Denitrifying Biofilters Nitrate contamination of water supplies is caused by widespread use of fertilizers, erosion due to changes in land use, and leaching. One of the most cost effective and environmentally responsible processes used to remove nitrates from groundwater is fixed-film biological denitrification. A possible concern with this process is the presence of antibiotics at in water supplies and their impact on dentrifying biofilm bacteria and their ability to reduce nitrate. Interestingly, recent work has shown that some antibiotics that might impede the activity of denitrifying bacteria may also be abiotically transformed in reducing conditions necessary for biological denitrification. This research attempts to understand whether antibiotics at environmentally-relevant concentrations will impact the activity and community structure of denitrifying biofilm bacteria, and whether the response of individual antibiotics to reducing environmental conditions will partially mitigate their impact(s). Using substrate utilization kinetic studies, a continuous-feed rotating annular bioreactor would be used to better understand the fate and impact of grouped antibiotics on denitrifying biofilm bacteria used for water treatment. Wunder, David Engineering Program for Sustainability Engineering Engineering Program for Sustainability Engineering Jesse Vander Wees Air Quality and Energy Value of Bagasse Charcoal Jonathan Gingrich Column Studies of Contaminant Removal in Bagasse Charcoal Wunder, David Prof Bascom, Johnathan Department Geology, Geography & Environmental Studies Funded by Student The Jansma Audrey Hughey, Family Brian Hilbrands Research Fund in the Sciences and Business, Esri (Environmental Systems Research Institute) Project Title and Abstract Publishing an Online Ethiopian Geography Using Intelligent Web Maps and Storytelling Templates New technologies and geospatial data are vastly expanding the potential of maps to tell geographic stories that actively engage its creators, readers and learners. This project relies on three features now available with Esri’s ArcGIS Online – intelligent web maps, storytelling templates and a new storybook app – to facilitate the construction of a new geography of Ethiopia. Bundles of related maps – coupled with narrative, which explicate them – become chapters for the book. This digital book will be "published" online and grow as a collaborative project, created with Ethiopian geographers. This summer’s project will construct a prototype of several chapters to pilot test with geographers in Ethiopia. Students will assemble raw materials, build web maps and publish them into templates Esri has developed to enable various kinds of storytelling. Bjelland, Mark Geology, Geography & Environmental Studies Calvin College Ian Noyes Geology, Geography & Environmental Studies Department Geographies of Deindustrialization and Environmental Contamination in Michigan Michigan’s governor Rick Snyder wants to replace our state’s Rust Belt image with a new image as the “Comeback State.” Reinventing Michigan, however, requires dealing with the state’s legacy of derelict, abandoned, and often environmentally contaminated brownfield sites. This research project involves assembling a geographic database and creating a series of maps depicting the patterns of deindustrialization and environmental contamination across Michigan. The student researcher will retrieve historic data from archival reports and maps. Fieldwork will document the reuse of older industrial buildings around Grand Rapids. Ferdinands, John Mathematics The Jack and & Statistics Lois Kuipers Applied Mathematics Endowment Andrew Hayes, Isaac Zylstra Selective Sums of Infinite Series The sum of a subset of the terms of an infinite series is called a selective sum of the series. The goal of the project is to determine the set of selective sums for some types of infinite series. Some results are known for series with real positive terms. Student researchers will investigate the question for other types of series, such as real alternating series and series with complex terms. Turner, James Mathematics The Jack and & Statistics Lois Kuipers Applied Mathematics Endowment, National Science Foundation David Zhang, Shamuel Auyeung, Joshua Ruiter Algebraic characterization of manifolds in higher dimensions There are well understood classifications of connected surfaces (i.e. 2-manifolds) obtained through algebraic methods (e.g. Euler characteristic, fundamental group). We will explore an analogous algebraic characterization for the classification of simply connected of 4manifolds through a device called Pi-algebras (which encodes how to construct such objects by gluing higher dimensional balls together along their spherical boundaries). It is expected that the methods we develop and the results we obtain can be extended to produce an algebraic classification of (n-1)-connected 2n-manifolds, for small values of n. There are several areas of applications for such an algebraic characterization of manifolds. In particular, the study of configuration spaces, which topologically model linkages and robot motion planning, can be studied effectively through such Pi-algebras. Similarly, such algebras can be used in the study of Grassmannians (arrangements of hyperplanes), which plays a useful role in computer simulation of vision and scattering amplitudes for subatomic particles. Prof Department Funded by Ayoola, Nursing The Henry and Adjoke, Peggy Gail Zandee Tazelaar Summer Student Research Fellowship, Calvin College Science Division, Robert Woods Johnson Foundation, Calvin Alumni Association Moes, Jesse; Byma, Elizabeth; Couzens, Suzan Nursing Student Megan Jongekrijg, Victoria Ellens, Erika Bosch, Tega Ebeye, Josianne Ishongore, Grace Lee, Kara Marshall, Samantha Orozco, Becca Broekhuis Michael Pryor The Jansma Family Research Fund in the Sciences and Business Project Title and Abstract Preconception reproductive knowledge promotion (PREKNOP) Unplanned pregnancy continues to be an ongoing public health problem in the United States which has a relatively higher rate than other developed countries. The social and economic cost of unplanned pregnancy and its associated adverse health outcomes on individuals and the society is enormous. Unplanned pregnancy rates and their adverse effects are even worse among minority and low-income women. The long-term objective of this research is to promote women’s reproductive health and positive pregnancy outcomes by examining the effectiveness of the “Preconception Reproductive Knowledge Promotion (PREKNOP)”, an intervention to increase women’s knowledge of their body, while reducing the risk of unplanned pregnancy and delayed pregnancy recognition. The social cognitive theory and the health promotion model guide this study. Based on a community-based participatory research approach, this study builds on residents’ reported concerns and recommendations as well as a longstanding partnership between the Calvin College nursing department and three racially diverse medically underserved low-income communities in southwest Michigan. One hundred and twenty women, 18-44 years old are randomly assigned into two groups, one control and one intervention at the time of recruitment. The PREKNOP intervention consist of 10 home visits during which women receive information on the female reproductive system and the expected monthly cyclical changes. Women in the intervention group receive 6 ovulation test kits (participants can request refills at any time), a 12 month menstrual calendar, a digital thermometer, and educational brochures covering: the female reproductive anatomy, hormones and menstrual cycle, how to recognize ovulation period, various methods of birth control and how they work, early pregnancy symptoms, and how to confirm pregnancy symptoms. Women in the control group receive information on healthy lifestyle. Teams of nursing students and community health workers administer the 12 month intervention and surveys in face-to-face interviews. Women of childbearing age, especially minorities and the medically underserved, need continuous monitoring and on-going educational approach to reduce disparity in health and improve pregnancy outcomes. Promoting better understanding of the reproductive changes in their bodies and actively involving women in their own care is a logical place to start. Heartside Healthy Feet Heartside Healthy Feet is a project designed to relieve pain during walking and improve overall activity levels in homeless adults. Participants will be recruited from various community organizations in the Heartside neighborhood in downtown Grand Rapids. Homeless adults will be given a pair of custom-fit shoes and told to maintain activity levels for six weeks. Before and after receiving the shoes, information about pain, foot health, and activity level will be collected. Prof Haarsma, Loren; Ubels, John Department Funded by Student Physics & Calvin College Jodie De Vries Astronomy Science Division Project Title and Abstract Investigating how UV exposure activates K+ channels in corneal epithelial cells using electrophysiology Earlier research, using electrophysiology and other methods, demonstrated that ultraviolet (UV) radiation at doses relevant to ambient levels of outdoor exposure (equivalent to less than one hour on a sunny day) activates K+ channels in corneal epithelial cells leading to rapid loss of intracellular K+. This loss of K+ appears to be an essential event in the UV-induced activation of apoptosis (programmed cell). We believe that the relatively high level of K+ in tear fluid (compared to normal extracellular fluid) helps maintain the normal balance between proliferation and shedding of corneal epithelial cells in the face of exposure to ambient UV. We will now investigate the intracellular signaling mechanisms by which UV activates K+ channels and apoptotic signaling pathways in corneal epithelial cells. We will transfect cells with siRNAs to knock down certain molecules (Fas and caspase-8) known to be important in the UV-activated apoptotic pathway. Using whole-cell patch clamping, we will compare UV-activation of K+ channels in transfected cells to control cells. We will also transfect cells with siRNA to knock down one K+ channel (KCNC4) known from prior work to be UV-activated, to determine if there are additional UV-activated K+ channels not yet identified. Harper, Paul Physics & Astronomy The Jack and Lois Kuipers Applied Mathematics Endowment Zachariah Strango Phase Behavior Studies of Minimal Surface Based Structures in Sugar-Lipid Mixtures Lipid phase transitions among the many types of lipid phases are highly relevant to understanding the behavior of membrane proteins and the cellular processes of pore formation, division, fusion, and infection. Likewise, sugars play a key role in stabilizing membranes against freezing and dehydration. This project has two main prongs toward better understanding these mixtures. The first is an experimental effort via DSC (differential scanning calorimetry) mapping out the phase behavior of monononadecenoin and sucrose; the second is computational, entailing making electron density models of lipid-water-sugar mixtures. Molnar, Larry Physics & Astronomy The John Van Zytveld Summer Student Research Fellowship, The Hubert A. Vander Plas Memorial Student Research Fellowship Christopher Spedden, Daniel Van Noord Modeling Fast and Unusual Binary Stars Though they often appear as a single star, even when magnified, binary stars are two stars held in mutual orbit around one another by gravity. Contact binary stars are so close together that their atmospheres touch as they rapidly orbit one another. While these so called “W UMa” systems are not uncommon, many aspects of their life cycle remain poorly understood, from formation to final state. They are identified by characteristic shapes of the light curves obtained with Calvin's telescopes. Using powerful search and analysis software, student researchers have already found and typed many new variable stars in recent years. Several of these are quite extraordinary and thus of significant interest to the astronomical community. This summer's work will follow up previous discoveries as well as seek new ones. Prof Molnar, Larry Walhout, Matthew Department Funded by Student Physics & Michigan Nathan Astronomy Space Grant McReynolds Consortium, Calvin College Science Division Physics & Astronomy National Science Foundation Jonathan Shomsky Project Title and Abstract Asteroid Collisions To a remarkable degree, the history of our solar system is recorded in the details of the orbits of the numerous small bodies that are left over: the asteroids. In the last few years, we have developed new techniques to read this history, especially in identifying the age and membership of asteroidal collisional families. One key parameter in models of the collisional history of the asteroid belt is the impact energy required to disrupt an asteroid. Theoretical estimates of this parameter vary widely. The main goal of this summer’s work is to establish this parameter observationally by careful study of the collisions that have occurred in the Koronis zone, an isolated region in the outer portion of the main asteroid belt. Towards this end we will use data from several large data bases. Trapping krypton and argon atoms with laser beams The team will expand the existing laboratory capabilities, so that two atomic species (krypton and argon) can be captured and studied in a magneto-optical trap. Students will work to measure and optimize the trap-loading rates for both species, and to begin characterizing the dynamics of cross-species (Ar-Kr) molecular interactions.
