We include students in our personal research because we believe that students learn biology best by conducting biological research. Get involved! Talk to a professor today and help discover something new about the living world around us.
- Assessing the Role of Endophytic Fungi in Managed and Natural Ecosystems
Students engaged in this research project will have an opportunity to explore how endophytic fungi impact plants. Endophytic fungi grow intercellularly within the shoots of many grasses and appear to protect the plants from insect herbivores. The mechanism of this protection is purported to be toxic alkaloids produced by the plant/fungal symbiotum. We have shown that grass endophytes mediate wound-induced resistance to insect herbivores. That is, the fungal endophytes are stimulated to provide heightened levels of protection for the plant following initial damage to the plant. One direction of current research is to assess the molecular basis of the induced response and determine if fungal and/or plant genes are responsible for the wound-induced response. Students will assist in formulating testable hypotheses concerning the interactions among endophytes, grasses and insect herbivores (e.g. aphids). Students will design methods of testing these hypotheses while learning various molecular techniques, and methods for fungal staining and detection, to determine the induction of fungal endophyte to down- or up-regulate the transcription of genes responsible for the production of defensive alkaloids. Students will use analytical chemistry and molecular biology to determine how the fungi impact herbivorous insects.
- Insect vector – fungal endophytes: are effects of the interaction dependent on fungal reproductive strategy?
Flies of the genus Botanophila are unusual in that they visit fungal (Epichloe spp.) fruiting bodies for feeding and oviposition. As they visit fungi, flies transfer spermatial spores among the self-incompatible fungal individuals. Thus, the flies act as “pollinators” of the fungi. Some species of Epichloe appear to require the services of the flies for “pollination” while others do not. Larval flies complete their development on the fungi. The aim of the project is to test the hypothesis that the reproductive mode of the fungus determines the dependence of Epichloe on Botanophila. Activities undertaken by students will comprise the evaluation of:
- Effectiveness of fly ontogenesis and fertility
- Reproductive success of fungal endophytes
- Presence of bacterial endosymbionts in the fungus-insect interaction
Research will be conducted both in the field and in a laboratory. Techniques used in the project will range from standard ecological to molecular and histo-cytological methods. Knowledge of the fungal endophyte-fly interaction will contribute to our understanding of evolutionary innovations in the interaction partners that have led to the diversity of life forms within the biosphere. The project is a multi-investigator, multi-national endeavor involving workers and labs from the United States, Switzerland and Poland. Field work will be conducted in Poland, while laboratory work will be conducted there, in Zurich, Switzerland, and at Hope College. Students will be involved in laboratory-based work at Hope and/or field work in Poland, thus the student needs to be amenable to international travel.
- Cell Growth and VACM-1/cul5
Research conducted in our lab focuses on elucidating the normal function for VACM-1/cul5, an endothelium specific gene product which shares sequence homology with cullins, a family of intracellular proteins that regulate diverse signaling pathways in response to changes in the cellular environment. Our work to date indicates that VACM-1 protein regulates cellular growth by a mechanism that distinguishes it from growth regulating factors, and from other cullins, and thus suggests a unique biological role for this largely uncharacterized protein. We have shown that both, in cancer cells and in endothelial cells, VACM-1 inhibits growth while expression of VACM-1 mutant has a dominant negative effect on cellular proliferation in vitro. Importantly, expression of VACM-1 mutant converts endothelial cells to the angiogenic phenotype. Consequently, VACM-1 may play a role as a potential novel suppressor of angiogenesis in vivo.
Thus, the goal of our recent research is to test the hypothesis that VACM-1 is involved in the regulation of endothelial cell growth, and to identify the mechanism of VACM-1 regulated angiogenesis in vitro. Specifically, we are examining the effects of posttranslational modification on the biological activity of VACM-1 and whether aberrant expression of VACM-1, or expression of mutated VACM-1, may lead to a disease, cancer in particular. Students will be involved in designing experiments that test different aspects of the structure-function properties of VACM-1. Students involved in our research projects will learn experimental procedures that include DNA isolation, site-directed mutagenesis, cell culture, immunocytochemistry, spectrophotometry, fluorescence polarization techniques, polyacrylamide gel analysis and Western blotting. Importantly, students will learn to read, discuss, and question research papers effectively and to prepare scientific manuscripts.
- Trafficking of a Membrane Transport System
In living organisms, routine metabolic processes result in the formation of many free radicals within the cellular environment that can be toxic to the cells themselves. My research tests the hypothesis that free radicals produced in metabolism regulate a membrane transport system, System xc-, that provides neurons and glia with the precursors required to synthesize a cellular antioxidant called glutathioine. System xc- is a plasma membrane transport system that catalyzes the stoichiometric exchange of extracellular cystine for intracellular glutamate in the brain. The internalized cystine is then used for glutathione synthesis which protects the brain from oxidative damage. While several groups have demonstrated transcriptional regulation of System xc- within 24 hours of exposure of cells to oxidants there have been essentially no studies which have examined the short-term regulation of transporter activity. My students and I have shown that oxidants appear to acutely (within minutes) regulate System xc- by modulating the cell surface expression of the transporter. These exciting findings suggest a novel form of regulation of System xc- that may serve as an extremely important component of the cellular defense system in protecting cells from oxidative insults. We are currently using biochemical and molecular techniques:
- To identify important trafficking motifs within the C-terminus of System xc-
- To describe the cellular signaling pathways that are involved in the hydrogen peroxide-regulated activity of System xc-
Ultimately, this work will provide us with a better understanding of molecular processes which acutely regulate System xc- and identify key proteins which regulate transporter trafficking. As such, this work may provide direction for future studies aimed at pharmacological manipulation of System xc- activity for therapeutic benefit.
Each student in the Chase lab has their own independent research project that fits into the overall research aims of the lab. Students also assist in formulating testable hypotheses and constructing appropriate experimental designs to test their hypotheses.
- Biology and domestication of dwaft ginseng
Healthcare for patients has been one of the major issues in the world including the U.S. Minimizing the chances that a person gets sick so that s/he lives a long-lasting healthy life is arguably the best way to drive down the healthcare cost and benefit the individual and the entire society. One approach to achieving the goal lies in the beneficial impact of chemicals known as adapsins produced in some plants such as the Dwarf ginseng (Panax trifolius). Native Americans have used the plant to help cure various diseases, and its close relatives American ginseng and Chinese ginseng have been widely used as herbal tea to strengthen human immune system. The dwarf ginseng occurs naturally and widely in the eastern and central Canada and U.S. In this study, we will gather plants of dwarf ginseng from various parts of its natural distribution, plant them in a common garden, quantify their production of active chemicals in roots, stems, leaves and fruits, selectively breed the ones with high chemical production, and explore genes that are involved in the pathways that produce the effective chemicals.
- Molecular Regulation of Fatty Acid Species
Lipids, are a particularly fascinating dietary component, as they comprise a structurally and functionally diverse group of compounds. They share as a common feature that they are all hydrophobic (“water-fearing”) compounds, yet structurally are very varied. One class of lipids, the fatty acids may be imported into cells and used as an energy source by the cell, or as building blocks in making other compounds that the cell needs. Different types of fatty acids have subtle, but important, structural differences that are crucial for function and cell survival. Some important structural differences in fatty acids occur in their length, and the presence (“unsaturated”) or absence (“saturated”) and the position in the chain of double bonds.
In this project, we are focused on how cells recognize these subtle differences. It is clear that cells do recognize these distinctions, because we can observe that cells differentially regulate genes in response to changing dietary conditions. For example, if you feed cells saturated fatty acids, you will see a small increase in the expression of the gene OLE1, which encodes the ∆9 desaturase. However, feed cells a particular class of unsaturated fatty acids, and they repress expression of OLE1. How does the cell “know” what type of fatty acid it has imported?
Initial work in our lab has used a molecular genetic and biochemical approach to identify the protein(s) that are involved in this recognition using the model organism Saccharomyces cerevisiae. We have isolated and performed initial characterization of a mutant defective in this process. Students working on this project will use both molecular genetic and biochemical approaches in their work. Experimental procedures will include some or all of the following: cell culture, cloning, DNA isolation, PCR, spectrophotometry, reporter gene assays, Western blotting, GC and GC-MS, and microscopy. In addition to experimentation, students will be expected to be full members of the research team-analyzing data, preparing figures, and reading and discussing research literature, and to write a manuscript at the end of the summer detailing their findings.
- Genomics of Wathershed Microbes
Dr. Aaron Best
Escherichia coli has been one of the primary model systems for understanding bacterial cellular processes and cellular structures in the field of microbiology. Likewise, it has become one of the best studied model species for developing approaches to and understanding the evolution of genomes. This is, in part, due to the clinical significance of many E. coli strains, leading to thousands of available genome sequences, but also to the broad genetic diversity that is observed among these strains. For example, when the full genome sequence of E. coli O157:H7 was published, it surprisingly contained over 1 million bases of DNA in a 5 megabase genome that are not found in laboratory strains of the model organism – fully 20% of the genome is different. This type of variation leads to questions about the very definition of a species in the bacterial world. Studies to characterize the extent of variation seen in isolates of E. coli from host-associated environments around the world fall into two broad categories: global studies of the Escherichia coli species through the analysis of representative fully sequenced genomes, and targeted studies of particular pathogen sub-types through the acquisition of up to hundreds of draft genome sequences of clinical isolates from the group in question. Both types of study lead to intriguing insights into the genus of Escherichia, challenging the notion of E. coli as being a relatively simple, model species of bacteria. However, none of these studies assess naturally occurring, non-host-associated populations of the genus Escherichia in a systematic, in-depth manner. Thus, questions arise as to the extent of habitats for Escherichia strains and the extent to which there are non-host-associated reservoirs for these bacteria that could provide opportunity for genetic exchange and evolution of the diversity of strains observed in the genus. In this study, we have a unique opportunity to perform a deep examination of Escherichia isolates derived from a non-host-associated environment — a watershed. The sources of Escherichia in a watershed can be many, including point sources associated with sewage treatment, livestock farming and wild animals and fowl; and non-point sources through sediment runoff from urban and agricultural environments. Several studies have pointed to the existence of "environmental" clades of Escherichia that fall outside of the traditional E. coli group. A very limited set of the environmental clade genomes exist in public databases (less than 10), yet well over 2000 Escherichia genomes from clinical, commensal and host-associated sources are available. This study will address this knowledge gap in one of the best studied groups of organisms by examining genome sequences of Escherichia isolates from a watershed environment coupled to a detailed surveys of microbial communities through 16S rRNA sequencing to track the composition and changes in microbial populations that occur in the watershed.
- Impacts of Hemlock Wolly Adelgids
Ottawa County is the epicenter of a developing invasion of Hemlock Wooly Adelgid (HWA), an exotic aphid-like insect that has already decimated populations of Eastern Hemlock trees in the eastern U.S. and promises to do the same in Michigan. Introduced to the U.S. in 1951, the insect was discovered in the Holland area in 2015 and at the Hope College Nature Preserve in August 2017. Heavily infested hemlocks often decline and die in 4–10 years. Because the understory beneath Eastern Hemlock canopies constitutes a distinctly different microenvironment than that beneath broadleaved trees, HWA-driven defoliation is likely to influence the recruitment and survivorship of tree seedlings on the forest floor. In addition, pronounced canopy defoliation and impacts on throughfall and leaf litter composition may affect communities of leaf litter arthropods beneath hemlock canopies. In turn, both plant species composition and litter decomposition rates may be altered in West Michigan dune forests.
We will assess hemlock condition and HWA establishment at several sites in Ottawa and Allegan County, and compare the density and composition of litter arthropod communities beneath hemlock and adjacent sugar maple canopies. We will also compare light environments, soil temperatures, seedling recruitment and photosynthetic rates of woody seedlings beneath hemlock and sugar maple canopies throughout the entire growing season, since the effects of Eastern Hemlock on the understory light environment are most pronounced before broadleaved trees leaf out in the spring. The proposed study will add to our understanding of how insect pests can exert major direct and indirect influences on forest ecosystems by altering the physical structure of the environment.
- Effec of HSV-1 latent infection on laster-induced axotomy
Over 20 percent of military personnel evacuated from Iraq and Afghanistan conflicts have had some type of blast-induced neurotrauma (BINT) (Warden, 2006). These soldiers have been diagnosed with cognitive and psychiatric disorders at increasing rates (Jett, 2010). One such pathology of BINT is the disruption of the blood-brain barrier. A damaged blood-brain barrier
increases the likelihood of circulating pathogens to enter the central nervous system to produce insults to the brain. One pathogen that is naturally attracted to neurons is Herpes Simplex Virus Type I (HSV-1). Over 60 percent of the U.S. population is infected with HSV-1 (Looker et al., 2015).
Alarmingly, the incidence of viral infections such as HSV-1 is higher among military personnel than civilians (Goyal et al., 2012). HSV-1 continues to be a leading infectious cause of corneal blindness and acute, sporadic encephalitis (Al-Dujaili et al., 2011). Additionally, HSV-1 infection has been linked with cognitive deficiencies, including a heightened increased risk of developing dementia (Tarter et al., 2014; Lovheim et al., 2015).
Wozniak and colleagues demonstrated that HSV-1 prompts the accumulation of amyloid beta plaques and neurofibrillary tangles, two pathological hallmarks of dementia and neurological damage induced by BINT (Wozniak et al., 2011). Taken together, these data support a central hypothesis that an existing infection of HSV-1 will exacerbate the cellular pathologies induced by mild shockwave-related BINT. This hypothesis will be tested via the following objectives:
- Objective 1. Test the hypothesis that mild shockwave-related BINT enhances HSV-1 reactivation from latency. HSV-1 forms a latent infection in sensory neurons in the peripheral nervous system. Reactivation of the virus allows virus particles to be released from these cells and potentially enter the central nervous system (CNS). Entry of HSV-1 into the CNS is associated with encephalitis as well as HSV-1 DNA presence has been linked to dementia (Mori et al., 2004; Piacentini et al., 2014). The proposal predicts that laser-treated dorsal root ganglion neurons latently with HSV-1 will exhibit higher rates of reactivation (marked by higher gene expression of viral genes ICP0 and HSV-1 Thymidine Kinase) compared to neurons infected with HSV-1 alone. Higher viral gene expression in shockwave-treated sensory neurons would indicate that BINT augments reactivation and would allow for more virions to enter the CNS.
- Objective 2. Test the hypothesis that HSV-1 exacerbates effects of shockwave-related BINT in CNS neurons. Shockwaves and BINT have been linked to a degradation of the blood-brain barrier. With this in mind, this objective will determine if HSV-1 infection increases cytopathy induced by shockwave-related BINT in hippocampal neuronal cultures. More specifically, this objective will evaluate if HSV-1 modulates decreases in GluR1 and synaptophysin as well as an increase in GFAP prompted by BINT alone. This result would mean HSV-1 presence in the CNS would act synergistically to compound the neural pathologies associated with BINT.
- Going native: restoring wildflowers and student's connection
Establishing mixed plantings of native plants like wildflowers creates a valuable reservoir of biodiversity. Not only do mixed plantings help conserve our floral biodiversity, they also facilitate restoration of habitats and ecosystem services. Mixed wildflower plantings increase ecosystem services by reducing rain water run-off, providing insect pest control by predators like spiders and providing food for our native pollinators.
We aim to create a mosaic of wildflower patches to restore native floral plants and fauna they support. In collaboration with local educators, we intend to use these gardens to increase authentic, scientific discovery by elementary and middle school students. In this project, a student will help establish a large, native wildflower patch next to Schaap Science Center by planting, watering and tending native wildflowers. Plants that may be included in this patch include common milkweed, goldenrod, New England aster, prairie coneflower, golden alexanders and wild bergamot. The student will also keep detailed notes, pictures and observations that can be used as a model by local area schools who are interested in establishing their own native wildflower patch for use in their science classes. The student will also develop scientific curricula appropriate for elementary or middle school students that are aligned with current state standards.
- Mechanisms of RNA Virus replication
Dr. Benjamin Kopek
Zika Virus (ZIKV) is a positive-stranded RNA arbovirus of the flavivirus genus that has recently caused a global health crisis associated with an increase of primary microcephaly, a congenital anomaly correlated with brain size and development. In this project, we are attempting to create genetic tools to study ZIKV replication in insect cell lines, specifically Drosophila melanogaster. Several ZIKV plasmid-based reverse genetics systems have been established for vertebrate systems, though they will not work in insect cells due to incompatible promoters. We believe establishing Drosophila as a model insect system for ZIKV will allow us to take advantage of Drosophila’s fully sequenced and well-annotated genome and the many tools available for genetic manipulation. We have recently been successfully at creating a plasmid-based replicon for Zika virus in Drosophila. This project will involve replacing the Zika virus structural proteins with a reporter gene to aid high-throughput studies in Drosophila.
- Assessment of an Innovative K-12 STEM Program
STREAM School is a middle school program provided through a partnership between Hamilton Community Schools and the Outdoor Discovery Center (ODC) Macatawa Greenway in Holland. STREAM School takes a non-traditional approach by connecting students to the outdoors through a project-based learning (PBL) approach. STREAM teachers work alongside local professionals and ODC staff to develop learning experiences for students that connect state-mandated content to real-world projects. Projects are designed to be authentic, engaging and educational within a framework allowing students to express their passions and interests. STREAM School places education outside the walls of the classroom and into authentic environments where students have opportunities to connect critical content with job skills.
One goal of my science education research lab at Hope College is to assess the STREAM school program using mixed methods techniques. Using data collected from interviews, test scores, surveys and observations, research assistants engaged in this summer project will attempt to answer the following research questions:
- How does STREAM School contribute to the non-cognitive skills of students (i.e., critical thinking, collaboration, personal accountability, etc.)?
- What types of projects best engage and motivate STREAM School students and why?
- How do STREAM School students’ understanding of science and mathematics change as a result of participation in the program?
- Does STREAM School contribute to the motivational resources of students, and if so, in what ways?
- What are the perceptions of STREAM School by Hope pre-service teachers who complete field placements at STREAM?
- How does STREAM School participation affect students' attitudes about future career choices?
Students will investigate these questions using both quantitative and qualitative research methodologies and generate written reports and articles for dissemination. Students will also learn to use research software packages such as SPSS and NVivo.
- Biochemical and behavioral effects of junk-food in the brain
My lab group is very interested in the role that the brain plays in obesity. In particular we are interested in the top-down control exerted by the prefrontal cortex on feeding behaviors. Significant similarities have been observed between obesity and drugs of abuse, particularly when examining the reward pathways of the brain. Reward areas of the brain receive a significant glutamatergic input from the prefrontal cortex as well as a dopaminergic input from the ventral tegmental area. While a significant number of researchers continue to explore the role of dopamine and the reward pathway on feeding behaviors, the role of the prefrontal cortex and executive control has been less well characterized.
Dopamine is often thought of as the reward signal in the brain, as rewarding experiences such as use of illicit drugs, sex and even eating, lead to a release of dopamine in the brain. The ventral tegmental area, one area of the brain that creates dopamine, innervates the reward pathways of the brain but also innervates the prefrontal cortex, suggesting that dopamine may exert influence on this important area. While significant research has examined the effects of drugs of abuse on the prefrontal cortex, little work has been done to examine the effects that a junk-food diet has on the prefrontal cortex.
My lab aims to explore the effects that a junk-food diet, and/or obesity development, has on the prefrontal cortex. In order to do this we will utilize a rat model in which animals are given access to a highly palatable junk-food diet consisting of potato chips, chocolate chip cookies, peanut butter and chocolate flavoring. Following chronic exposure to this diet behaviors mediated by the prefrontal cortex are examined in an effort to explore whether or not a junk-food diet or obesity development might lead to deficits in certain cognitive functions. To compliment these behavioral studies, biochemical analysis will be performed to explore potential molecular mechanisms that may lead to deficits. Specifically, we are interested in examining potential deficits in dopamine signaling that may be present, as alterations in dopamine signaling within the prefrontal cortex have been linked to deficits in executive functions such as inhibitory control, working memory and decision-making.
Understanding the effects of a junk-food diet on the prefrontal cortex may lead to a better understanding of obesity and the struggle that many individuals have with long term weight loss.
- City of Holland Tree Canopy and GHG Assessment
Dr. Kathy Winnett-Murray and Dr. Greg Murray
The City of Holland Sustainability Committee has created this Hope College student research project as a way to coordinate a project between the committee, the city’s Parks Department and Hope College, to further inventory the urban tree canopy within the city. The student researcher will assist the City of Holland update its urban tree canopy inventory through a GIS program, assess greenhouse gas carbon sequestration value of trees and help develop a program/platform for engaging community members and K–12 students in citizen science. The proposed study will add to our understanding of the various ways to assess the value of trees and how they contribute to ecosystem services that benefit the community at large. The student will collect data such as tree species, size, relative age and quantities within the designated areas. These data will be used for projects such as the 40-year community energy plan, Holland in Bloom and Tree City/Tree Campus USA.
“Trees are sustainability power tools: They clean and cool the air, regulate temperatures, counteract the urban ‘heat island’ effect, and support water quality and manage flow.” (“Cities Should Think About Trees As Public Health Infrastructure,” October 2, 2017)
Hope College faculty will assist in calculating the carbon sequestration value of the trees and tree identification as needed.
Start and end dates are flexible and should be arranged in advance such that the five-week project is completed by July 13, 2018.
A. Paul Schaap Science Center35 East 12th StreetRoom 2103Holland, MI 49423