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Summer Research: 2014 Project Proposals Details

Application submission deadline: February 17, 2014

Biology projects

Ryan Bebej, Biology
Project #1 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 trip may also involve day trips to the Museums of Zoology and
Paleontology at the University of Michigan to collect additional data as needed.
Benefit to student: The student will gain firsthand experience utilizing a comparative anatomical approach to reconstructing behaviors in fossil animals based on how they compare to living animals. In so doing, the student will gain basic knowledge about anatomy, functional morphology, and what types of anatomical changes take place during adaptive radiations. The student will also gain proficiency in working with and managing substantial datasets. The student will be exposed to different approaches for analyzing such data using multivariate techniques, and he/she will be given the opportunity to creatively explore the data on his/her own. Finally, the student will also gain substantial experience in reading primary literature, preparing a scientific seminar, and eventually writing up results and submitting them to a journal for review.
Additional Project Details

Randall De Jong and John Wertz, Biology
Project #2 Exploring Bacteriophages in Microbe-Host Symbiotic Systems
There are estimated to be 10^31 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. Applicants should have an interest in learning some bioinformatics and have had
prior training in basic microbiological techniques.
Benefit to student: Student will learn bioinformatics and genomic analysis techniques. Student will learn molecular biology lab techniques – PCR, quantitative PCR, digital PCR, and DNA sequencing. Student will perfect their sterile technique. Student will play an important role in analyzing data to be published.
Additional Calvin faculty working on project: Serita Nelesen, Computer Science

Randall DeJong, Biology
Project #3 Microbial monitoring of the Lower Grand River watershed in Kent County, MI
The Grand River is the longest river in Michigan and is a significant tributary to Lake Michigan. The river runs through the heart of Grand Rapids, but the namesake rapids were eliminated more than 150 years ago. Currently, plans for restoring the rapids are under development, with a vision of increased aesthetics, river health, wildlife habitat, and recreational opportunities. There is a need to incorporate knowledge about microbial source pollution in the Grand Rapids area into restoration plans and their implementation. This project will survey at least 10 sites in the Grand River watershed twice each week to collect samples, and will analyze the samples with both conventional microbiological and advanced
molecular techniques. The molecular techniques will utilize a new high throughput instrument that is only
the 3rd of its kind in the state of Michigan. This project is a collaboration with the Michigan Department of
Environmental Quality and is dependent upon pending proposals.
Benefit to student: Students will learn microbiological techniques and standardized water quality procedures. Students will learn advanced molecular techniques, including quantitative and digital PCR. Student may benefit from contact with and training from Michigan DEQ personnel.
Additional Calvin faculty working on project: David Warners (Biology), Gail Heffner (Director of Community Engagement) and Mike Ryskamp (Program Coordinator, Plaster Creek Stewards, Biology) will be consultants.

Keith Grasman, Biology
Project #4 Fish-Eating Birds as Sentinels for Pollution in Aquatic Ecosystems
Description: 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 fish-eating 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.
Benefit to student: Students will gain extensive experience in both ecological field studies and laboratory assays. They will benefit from interactions with other members of the Calvin research team (students and faculty) and with scientists in governmental wildlife agencies (US Fish and Wildlife Service, New York Department of Environmental Conservation) and conservation organizations (Biodiversity Research Institute, Wildlife Conservation Society/Bronx Zoo).

David Koetje, Biology; Herb Fynewever, Chemistry & Biochemistry
Project #5 Assessing the Effectiveness of Investigative Labs in Biology 224 and 225
Description: Two students, co-supervised by Dave Koetje (50%) and Herb Fynewever (50%), 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. Students with interests in analyzing quantitative and qualitative data, writing, and education are strongly encouraged to apply.
Benefit to student: Students will be mentored in a type of research associated with the scholarship of teaching and learning (SoTL). This will involve data analysis, literature review, writing, and collaborative discussions with other science educators. We expect to produce professional-quality learning materials for wide dissemination and to publish a manuscript in a peer-reviewed SoTL journal. Students and faculty will also present this work at professional conferences.
Additional Calvin faculty working on project: Amy Wilsterman (Biology)

Darren Proppe, Biology
Project #6 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 red-breasted 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. Willingness to work in the field and the ability to begin research around sunrise is required. Previous knowledge of bird identification through sight and sound is preferred, but not required (must be committed to developing proficiency in common species before summer begins). The ability to start working 5-10 hours/week during the semester in April and May is a plus, shifting to full time immediately after the semester ends. The student researchers will reside at the Au Sable Institute for 10 weeks and be a member of their summer research program ( Students will complete 2 hours of coursework in research methods and one additional 4 hour course of their choosing. Housing and tuition costs are discounted at $145/week and $2500 for the coursework. In sum, students will gain research experience and complete six hours of academic credit through this program.
Benefit to student:The student involved in this project will learn to identify birds by sight and sound. Further, they will learn techniques for surveying birds and establishing residency at a site. They will also become proficient in finding and monitoring songbird nests for the purpose of determining reproductive success. In addition, the student will spend ample time in the field, providing a valuable introduction to this type of research. This will help the student determine whether field ecology is a career they wish to pursue, while adding research experience to their resume. Their participation with the Au Sable Institute will also provide them with the opportunity to take summer courses and receive 6 hours of academic credit. Lastly, their research results will lead to opportunity for participation at the annual conference for the Michigan Bird Conservation Initiative.
Additional Project Details

Anding Shen, Biology
Project #7 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. Students who have taken Bio333 (The Immunology Course) or who had tissue culture experience are preferred.
Benefit to student: Students will learn valuable research skills and will be trained in scientific reasoning and problem solving.

John Ubels, Biology
Project #8 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.
Benefit to student:
Students will learn state of the art cell and molecular biology techniques, experimental design, data analysis and preparation of manuscripts for publication.
Additional Calvin faculty working on project: Loren Haarsma (Physics)

Randy Van Dragt, Biology
Project #9 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.
Benefit to student:
The project will give students strong experience in field data recording, tree identification, GIS mapping, and the processing of large data sets.
Additional Project Details

Randy Van Dragt, Biology
Project #10 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.
Benefit to student: The project will introduce the student to research at the level of the biological community and will involve sampling design, becoming familiar with insect taxonomy and identification, the use of community diversity and similarity indices, and statistical analysis of large data sets.
Additional Calvin faculty working on project: None directly though the project is coordinated with the phenological work done by Dave Warner's student at Flat Iron Lake.
Additional Calvin faculty working on project: Dave Warners, Biology, will interact on some of the restoration activities the stewards engage in.

Randy Van Dragt, Biology
Project #11 Land Stewardship in the Ecosystem Preserve
Description: 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. The work consists of about 50% management and maintenance and 50%
research related activities. The stewardship position runs for 12 weeks.
Benefit to student: Students will learn the natural history and ecology of many animals native to West Michigan. They will learn techniques for sampling mammal populations and for describing the breeding behavior of the birds that frequent the preserve. They will also be exposed to and gain proficiency in a wide variety of techniques used in habitat maintenance.

Dave Warners, Biology
Project #12
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. Students interested in this project
will be willing to work outdoors in all kinds of weather and willing to invest in challenging physical labor.
Benefit to student: Ecological restoration skills will be gained, along with experience conducting field experiments.
Additional Calvin faculty working on project: Gail Heffner (Director of Community Engagement)

Warners, Dave, Biology
Project #13 Plant Responses to Climate Change at Flat Iron Lake Preserve
This project will take place at Flat Iron Lake, during which time the student will be expected to live in a Calvin-owned house at Flat Iron Lake with one other student. 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. The student who takes on this project 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.
Benefit to student: It will provide a hands-on field botany experience, as well as involvement in field-based scientific research.

Warners, Dave, Biology
Project #14 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.
Benefit to student: This student will be involved in basic, field based data collection and processing with real world implications. The water quality project will follow protocol developed by the Michigan Department of Environmental Quality, providing students with valuable preparation for graduate school or job applications.
Additional Calvin faculty working on project: Gail Heffner (Director of Community Engagement) and Mike Ryskamp (Program Coordinator, Plaster Creek Stewards, Biology)

John Wertz, Biology
Project #15
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). Applicants will need to have prior training in basic microbiological techniques.
Benefit to student: The student will benefit from the preparation (including background research), implementation, correct recording, and troubleshooting of laboratory experiments. The student will also learn how to communicate effectively and work both independently and as part of a larger research team. He/she will learn classic microbiological and chemical techniques (e.g. media preparation, spec-trophotometry, HPLC) and use cutting edge equipment (e.g. Fluidigm Biomark) to engage the microbes ecophysiologically using systems thinking. They will be expected to translate these results, using systems thinking, into hypotheses about the role of these bacteria in the ant gut. The student will deeply engage the literature regarding physiological characterization and naming of novel bacteria, garnering expertise from others within that field via direct communications. The student will also need to communicate with and report findings to collaborators at Drexel University and The Field Museum. Thorough characterization, proper naming, and engagement in the writing process will earn the student the opportunity to participate as a co-author on a peer-reviewed publication.

Chemistry & Biochemistry projects

Carolyn Anderson, Chemistry & Biochemistry
Project #16 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 N-alkyl 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.
Benefit to student: 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.
Additional Calvin faculty working on project:
Roger DeKock, Chemistry & Biochemistry

Carolyn Anderson, Chemistry & Biochemistry
Project #17 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.
Benefit to student: 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.

Carolyn Anderson, Chemistry & Biochemistry
Project #18 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 $- and %-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
Benefit to student: The students will gain experience with synthetic organic chemistry techniques, including: running reactions, purification, organic spectroscopy, and experimental design.

Eric Arnoys, Chemistry & Biochemistry
Project #19 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.
The student will serve as a research collaborator in a collaborative project with Profs. Louters and
Looyenga, learning both common and state-of-the-art biochemistry experimental techniques. In addition
to learning about how research works, he or she will also gain valuable experience and will have the
opportunity to serve as a co-author on research papers. No previous research experience or biochemistry
coursework is required; a love of lab work and at least one college-level chemistry course are a must.
Students interested in a multi-year research experience are strongly encouraged to apply.
Benefit to student: The student will serve as a research collaborator, learning both common and state-of-the-art biochemistry experimental techniques. In addition to learning about how research works, he or she will also gain valuable experience and will have the opportunity to serve as a co-author on research papers. Other students have already benefitted from this project, as it has provided independent projects for 40+ students in Chem 383 over the last few years.
Additional Calvin faculty working on project: Larry Louters and Brendan Looyenga (Chemistry & Biochemistry)

Michael Barbachyhn, Chemistry & Biochemistry
Project #20 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.
Benefit to student:
Students participating in this research will learn fundamental laboratory techniques associated with organic synthesis. These include handling air-sensitive reagents, running temperature controlled reactions, and learning extractive workup techniques and purification methods, especially column chromatography. Analytical methods, including spectral determinations (NMR, IR, MS) and HPLC purity assessments will also be experienced. The developed methodology may have utility in the subsequent synthesis of derivatives with therapeutic potential. Finally, presentation of this work in a poster(s) and publication of this work in peer-reviewed journals will provide the student with external visibility in the scientific community.

David Benson, Chemistry & Biochemistry
Project #21 Proteins as antioxidants
Most antioxidants are low molecular weight molecules that are sacrificially oxidized in the presence of oxidants produced by the immune system. The Benson laboratory has found that a covalent cross 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.
Benefit to student:
Students performing this research will be provided with a biochemical research experience. They will know how to purify and characterize a protein using recombinant DNA techniques and chromatography

Roger De Kock, Chemistry & Biochemistry
Project #22 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).
Benefit to student:
The student will learn about computer modeling in chemistry. Specifically, the student will learn about Hartree Fock theory, and how it is implemented in GAMESS (General Atomic and Molecular Electronic Structure System). The student will also learn much about reading the literature in the field, and
preparing written, oral, and poster reports on the project.
Additional Project Details

Brendan Looyenga, Chemistry & Biochemistry
Project #23 Cell Signaling and Endocytosis in Kidney Cancer
Recent work in the field of cancer research has demonstrated that functional alterations of the cellular trafficking machinery that regulates important cell signaling proteins is 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 activity3due to its genomic
amplification or mutation3modifies 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.
This project provides an excellent basis for training undergraduate students in the principles of cellular
transformation, as well as the experimental tools required to answer mechanistic questions about these
principles in the laboratory.
Benefit to student: This proposal impinges on the three core disciplines of molecular cell biology research. Students will be presented with the genetic basis of cancer (gene amplification and mutation), the unique cell biology of cancer cells (proliferation, survival, contact independence, anchorage independent growth), and the biochemistry of cell signaling (kinase cascades). Though these examples are specifically applied to oncology, the research concepts are formative for nearly all fields of molecular and biomedical research.
Three central educational purposes of this proposal are: 1) to provide training for undergraduate students
in the intellectual discipline of research; 2) to provide training in a variety of research techniques; 3) to
provide training in scientific communication, both oral and written. Students will be involved in all phases
of the proposed research including: cell culture, cell transfection/infection, biochemical assays (ELISA,
immunoblot), microscopy, and data analysis. Each student will work side-by-side with the principle
investigator and/or a senior research student until she or he has mastered the appropriate technique and
is able to function independently.
Additional Calvin faculty working on project: Larry Louters and Eric Arnoys (Chemistry & Biochemistry)
Additional Project Details

Larry Louters, Chemistry & Biochemistry
Project #24 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. The research groups of Professors Arnoys, Looyenga and will be integrated into a single team.
Benefit to student:
Learn to do research in a team setting.
Additional Calvin faculty working on project: Eric Arnoys and Brendan Looyenga, Chemistry & Biochemistry

Larry Louters, Chemistry & Biochemistry
Project #25 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. The research groups of Professors Arnoys, Looyenga and will be integrated into a single team.
Benefit to student: Students will learn to do research in a team setting.
Additional Calvin faculty working on project: Eric Arnoys and Brendan Looyenga, Chemistry & Biochemistry

Mark Muyskens, Chemistry & Biochemistry
Project #26 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.
Benefit to student: The student will gain experience applying models for analysis of new experimental data with a focus on preparing publication.

Kumar Sinniah, Chemistry & Biochemistry
Project #27 Characterizing Riboflavin Conjugated Nanoparticles for Targeted Drug Delivery in Chemotherapeutics
Description: 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. This project is suitable for a student interested in
Benefit to student: This is a biomedical research project which involves collaboration with a team of scientists in the biomedical sciences program at the University of Michigan. The students will benefit from developing experimental skills, preparing surfaces for nanoscale measurements, learning to operate the atomic force microscope, and analyzing data based on models for single molecule analysis. The student will be mentored by a senior student and Dr. Sinniah.

Kumar Sinniah, Chemistry & Biochemistry
Project #28 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.
Benefit to student:
Students will be trained in research methodologies, learn critical thinking skills and get to do hands-on scientific research. Students will learn how to operate the isothermal titration calorimeter and the differential scanning calorimeter. These instruments provide the gold standard for measuring thermodynamic parameters for protein-ligand interactions. Student working on this project will work alongside a senior student and mentored by Dr. Sinniah.

Douglas Vander Griend, Chemistry & Biochemistry
Project #29 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. I anticipate that the students will not only get ample hands on experience with making up solutions and mastering several analytical devices, but also have a chance to interact with other research labs. It is ideal for first or second year students.
Benefit to student: Students on this project will
1) learn to prepare, study, and characterize solution phase systems
2) conduct their own arm of research on a particular system
3) present their research to other researchers
4) learn to write about their research in a succinct and professional manner
5) familiarize themselves with the graduate school environment for chemistry

Computer Science projects

Joel Adams, Computer Science
Project #30 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
Benefit to student: By the end of the summer, these students will be more knowledgable about parallel / high performance computing technologies than most college computer science professors. The experience will look great on graduate school applications, especially if the students present at the SC14 conference. The students will also have the opportunity to meet and network with other students who are working on this project from Macalester, St Olaf, and other colleges.

Victor Norman, Computer Science
Project #31 Developing a Scratch interface for the Greenfoot programming environment
Description: Most CS outreach programs introduce students to program using MIT's Scratch programming environment -- a wonderful drag-and-drop graphical programming environment that students love. However, soon students tire of the limited capabilities of Scratch and need to learn to program in a "real" language, like Java. The Greenfoot programming environment uses Java, but has many similarities to Scratch -- a 2D canvas to work on, support to representing objects with images, and a built-in event loop to run actions. However, it lacks the full interface that Scratch has for moving objects, detecting
collisions, drawing, etc. Its biggest difference, however, is in a lack of support for multi-threading. In
Scratch, you can build multiple "action loops" that operate on one object. Students get used to this
programming style, and then find it missing in Greenfoot. The goal of this research is to alter Greenfoot's
source code to support this multi-threading interface, thus allowing a smoother transition for students
from Scratch to Greenfoot/Java.
Benefit to student: The student researcher will learn:
1. how to read, navigate, and alter a large source code project that they have not written.
2. the inner workings of multi-threading in Java.
3. how to design and implement an interface to provide multi-threading support for the introductory programmer.
4. how. to test their code.
5. how to write a paper describing their results

Harry Plantinga, Computer Science
Project #32 Research on the Semantic Web
In this project the student will learn about and use semantic web technologies and a semantic reasoning system to create an information page about books, people, places, or other entitites. Information will be gathered from knowledge repositories such as DBPedia and Freebase. Some of the information may be generated by deduction from other facts. The resulting pages will be used by millions of people each year at
Benefit to students: The student will learn web development, semantic web technologies, and reasoning systems.

Engineering projects

Xiuhua Si, Engineering
Project #33 Electric and Magnetic Focusing and Navigation for Ingtranasal Target Drug Delivery
Intranasal olfactory drug delivery provides a noninvasive practical method of bypassing the BBB(Blood- Brain-Barrier) and directly delivers the medications to the brain and spinal cord. The BBB has forestalled the use of many new genetically engineered drugs for treating central nervous systems (CNS) disorders such as Alzheimer’s [1,2]. 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 [1]. However, demonstration of its clinical feasibility is still in adolescence due to the lack of devices that effectively deliver medications to the olfactory epithelium. While there are vast options of nasal delivery devices available on the market, devices designed for selective olfactory deposition have not yet been found [2]. Without better options, the limitations of conventional nasal devices are obvious, only a very small faction of therapeutic agents deposits in the olfactory region, which may possibly enter the brain via the extracellular epithelial pathway [3]. Previous studies [4, 5] have shown that less than 1% of nasalinhaled particles could reach the olfactory nerves which are secluded in the upmost nasal cavity
Therefore, 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. The feasibility of this method was numerically
evaluated with three designs in an idealized 2-D model [6,7]. The influences of drug release positions at
the nostrils were also studied. It was observed that applying electrophoretic forces significantly enhanced
the dosage to the olfactory region.
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.
With similar mechanism of electrophoretic drug delivery, magnetic force is the other applicable one to
control the aerosol particles through nasal airway to the targeted area if the aerosol particles are
magnetized. 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.
[1] Mistry, A., Stolnik, S., and Illum, L., 2009, “Nanoparticles for Direct Nose-to-Brain Delivery of Drugs,”
Int. J. Pharm., 379, pp. 146-157.
[2] Hanson, L., and Frey, W., 2007, “Strategies for Intranasal Delivery of Therapeutics for the Prevention
and Treatment of NeuroAIDS,” J. Neuroimmune Pharmacol., 2, pp. 81-86
[3] Misra, A., and Kher, G., 2012, “Drug Delivery Systems from Nose to Brain,” Curr. Pharm. Biotechnol.,
13, pp. 2355-2379
[4] Shi, H., Kleinstreuer, C., and Zhang, Z., 2006, “Laminar Airflow and Nanoparticle or Vapor Deposition
in a Human Nasal Cavity Model,” J. Biomech. Eng.- T ASME, 128, pp. 697-706
[5] Si, X., Xi, J., Kim, J. W., Zhou, Y., and Zhong, H., 2013, “Modeling of Release Position and Ventilation
Effects on Olfactory Aerosol Drug Delivery,” Respir. Physiol. Neurobiol., 186(1), pp. 22-32.
[6] Jinxiang Xi, Xiuhua Si, and Rachel Gaide, 2014, “Electrophoretic Particle Guidance Signicantly
Enhances Olfactory Drug Delivery: A feasibility Study” PLOS ONE, 9(1), e86593.
Benefit to student: Students will work closely with the professor during this whole project. The students will learn how to do research and solve different problems with their knowledge learned in class. This will enhance their understanding of their class study. Students will also learn to use different instruments to do experiments and learn to use engineering software Comsol Multiphysics, which is a powerful multidisciplinary tool and becomes more and more popular among engineering companies. Comsol software will be a great tool to use to solve problems in students’ future course study and for their future job. This skill will be a good selling point for students’ job hunting.
Additional Project Details

David Wunder, Engineering
Project #34 Bagasse Charcoal: A Novel Water Treatment Approach for Developing Global Regions
Wood charcoal (WC) is broadly used in developing global regions (DGR) for heating and cooking. In many regions, WC production contributes to deforestation, which can exacerbate global climate change and increase the adverse effects of soil erosion and flooding. Bagasse, the sugarcane residual from processing, is an alternative and sustainable source for charcoal. Although studied as a fuel source,
bagasse charcoal (BC) also has potential additional value for water treatment. This research builds on
earlier investigations of the sorption of fluoride and pesticides to bagasse charcoal , focuses on the
evaluation of bench-scale BC columns for water treatment and the development of field study
methodolody for (future) in-country testing of BC for water treatment.
Benefit to student: Research experience. Experimental and prototype design experience. Linking passions with gifts.
Additional Project Details: Combines research that has basic/applied elements, along with great potential for service-learning experiences (and scholarship).

David Wunder, Engineering
Project #35 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.
Benefit to students: Research experience. Experiment and system design experience. Combining passions with gifts.
Additional Project Details: This line of research continues successful publication of externally funded research.

Geology, Geography & Environmental Studies projects

Jonathan Bascom, Geology, Geography & Environmental Studies
Project #36 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.
Mesfin Woldemariam’s An Introductory Geography of Ethiopia (1972) is the only published geography of
Ethiopia, which is now the 12th largest country in the world. Lack of a recent text hampers teaching,
learning and the advancement of scholarly research. A replacement is long overdue. Aided by Fulbright
grants in Ethiopia during the last two years, Professor Bascom worked with geographers from all seven
graduate programs in the country to launch a new geography of Ethiopia. We have produced a
preliminary set of maps and written more than 100,000 words of narrative, which are currently being
edited with grant support.
Significantly, this online book – A Contemporary Geography of Ethiopia – will support the delivery of the
recently harmonized geography curriculum for the twenty-nine geography departments in Ethiopian
universities. The ultimate goal is to produce a book with a chapter for each of twenty geography courses
that comprise the curriculum for university-level geography in Ethiopia. While printable, a cloud-accessed
text allows for expansion, feedback, updates, unlimited color graphics, data banks behind pages, portals
to related sites and more.
Helping to change the culture of learning and teaching is a central aim of this project. Although lecturing
and rote memorization are the normative modes in most developing countries like Ethiopia, teaching by
way of interactive story maps, will help transform the relatively passive pedagogy. Our aim is to supply
both professors and students with Ethiopian spatial data, steer their interaction with that data, assist
them to build web maps with storytelling templates and to substantiate the geographic story associated
with a given map. The goal is for students to become cartographic authors. The power of such an
approach is that it moves move students into active learning, critical thinking and problem-solving
The next step is to transfer the project into Esri’s storybook app, which will serve as its platform. This
summer’s project will construct a prototype of several chapters to pilot test with geographers in Ethiopia.
The selected student(s) will assemble raw materials, build web maps and publish them into templates.
Esri has developed to enable various kinds of storytelling. (See for examples of
various templates.)
This project has five main aims:
1. To publish a new geography of Ethiopia;
2. To facilitate collaborate authorship between students and professors, both in the US and Ethiopia;
3. To demonstrate the capability of Esri’s templates and apps to construct a web-based academic
4. To demonstrate the value of storytelling maps as a method for learning, teaching and doing
5. To illustrate the utility of a storytelling textbook to serve a university curriculum in a developing
Benefit to student: Students will benefit by learning the geography of Ethiopia as well as how to create effect interactive web maps. The selected student(s) are likely to accompany Professor Bascom on a trip to Esri headquarters in Redlands, CA to consult with the storytelling-with-maps team about The Contemporary Geography of Ethiopia book project. (Allen Carroll, former chief cartographer at National Geographic, leads a team at Esri that publishes story maps.) The recipient(s) will contribute to a significant educational development project.

Mark Bjelland, Geology, Geography & Environmental Studies
Project #37 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. GIS skills equivalent to GEOG-261 are required.
Benefit to student: Students will gain experience with research design, archival research, and the use of ArcGIS and spreadsheet software. Students will also develop a much greater appreciation for the geography of Michigan and the manufacturing legacy of its towns and cities.
Additional Project Details

Mathematics & Statistics projects

John Ferdinands, Mathematics & Statistics
Project #38 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.
Benefit to student: They will experience doing mathematical research in a familiar area, one that they saw in second semester calculus.

James Turner, Mathematics & Statistics
Project #39 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 4-manifolds 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.
Benefit to student: First, the project will expose students to some current trends in research in algebraic topology. They will thus gain experience in working with graduate level mathematics which will be beneficial for their advancement. They will also gain experience writing up results and submitting them for publication, as well as, presenting their results in colloquia and conferences.

Nursing projects

Adejoke Ayoola, Nursing
Project #40 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.
Benefit to student: We are in the second year of this project, we are still recruiting participants and nursing students have been involved in recruitment, delivering the intervention, and conducting surveys at the different stages of this study. Nursing student/CHW teams will start 12 months survey in 2014 spring semester. Six nursing student research assistants will be hired for 2014 summer semester to complete home visits. Nursing student research assistant/CHW teams will provide monthly home visits during the 3rd to 6th month, and conduct the 6-month, 12 month, and 18 month survey as needed during the summer
semester. These students will also be involved in entering study data. The Center for Social Research will
provide training for the nursing research assistants in survey data entry and direct student-to-student
support for database and methodological issues. This involvement will provide opportunities to develop
students’ knowledge in evidence-based practice, especially in the area of maternal/child health nursing. Additional Calvin faculty working on project: Gail Zandee, Nursing
Additional Project Details

Jesse Moes, Nursing
Project #41 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. Preference will be given to nursing students interested in pursuing graduate education.
Benefit to student: Students interested in participating in this project will gain research experience in recruiting and retaining participants, conducting interviews/completing surveys, collecting, entering, and analyzing data, and presenting project findings during a poster presentation. In addition, students will rely on strong organizational skills, critical thinking, and self-sufficiency. Students will also learn about the relationships among pain, activity, and foot health.
Additional Calvin faculty working on project: Elizabeth Byma, Suzan Couzens and Renae Boss Potts, Nursing. Dr. Elizabeth Byma has significant expertise in the areas of pain and symptom management. Suzan Couzens is also assisting with the project design and implementation. Suzan is a community health nurse and has extensive partnerships with homeless residents and community organizations in the Heartside neighborhood. Renae Boss Potts has extensive clinical experience and will assist with conducting focused foot health assessments.
Additional Project Details

Physics & Astronomy projects

Loren Haarsma, Physics & Astronomy
Project #42 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.
Benefit to student: The student will gain knowledge of ion channels, corneal epithelial cells, cell culturing techniques, and siRNA transfection methods. The student will gain extensive experience with whole-cell patch-clamp electrophysiology techniques and data analysis.
Additional Calvin faculty working on project: John Ubels, Biology
Additional Project Details

Loren Haarsma, Physics & Astronomy
Project #43 Programming and optimizing an agent-based computer simulation of a self-organized, interdependent economy
Over the last several summers, Calvin undergraduates have programmed an “agent-based” computer simulation similar to computer games such as SimCity and Life. In this simulation, computer agents gather resources, invent tools and trade with other agents. Over time a complex network of
interdependencies develops among the agents. This is a model of the development of economic
relationships that exist in modern, technologically-advanced economies. The purpose of this model is to
investigate the variables which affect the growth of wealth and inequality within such an interdependent
economy. This summer, a student will work with professors in economics, computer science, and physics
to add functionality to the existing computer model by adding human virtues and vices to agent behavior
and social institutions to the trading scenarios. The programming project might also include
“parallelizing” the code, to vastly reduce runtime. Students should know or be able to quickly learn the
C++ programming language. Students having had at least one economics course are preferred.
Benefit to student:
The student will gain knowledge of and experience with computer modeling methods. The student will both write computer code and work with the professors in evaluating the performance of the model. The model will be based on agent-interaction, and features of this computer model are inspired by economics and evolutionary biology. Thus, many of the skills learned in this project should be transferable to other computer modeling projects in the natural and social sciences. We will also write a paper based on the results for submission to a professional journal.
Additional Calvin faculty working on project: Becky Haney (Economics) and Vic Norman (Computer Science) Prof. Haney has expertise in both economics and computer modeling. Prof. Norman has
expertise in computer programming, code optimization, and open-source software.
Additional Project Details

Paul Harper, Physics & Astronomy
Project #44 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. The results of this work will be utilized in upcoming X-ray diffraction
measurements that I will be making in collaboration with Prof. Horia Petrache of IUPUI (Indiana
University, Purdue University at Indianapolis).
Benefit to student: Students will benefit by performing original research on lipid kinetics, constructing samples, taking and analyzing data, and devising models of the observed behavior. Potentially, their results will be presented at the national Biophysical Society Meeting and published.

Larry Molnar, Physics & Astronomy
Project #45 Asteroid Collisions
Description: 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.
Benefit to student: In general, a project like this is an opportunity for the student to learn the observational techniques of photometric astronomy (precise determination of brightness with time) and the theoretical techniques of orbital dynamics, and to coauthor a significant research paper. Previous students on this project have coauthored research papers and received offers of fellowships to graduate programs.
Additional Project Details

Larry Molnar, Physics & Astronomy
Project #46 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
Benefit to student:
In general, a project like this is an opportunity for the student to learn the observational techniques of photometric astronomy (precise determination of brightness with time) and the theory of synthesizing light curves (variation of brightness over time as the stars orbit), and to coauthor a significant research paper. Previous students on this project have coauthored research papers.
Additional Project Details

Matthew Walhout, Physics & Astronomy
Project #47 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.
Benefit to student: Students will become familiar with laboratory techniques that are essential in university-level research today. Experience in this laboratory has been a significant strength in the grad-school applications of recent Calvin graduates. Current support from the NSF lends credibility to the scientific relevance of the students' training.



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Past funding