2015 On-campus Summer Research Projects

2015 On-campus Summer Research Projects
Bebej, Ryan
Funded by
Project Title and Abstract
Evaluating changes in hind limb form and function to assess evolution of swimming mode in early cetaceans 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 limb-powered to tail-powered swimming 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 for
understanding the functional implications of hind limb morphology (particularly of the pelvis and femur) in fossil whales in
the context of modern mammals. It will involve working with zoological and paleontological museum specimens to document
and quantify differences in hind limb form and function. Analytical techniques will incorporate multivariate statistical
analyses and possible exploration of geometric morphometrics, but student-initiated approaches to analyzing data will be
Research will involve trips to the University of Michigan Museums of Zoology and Paleontology, work with modern and
fossil skeletal material, and introductions to specimen photography and data analysis.
Andre Otte,
Thuy Tien
YeaEun Lee
Department of
Geographic and Taxonomic Sourcing of Bacterial Contamination in Plaster Creek E. coli levels in Plaster Creek
consistently exceed state standards for total and partial body contact (some samples from 2014 revealed levels 50x higher
than what is considered safe for partial body contact). Most of these samples were collected from the main channel of Plaster
Creek, and this sampling shows large fluctuations over time. Therefore, it has been difficult to specify the primary source(s)
of bacterial contamination. The goals of this project are 1) to understand the relative contributions of E. coli loading into
Plaster Creek from 10 major tributaries and prioritize the five most egregious contributors; 2) to identify primary taxonomic
sources within the highest 5 sub-watersheds using molecular markers; and 3) to pinpoint E. coli loading locations in the
highest 5 sub-watersheds using molecular markers and using scent-trained canines in sub-watersheds where human E. coli
has been identified. Students will also help to assemble, organize, and interpret the resulting dataset of E. coli concentrations
(CFUs/100 ml), under both wet and dry conditions, from the main tributaries of Plaster Creek. An additional objective of this
project will be to consolidate all known bacterial sampling data that has been done in Plaster Creek (from work done by
MDEQ, WMEAC, Health Department, and Calvin College) into one cohesive data set. This standardized data set will be
useful for understanding long term fluctuations and for identifying seasonal and weather-related patterns in E. coli
abundance, as well as helping to identify the major entry points of bacteria into Plaster Creek.‚Äč
Grasman, Keith Biology
Alaina Mahn,
Jenna Van
Bruggen, David
The William H.
and Celia I.
DeVries Family
The Clarence
(Bud) Star and
Arlene Talen
Star Student
US Fish &
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 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
Proppe, Darren Biology
The Jansma
Research Fund
in the Sciences
and Business
Conspecific attraction: Does noise reduce songbird establishment in areas with song playback? Songbirds are less likely
to be found in areas with high levels of noise. However, 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. The goal of this research
is ultimately to test whether conspecific playback can be used in urban areas to enhance songbird diversity. The work is being
conducted in three stages. The first, completed last summer, was to test conspecific playback as a tool to increase bird
populations in non-noisy areas. The final stage will be to test conspecific playback in the urban setting. However, first we
need to test the effects of noise in a context free of other changes that are found in urban environments. To do this, I am
seeking two student researchers that will assess bird populations in undeveloped forest in Northern Michigan near the Au
Sable Institute. The selected students will survey birds daily by sight and sound at 18-20 field sites, and potentially capture
songbirds with mist nets to assess productivity within those sites. 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. This research is being conducted jointly with the Au Sable Institute for Environmental Studies (ausable.org). The
students will reside at the Au Sable Institute from May 18 - August 14, 2015. As part of their experience, students will enroll
in a May term course on Field Ecology of Birds (4 hours, 300 level credit towards biology major) and a Summer I and II
course in Research Methods (2 hours). Research students are asked not to enroll in additional coursework during Summer
Session I, but may opt to take an additional course during Summer Session II. Room and board is covered by the Au Sable
Institute. Courses fees are reduced by 50% for student researchers ($317.50/credit). Students will receive the normal $3800
stipend from the Calvin College Science Division. Unless already completed, biology students are normally expected enroll
in Biol 399 the following fall semester.
Shen, Anding
Praamsma, Seth
Verkaik, Jared
Institutes of
Health (NIH),
Grand Valley
The roles of endothelial cells on HIV-1 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 CD4+ T cell
numbers. However, a major latent reservoir identified in resting CD4+ T cells poses a great barrier to eradication and ensures
viral persistence in patients. The understanding of how such a latent reservoir is formed is quite limited. A more complete
understanding of the mechanisms contributing to the establishment of the reservoir will influence the strategies in battling
viral persistence. The overall goal of this study is to investigate the roles of endothelial cells on HIV-1 infection and latency
in resting CD4+ T cells. Students will be working with human blood cells and a non-infectious pseudotyped virus. The
knowledge gained from this study will significantly improve the understanding of HIV latent reservoir formation and will
influence the strategies in battling viral persistence. It will also provide insight into the mechanisms contributing to HIV
infection of CD4+ T cells and may contribute to potential innovative intervention.
Ubels, John
John Leerar,
Micah Warners
Institutes of
Health (NIH)
Protection of the cornea from UVB radiation by elevated potassium in tears
Warners, David Biology
Gail Heffner
Habitat Restoration with Green Team High School Students These college students will help supervise and work
alongside the Plaster Creek Stewards summer Green Team, a group of paid high school students who gain experience
learning how to implement and maintain green-infrastructure development projects. Responsibilities will include greenhouse
and nursery management, off campus project installations, seed collecting, and planning and guiding the high school student
activities. This position will afford opportunities for coordinating efforts between the Plaster Creek Green Team and a new
Green Team that is starting up in the Rogue River Watershed (near Rockford, Michigan). Besides helping to educate high
school students this work will also provide opportunities to practice Spanish and engage in cross-cultural relationships.
Warners, David Biology
Jeremy Brands, Fritz and Carol
Plant Responses to Climate Change at Flat Iron Lake Preserve This project will take place at Flat Iron Lake. It 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. In addition the student will collect data on the impacts of spring controlled
burning on the composition and productivity of the prairie ecosystem at Flat Iron Lake. This student will be contributing to a
long term data set on the flowering period of several native prairie species. This year the student will also be collecting data
to assess the impact of controlled burning on litter consumption and biomass productivity.
Warners, David Biology
Wes Dykstra,
Dena Kryger
Ecological Restoration in the Plaster Creek Watershed Students will work closely with Mr. Michael Ryskamp in the
preparation and installation of a variety of restoration projects from small residential rain gardens to large-scale habitat
restorations and bio-retention projects. Additionally, these students will assist in the maintenance of restored areas, and will
become involved in all aspects of plant propagation from seed collecting to out-planting. This work will provide students
with practical, hands-on opportunities to learn about low-impact development and green infrastructure best practices.
Department of
Quality; The
Warners, David Biology
Leanna DeJong Calvin College Experimental Approach to Restoring Native Habitats in Urban Landscapes In this project, the student will work in
Calvin’s greenhouses, tree nursery, and at sites on and off campus investigating the re-introduction of native plants and native
habitats into urban areas. Part of this work will involve collecting and processing data from an experimental prairie planting
near the Prince Conference Center, assessing the best soil conditions for establishing native prairie plants. The student will
also work with Dr. Warners in designing and installing an expansion of this experimental restoration planting. This student
will also assist with restoration projects done off campus by Plaster Creek Stewards, with particular focus on developing
sampling protocol to monitor the success of these projects over time.
Warners, David Biology
Leisman, Emily Foundation;
Van Staalduinen Land
Conservancy of
West Michigan;
Calvin College
Historical Field Botany: A 100-year retrospective assessment of Emma Cole’s Grand Rapids Flora (1901) Over 100
years ago an outstanding botanist named Emma J. Cole published Grand Rapids Flora: A Catalogue of the Flowering Plants
and Ferns Growing Without Cultivation in the Vicinity of Grand Rapids, Michigan (Cole 1901). Since those “horse and
buggy” days enormous changes have taken place within and around Grand Rapids that have impacted the botanical richness
of our region. Yet, Cole’s book remains the most recent comprehensive botanical inventory of Greater Grand Rapids. The
primary goals of this research project are to identify and gain access to as many of the specific locations described by Cole as
possible, evaluating their present-day status compared with her descriptions from 1901. In some cases, whole natural areas
have been lost, whereas in some cases remnant vegetation has persisted. The project will involve collecting and identifying
the plants of these areas, with specimens deposited in the Calvin College Herbarium to document the study. Certain sites
deemed as potentially high quality will receive more concentrated investigation. Students involved in this project will also
help to determine the current status of the 34 species listed by Cole that are presently considered rare and endangered in the
state of Michigan. These students will work closely with Drs. Garrett Crow and David Warners, and will collaborate with the
lead botanist of the Michigan Natural Features Inventory with respect to rare plants. The work from this project will
eventually contribute to an updated manuscript, Flora of the Grand Rapids Area.
Wertz, John
Identifying how the ecological and evolutionary interactions between host and symbiont shape holobiont biodiversity
The close association of bacteria with animals and plants, forming complex symbioses, is considered to be a critical factor
behind the evolutionary success of higher eukaryotes. Because the bacteria and host are so intricately connected
physiologically, the two can be considered together as one entity, a “holobiont.” Though there have been many studies on the
diversification of plants and animals, very few have taken into account how the bacteria function in the process of
diversification. In order to study this, we use the model system of the turtle ant. These ants span a broad tropical geographical
range, are taxonomically diverse, and have different feeding habits. Hence, they are ideal for asking questions about the role
of the gut bacteria in geographic and dietary expansion/changes, and eventual diversification. Recently in our lab we have
been able to cultivate several members of the turtle ant gut microbiota, including ones that are unique enough to warrant
placing them into new genera or families of bacteria. 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). Additionally this project will focus on the isolation of additional bacteria from
different genera of Cephalotes ants and making phylogenetic comparisons. Successful applicants will have had prior training
in basic microbiological techniques.
Thomas and
Bonnie Juett
and Gladys and
Ruth Wierenga
Cancer Curriculum Initiative The goal of the CCI is to develop a library of quality, engaging, age-appropriate materials for
children in grades K-12 focused on the topic of cancer for use by classroom teachers (curriculum standards included in lesson
plans) and hospital educators. A student working on this project will assist in the development of educational materials,
assessment tools, and a website to facilitate dissemination of resources. A student that is able to continue work into the
academic year will assist in classroom visits, assessment analysis, and preparation of grant proposals.
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 will 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 in 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, using
the microwave reactor, and experimental design.
Evan Romero
Organic Chemistry: Asymmetric 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 chiral N-substituted pyridones; an interesting functional group found in a series of
pharmacologically interesting compounds. To date, wehave developed a gold(III)-catalyzed method for accessing this motif
by rearranging a related system in a racemic fashion. The student working in this area will be responsible for trying to
develop an asymmetric version of this rearrangement. The student will gain experience with synthetic organic chemistry and
analytical techniques, including: running reactions, purification, organic spectroscopy, chiral HPLC and experimental design.
Connor Reidy
Organic Chemistry: 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 students working in this area will be responsible for exploring and optimizing the
gold(I)-catalyzed rearrangement. The students 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.
Karine Rose
Synthesis of Beta- and Gamma-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 beta- and gamma-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 student working
in this area will continue to seek conditions for the preparation of this intermediate and its conversion into the desired amino
acids. The student will gain experience with synthetic organic chemistry techniques, including: running reactions,
purification, organic spectroscopy, and experimental design.
Arnoys, Eric
Adam Doorn,
Institutes of
Health (NIH)
Watching Membrane Proteins in Living Cells 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 Prof. Louters and Prof. 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.
Baker, Rachael Chemistry
Luke and
Pauline Schaap
The Role of Ubiquitination in Ras-Driven Signaling More than one third of all human cancers are caused by small changes
in the protein Ras. Recently, Ras was shown to be modified by a second protein, ubiquitin, in a process called ubiquitination.
Intriguingly, pancreatic Ras-driven tumors are smaller in the absence of ubiquitination. These findings suggest that
ubiquitination may be important for how Ras causes cancer. I previously developed a novel method to add ubiquitin to Ras in
vitro and performed detailed studies that showed how ubiquitination alters Ras activation. However, questions still remain
about the role of ubiquitination in Ras signaling in vivo. One challenge impeding progress is that Ras regulation and
signaling in human cells is complex, making it difficult to isolate the effect of a single event like ubiquitination. We will
study Ras ubiquitination in the yeast model system, where signaling pathways are conserved, yet simplified, and powerful
genetic tools are available. We hypothesize that site- and isoform-specific ubiquitination of Ras will be important for pathway
activation. Students working on the project will gain experience with experimental techniques including cloning, western
blots, yeast cell culture, protein purification, biochemical assays, and experimental design.
Alex Boomsma,
Sherrice Zhang
The Enno
Brummel Chair
The Iodocyclocarbamation Reaction of N-Allyl-, N-Dienylmethyl-, and N-Allenylmethyl-N-arylcarbamates: Scope and
Limitations The 5-substituted 3-aryl-2-oxazolidinone ring system can be considered a privileged chemical scaffold by virtue
of its being a core structural feature of marketed therapeutic agents such as linezolid (antibacterial agent), rivaroxaban
(anticoagulant) and toloxatone (antidepressant), amongst others. The iodocyclocarbamation reaction of N-allyl-Narylcarbamates, available in two steps from commercially available aromatic amine precursors, provides ready access to
racemic 5-(iodomethyl)-3-aryl-2-oxazolidinones. In 2014 we prepared >12 oxazolidinone derivatives of this type. These
advanced intermediates have utility in allowing synthetic access to privileged substances such as those mentioned above. In
fact, we completed a total synthesis of racemic linezolid from the requisite substituted aniline in 6 steps and ~50% overall
yield. To our knowledge, there is only one published example of this N-aryl variation of the classic iodocyclocarbamation
reaction and much more work remains to be done in order to establish the scope and limitations of this synthetic approach.
Some additional examples in the N-allylated series will be prepared. We will also explore the extension of this chemistry to
new N-dienylmethyl and N-allenylmethyl N-arylcarbamates to further probe the generality of the iodocyclocarbamation
process and provide access to uniquely functionalized oxazolidinone C-5 side chains.
Benson, David Chemistry
Susan Hromada, Beckman
Anti-Oxidant Nature of Tyrosine-Cysteine Crosslinks in BF4112 The covalent bond between tyrosine and cysteine amino
acid sidechains in proteins could potentially provide anti-oxidant chemistry. This project will characterize how the covalent
bond (crosslink) between a tyrosine and cysteine in an orphan protein (BF4112) occurs. Our research group found this
crosslink for the first time, but we are using this protein to "test drive" a variety of formation chemistries. We are
interested in copper, iron, and manganese-based oxidations that are biologically inspired.
DeKock, Roger Chemistry
Jared Weidman,
Matt Genzink
(student at
Grove City
College), Lucas
Van Laar
Trends in the Electronic Structure of Atoms We plan to complete theoretical studies on several atomic systems 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, 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, and 3) a theoretical interpretation of the relationship between atomic size and sequential atomic
ionization energies. We employ the GAMESS software, and the Constrained Unrestricted Hartree-Fock (CUHF) model
within GAMESS (General Atomic and Molecular Electronic Structure System).
Camille and
Henry Drefus
Stephen Lander, National
Kylee Rosette Institutes of
Health (NIH)
Cooperation of LRRK2 and MET in Renal Cancer Growth factor receptors such as MET play an important role in many
different cancers. The genes for growth factor receptors are often amplified, mutated or overexpressed, leading to hyperactive
cell growth. Despite the importance of these genetic changes, however, they are not sufficient to cause cancer by themselves.
Other additional mutations to secondary genes are required to complete the transformation of a normal cell into a cancer cell.
In this study we will focus on the cooperation of two genes--MET and LRRK2--in the context of a kidney cancer called
papillary renal cell carcinoma (pRCC). Both genes are amplified and overexpressed in this cancer, and prior studies from my
lab have shown that LRRK2 amplifies the activity of MET by allowing it to interface with signaling pathways that are not
usually prominently activated by this receptors. We hypothesize that LRRK2 regulates the intracellular sorting of MET
receptors after they are internalized by endocytosis, leading to prolonged retention in the endosome and recycling back to the
cell surface. We will primarily use cell culture models and a variety of biochemical and molecular biology methods to study
this process.
Louters, Larry Chemistry
The role of lipid rafts in the regulation of GLUT1, the predominant glucose transporter in cancer cells It has been
established that activity of membrane proteins can be regulated by its lipid environment. Some transport or receptor proteins
have greater activity when they are moved into small membrane domains known as lipid rafts. We will determine if GLUT1,
a glucose transport protein, moves into or out of these domains when it is activated.
Louters, Larry Chemistry
Leesha Gunnink National
Institutes of
Health (NIH)
Effects of glucose uptake activators on the membrane distribution of GLUT1 Acute activators of glucose uptake such as
hydroxylamine or berberine treatment appear to activate the glucose transporter, GLUT1, without changing the surface
concentration of the transporter. However, the activation may cause a redistribution of the transporter into lipid rafts. We will
explore this possibility by the biochemical isolation of lipid raft protein pre and post activation and determine is altered when
lipid rafts are disrupted. The research groups of Professors Arnoys, Looyenga and will be integrated into a single team.
Louters, Larry Chemistry
Institutes of
Health (NIH)
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.
Shane Bolhuis, The Thedford
P. Dirkse
Photochemistry: Research in Fluorescence of Woody Material Extracts from Local Trees We will investigate the
chemical structure of the highly fluorescent components of the aqueous extracts of woody material in local trees. This project
continues an effort to identify the fluorescent compounds from sycamore wood. The work involves extraction of soluble
compounds, liquid chromatography and other separation techniques and use the full suite of fluorescence spectroscopy tools
available to us.
Ken and
Marcia Wierda
Sinniah, Kumar Chemistry
Lydia DeJonge, The Rollin M.
Abby Leistra
TheDr. Daniel
J. Visser
Fellowship in
the Medical
Brummel Chair
Investigating the Binding of Hexameric Insulin with G-Quadruplex DNA G-quadruplexes are noncanonical DNA
structures formed from guanine-rich DNA sequences in the presence of monovalent cations such as potassium or sodium
ions. These structures are of significant interest due to their role in gene promoter and telomere regions. Over 376,000 sites
in the human genome have been identified as having the potential to form G-quadruplexes. Proteins that bind to Gquadruplex DNA are likely to provide a clue to the role of G-quadruplex DNA in biology. Our group is interested in
studying the physical properties of the interaction between hexameric insulin and the consensus sequence of G-quadruplex
DNA found in the insulin linked polymorphic region. This project is suitable for a student interested in biochemistry or
Sinniah, Kumar Chemistry
Kayla Scholten TheDr. Daniel
J. Visser
Fellowship in
the Medical
Aggregation of Insulin at Interfaces – An Atomic Force Microscopy Study Insulin is one of the most important
pharmaceutical peptides for diabetes treatment. This hormone is produced by pancreatic beta cells and stored predominantly
as zinc-coordinated hexamers in the secretory granules within pancreatic islets. When insulin is released into the blood
stream, insulin binds to its receptor in a monomeric form to regulate glucose metabolism. However, aggregation of insulin
can occur under various conditions such as acidic pH, elevated temperature, hydrophobic interface, ionic strength and
mechanical agitation. In this study we plan to investigate the aggregation of insulin in the presence of G-quadruplex DNA.
We will investigate if the length of G-quadruplex DNA influences the physical and chemical properties of insulin.
Vander Griend, Chemistry
Tasha Thong,
(NSF); Camille
and Henry
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 (at Michigan
State University) to investigate the solution chemistry of variousinorganic and biochemical molecular building blocks as they
interact under conditions of dynamic equilibrium to form nanostructures. A significant element of the research also involves
modeling multi-equilibria systems. This includes modeling artificial data to probe the limits of our mathematical techniques
so that we can better evaluate our models of real data.
Adams, Joel
Chris Dilley,
Patrick Crain
CSinParallel: Tools for Parallel Computing Nearly every modern desktop, laptop, tablet, or phone contains a multicore
processor, which allows it to perform multiple actions simultaneously. Traditional sequential programs only use one of a
processor's cores, leaving the others idle. To take full advantage of such hardware, programs must be written as parallel
programs instead of sequential programs. The two students who work on this NSF-funded project will develop graphical
tools, visualizations, and other educational materials that CS instructors throughout the world can use to teach their students
about parallel computing.
Nelesen, Serita Computer
Javin Unger
The Jansma
Research Fund
in the Sciences
and Business
Educational Impacts in Computer Science Many students' first impressions of computer science come from a college level
course. Thus, their learning experiences in their first course at Calvin (or elsewhere) have an impact on their understanding
of their aptitude in the area and their general understanding of the field. Making this first course the best it can possibly be
then is important for recruitment and retention of students from all populations. Prof. Nelesen has been compiling data to
assess pedagogical interventions in introductory computing classes. This project will involve codifying the various forms of
data collected, and then determining which (if any) interventions had positive impacts on learning. We will write up our
results for publication in a technical conference or journal.
Norman, Victor Computer
Isaac Zylstra
The Jansma
Research Fund
in the Sciences
and Business
Creating a Kinect2Scratch server In the past, a program existed to interface between a Microsoft Kinect and the Scratch
programming environment, allowing users to control Scratch using their bodies. Students have found the combination of
Kinect+Scratch to be great fun. The new version of Scratch (2.0) has a new interface for interacting with external programs or
devices; additionally, a new version of the Microsoft Kinect hardware has been released. Thus, we need to build a new server
to interface between these two. The candidate must be able to program in C#.
DeJong, Rich
Heun, Matt
Toyota Motors Wind Noise Assessment of Toyota Tundra Truck We will be conducting wind tunnel tests of a scale model of the truck
Rovedatti, Jacob Co.
and then assisting in measurements at their test track to develop computer models of the wind noise sources.
Curtis Kortman Program for
Internet of Things Meets Building Energy Efficiency
Kim, Yoon
David Dadzie
Kim, Yoon
Alexis Bonnema Program for
Development of Solar Simulator System with High-Power Multi-Array LEDs
Michmerhuizen Engineering
, Mark
Simulation and Modeling of LED Optical Characteristics
Sykes, Aubrey Engineering
Ha Ram (David) Program for
Program for
Program for
Development of Constant-Current DC-DC Converter Modules for High Power LEDs
Impacts of Green Roofs on Energy Use
Ryan De Groot Michigan
Department of
Aay, Henk
Matt Raybaud
Geography &
Meijer Chair,
Geography &
Department of Geographic Information System (GIS) Development for Plaster Creek Watershed Students will join Professor Jason
Environment-al VanHorn to redesign an interface to make the Plaster Creek GIS Database more accessible to local government officials,
developers and other watershed stakeholders. Dr. Jason VanHorn and two research assistants will produce additional layers
(5-10) in the Plaster Creek watershed to include new layers developed by third parties in the next two years. These (and
existing) layers will be used to develop 1-3 new spatial analysis tools focused on hydrology modeling. They will also create a
series of short videos (about 20) to demonstrate all aspects of the interface to help educate users about this GIS system, about
analysis approaches to understand the watershed, and about the watershed itself. It is good for students to have completed
Geography 261, Introduction to GIS, prior to this research experience.
Turner, James
Mathematics & David Zhang
The Jack and
Lois Kuipers
Hydrologic Modeling of Effects of Stormwater Runoff in Plaster Creek Watershed The student selected for this project
will assist Professors Wildschut and Hoeksema (Engineering Department) in constructing a hydrologic model of the Plaster
Creek watershed to better prioritize future stormwater reduction projects and evaluate the relative success of these future
projects, a practice identified as critical for effective stream restoration. The model will initially be constructed on HEC-HMS
using available GIS data (funded by grant 2012-0023). The student will also help plan where to install twelve Leveloggers,
each stationed just above the point where a major tributary drains into the main channel of Plaster Creek, and also install
them. Data from these Leveloggers, together with field-collected data will be used to calibrate the model. This model will
assist Plaster Creek Stewards to better assess the relative contributions of the twelve tributaries to the flashiness of the main
channel after rainfall events. A student interested in this position should be able to work independently, learn new software,
and keep data organized. Ideally, they would have some background understanding of GIS and hydrologic modeling or
GIS Mapping and Analysis of Dutch Immigration Databases Robert Swierenga is the pre-eminent historian of Dutch
immigration to the US and the compiler of the most comprehensive databases related to this immigration. Sources for these
databases include US census records, ship manifests, and Dutch provincial and municipal emigration records.
Swierenga’s databases were created during the 1980s and used punch cards for the records and the analysis. Recently, several
Calvin senior computer science students converted these databases into comma separated values (CSV) ones that today’s
software (including GIS) can read. A systematic geographical (spatial) analysis of these databases has never been conducted
even though they contain much spatial information (especially for Dutch geographical origins and American destinations).
This research project will apply GIS to these databases and produce maps and spatial analysis for publication. Some of the
maps produced will be included in an ongoing project: The Atlas of Dutch American History and Culture.
Explorations in the Algebra of Homotopy Operations Homotopy operations provide an algebraic approach to understand
the topology of geometric objects. This project will focus on one or both of two aspects of this area. First, in a continuation of
a project begun last summer, we will seek an algebraic classification of the homotopy types for (n-1)-connected 2ndimensional manifolds by characterizing them through homotopy groups of spheres. The second aspect will focus on
developing means to systematically construct resolutions of homotopy operations and apply the results to determining when
certain algebraic maps can be lifted topologically. Possible applications of these results include determining the global
behavior of configuration spaces relevant to phase spaces in mechanics, end-effector spaces for robot motion planning, or nparticle arrangements in statistical mechanics.
Adejoke; Gail
Sytsma, Elise
Veurink, Tega
Ebeye, Katie
The Jansma
Research Fund
in the Sciences
and Business;
Robert Wood
Johnson grant
Preconception reproductive knowledge promotion (PREKNOP) Intended pregnancies decreased and unintended
pregnancies increased between 2001 and 2008 in the U.S., this is a shift that was previously unobserved. A Healthy People
2020 goal is to increase the percentage of intended pregnancies to 56%. It is essential to increase the percentage of intended
pregnancies considering the numerous risks and undesired consequences associated with unintended pregnancies. Unintended
pregnancies are associated with delayed recognition of pregnancies, and adverse birth outcomes such as preterm birth, low
birth weight, and negative physical and mental health effects in children. Unintended 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. The hypothesis
is that the PREKNOP program will reduce the risk of unplanned pregnancy and improve women’s ability to manage their
reproductive health. A sample of 125 women, 18-44 years old have been recruited into the study and are randomly assigned
into two groups—control (healthy lifestyle) and intervention (reproductive knowledge promotion)—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. Teams of nursing students and community health workers
administer the 12 month intervention and six surveys in face-to-face interviews. The PREKNOP intervention consist of
receiving a Knowing your Body Kit, which consists of 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 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. A logical place to start is by promoting women’s understanding of the reproductive changes in
their bodies and actively involving them in their own.
Balili, Ryan
Physics &
Matthew Link
The John Van
Instrumentation and experiments on novel quantum effects in semiconductor optics The project is aimed at building
spectroscopic experimental setups and implementing computer automation and control for experiments intended towards the
development of novel devices in semiconductor optics. Students will have a first hand experience with standard equipment
used in semiconductor research and industry as well as develop some skill in automation, optical experimentation and
computer programming.
Loren; Ubels,
Physics &
Peter Boersma
Elucidating the Signaling Pathway of UVB Induced Potassium Efflux 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 molecules 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.
Harper, Paul
Physics &
The Jack and
Lois Kuipers
Structural studies of cubic and hexagonal phases in lipids. Lipids are the basic building blocks of cell membranes and
form a beautiful variety of structures, including minimal surface based phases that form cubic lattices and the curled up
cylinders of the inverted hexagonal phase. We’ll be working on two projects, the first of which is examining lipid-sugar
interactions using several techniques, including DSC (differential scanning calorimetry). The second project will be utilizing
X-ray data to make electron density reconstructions of the hexagonal phase formed by lipids and an essential lung protein.
The second project is part of a larger effort to understand how the protein works and to potentially devise a therapeutic
Molnar, Larry
Physics &
Space Grant
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, along with some strategic
complementary data from our own telescope.
Molnar, Larry
Physics &
Cara Alexander Hubert A.
Vander Plas
Period changes in contact binary systems 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 contact systems are not uncommon, many aspects of their life cycle remain
poorly understood, from formation to final state. The current state of any system (masses, temperatures, radii) can be
determined by analysis of light curves (brightness vs. time as the system rotates) and spectra (which yield radial velocities).
Indications of change over time can be found by precise monitoring of the orbital period. This summer's work will
particularly follow up two systems whose periods we have found to be changing in dramatic ways.
Physics &
Zachary Bruce
Distinguishing Stellar Populations within Milky Way Globular Star Clusters Globular star clusters have long been
considered simple stellar populations – organizations of stars that all formed at once and evolve together. This assumption
has allowed astronomers to study stellar evolution with great success. Over the past two decades, evidence has accumulated
which suggests that globular clusters (GCs) may not actually be single population groups, but rather appear to have
undergone multiple epochs of star formation on cosmologically short timescales. While theoretical work is somewhat
divided on the issue, fewer than half of the ~160 GCs in the Milky Way have been studied observationally. In this project,
we will obtain and analyze data from clusters that have not been thoroughly studied within the Milky Way that may continue
to shed light on the evolutionary history of individual clusters and the population of Milky Way GCs as a whole.
The John Van
Walhout, Matt Physics &
Aaron Abma
Helder, Emily; Psychology
Bethany Gorter, Alumni Grant;
Ye In Oh
Ken and
Marcia Wierda
Calvin College
Longitudinal outcomes among internationally adopted children and their families The proposed project seeks to gather
information about how children are adjusting and developing following adoption from international orphanages into families
in West Michigan. Forty-nine children have been enrolled in the study and data has already been collected during the
summers of 2010, 2011, and 2012. These same children will return during the summer of 2015 to assess cognitive, emotional,
and behavioral outcomes as well as adoptive family functioning. Student research assistants will be trained to administer
cognitive tests and semi-structured interviews so that they can assist in data collection. Students will also participate in data
entry, literature reviews, and manuscript preparation. Students interested in pursuing graduate training in clinical psychology
are especially encouraged to apply.
Jones, Eric
After the Exoneration: Effects of Wrongful Convictions on Career Prospects It is believed that thousands of innocent
people may be convicted each year. According to the Innocence Project, over 300 people have been exonerated through DNA
evidence after being wrongfully convicted. Much research has investigated the causes of these errors and their solutions.
Nevertheless, far less research has examined the consequences of being wrongfully convicted and then later released from
prison. This research project aims to explore the potential obstacles that exonerees face when applying for jobs. It is wellknown that employers discriminate against ex-convicts. However, wrongfully-convicted people should theoretically have no
criminal record. Therefore, this project will examine how a sample of businesspeople respond to job candidates with and
without criminal records.
Optical Methods for Trapping Atoms and Making Cold Molecules The student researcher(s) will utilize a system of
lasers, optics, electronics, computers, and vacuum equipment to produce ultra cold clouds of argon and krypton atoms, and to
study molecules that form when the clouds are exposed to laser light at specific optical frequencies.
(NSF); Science
students (48 men, 37 women)
Two students did interdisciplinary research
Julie Yonker
Psychology and Nicole Karl,
(Psychology) Business
and Brian
53% externally funded by grants from outside Calvin College
32% funded by private donors
15% funded from within Calvin College
Virtues & Character Strengths in Young Adults: What’s the Impact? Christian higher education often strives for
learning and growth that go beyond utilitarian skills. These include a focus on formation of virtuous dispositions, character
strengths and holistic spiritual formation. Need for assessment of educational outcomes places pressure on the measurable,
creating a challenge for those foci that are not easily countable. Our project aims to understand the outcomes of virtues and
character strengths for emerging adults as measured through a meta-analysis of existing empirical studies. The results will
inform future work on how Calvin College can best incorporate a virtues framework as detailed in the Core Curriculum. We
expect that the results of our project will help fill some gaps in our understanding of how virtues and character strengths can
influence adolescents and emerging adults.
2015 Off-campus researchers who presented posters at the Science Division Summer Research Poster Fair
Marc Scanio,
PhD; Thomas
Van Geldern,
PhD; Professor
Jeffrey Rohde,
PhD; Dale
Kempf, PhD
Funded by
Institute for
World Health
(FIWH) &
AbbVie Inc.
Garrett Bazany Dr. William D. National
(NSF) and
Joshua Budi
Dr. Fred Van
Dyke, Dr.
Benjamin W.
Van Ee
Project Title and Location
Initial Structural-Activity Relationship (SAR) Development of Arylcarbamate Series for the Treatment of Neglected Filarial Tropical
Diseases AbbVie Inc., North Chicago, IL
Investigating the role of dimethyl fumarate in activating Nrf2 pathway associated genes and in the survival of motor neurons following
MeHg-toxicity Michigan State University
Little River
Spatial Distribution and Identification of the Mottled Sculpin (Cottus bairdii ) for Stream Quality Analysis in the Manistee River
Band of Ottawa Watershed Au Sable Institute of Environmental Studies, Mancelona, Michigan
Stephan Buiter Dr. David R.
Profilin and its effects on cytokinesis in fission yeast University of Chicago, Illinois
Joy Christopher Dr. Ken Inoki
Uncovering the Role of BASP1 as a Key Regulator of Amino Acid Sensing by mTOR University of Michigan Life Sciences Institute, Ann
Arbor, MI
Lydia Cupery
Location Detection and Display in Next Generation 9-1-1 Systems Department of Computer Science, University of Houston, Texas
Dr. Stephen
Kathryn Gerber Paul Schramm,
Dr. Shubhayu
Ridge Institute
Saha, Arie
of Science and
Worldwide meta-analysis of relationship between allergenic pollen and climate change Centers for Disease Control and Prevention,
Atlanta, Georgia
Jacob Hall
Giselle L.
Sholler M.D.,
Ping Zhao,
BKM120 (Buparlisib) induces apoptosis in medulloblastoma through the inhibition of the PI3K signalling pathway and prevention of
Health, The
cell proliferation Helen DeVos Children's Hospital, Grand Rapids, MI
Meryl &
Charles Witmer
Beat NB
Marko Ivancich Dr. Neelu Puri, SMaRT
Mechanism of Action of Oligonucleotides Homologous to the Telomere Overhang and Development of a Nano-Delivery for Melanoma
to Increase its Efficacy University of Illinois College of Medicine at Rockford
Nicole Joseph
Carrie Graveel, Van Andel
MET Signaling in Triple Negative Breast Cancer Van Andel Research Institute, Grand Rapids, MI
Elizabeth Tovar Research
Institute, Grand
Diegel-Zylstra, Institutes of
Dr. Bart
Health (NIH)
Conditional Knockdown of Wnt3a Using the CRISPR/Cas9 System Van Andel Research Institute, Williams Lab, Grand Rapids, MI
Evans Lodge
Dr. John Drake, National
Protective Population Behavior Change in Outbreaks of Emerging Infectious Diseases Odum School of Ecology, University of Georgia
Matthew Oram Dr. Ormand
PhD, Dr.
Hiroyuki Mori,
M.D., PhD
Kara Smit and David Dornbos,
Phil Tubergen PhD, Sara
Syswerda, PhD
Calvin Biology Wnt signalling increases β-oxidation in adipocytes University of Michigan
Megan Van
Van Andel
Dr. Jeff
Kellie Sisson,
Matt Kortus
Influence of Autumn Olive on Plant Community and Soil Composition Pierce Cedar Creek Institute
Research Grant
for the
When Broken Brakes are a Problem: Developing a TSC Cell-Based Screen for Compound Sensitivity Laboratory of Systems Biology,
Van Andel Institute, Grand Rapids, MI