/ Biology Department

Research

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.

Faculty Research

Assessing the Role of Endophytic Fungi in Managed and Natural Ecosystems
Principle Investigator

Dr. Thomas Bultman

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?
Principle Investigator

Dr. Thomas Bultman

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: (1) effectiveness of fly ontogenesis and fertility, (2) reproductive success of fungal endophytes and (3) 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.

Can Students at Hope College Help Find a Cure for Cancer?
Principle Investigator

Dr. Maria Burnatowska-Hledin

We have cloned a novel, endothelium specific protein, VACM-1, which shares sequence homology with cullins, a family of intracellular proteins that regulate diverse cellular functions. Our work 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 cul gene product. In cancer cell line and in endothelial cells VACM-1 inhibits growth while expression of VACM-1 mutant has a dominant negative effect on cellular proliferation in vitro as it increases cellular growth, and, importantly, 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 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. Students will be involved in designing experiments that test different aspects of the functional relationships between VACM-1 and cellular growth under different extra-cellular environmental conditions. Students involved in our research projects will learn experimental procedures that include 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.

Regulation of Membrane Transporters by Reactive Oxygen Species
Principle Investigator

Dr. Leah Chase

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 the neurotransmitter transport system, System xc-, provides neurons and glia with the precursors required to synthesize glutathioine in the cellular defense against oxidative insult. Specifically, the build up of H2O2 and other reactive oxygen species leads to depletion of cellular glutathione, and ultimately oxidative stress-mediated neuronal death. The molecular events that underlie the development of increased oxidative stress in the neurons of Parkinson’s Disease patients is currently not understood. Previous studies in my lab have shown that the metabolite, H2O2, acutely regulates the activity of System xc- in glioma and dopaminergic cells by triggering the trafficking of the transporter to the plasma membrane. This trafficking event directly results in the rapid recovery of cellular glutathione levels within the cell. Thus, the oxidant-regulated trafficking of System xc- is likely to play a key role in the defense against oxidative stress immediately following an oxidative insult. We are currently using biochemical and cell biological techniques 1) to describe the cellular signaling pathways that control constitutive (basal) and H2O2-regulated activity of system xc- in cultured glioma cells and dopaminergic cells and 2) to determine if the upregulation of transporter activity decreases sensitivity oxidative cell death. Each student in the Chase lab has their own independent research project that fits into the overall research aims of the lab. Students will assist in formulating testable hypotheses and construct appropriate experimental design to test their hypotheses.

Horizontal Gene Transfer of Cholorplast Genes in the Parasitic Plant Balanophora
Principle Investigator

Dr. Jianhua Li

Both abiotic and biotic environmental factors have impact on biological systems, and the impact is reflected at different levels from molecules to ecosystems. This project involves a holoparasitic plant and its host at the molecular level. Blanophora is a holoparasitic plant genus in southeast Asia with either 1 or 15 species depending on authors. It has been placed in the Santalales (e.g., mistletoes) based on morphological data and this placement is supported by molecular data. However, our preliminary chloroplast DNA sequence data suggest its close relationship with Fabales (legumes, e.g. beans and peas). It is possible that there has occurred a horizontal gene transfer from its photosynthetic host to the parasite. However, there have been few reports of GHT of chloroplast genes. We will gather more chloroplast genes from a few populations of Balanophora as well as the roots of its hosts. If genes from Balanophora are most similar to those in the host, then we have evidence that plastome HGT is involved in the host-parasite system.

Molecular Regulation of Lipid Metabolism
Principle Investigator

Dr. Virginia McDonough

Microorganisms maintain growth and reproduction by utilizing nutrients in their environment for energy. My research interests center on the exploration of the regulation of lipid metabolism, using the model eukaryote Saccharomyces cerevisiae. My research tests the hypothesis that specific genetic mutations will prevent S. cerevisiae from sensing and utilizing lipids in their environment. In recent work, we have isolated mutants in S. cerevisiae that exhibit increased growth sensitivity to a mildly toxic fatty acid, and appear deficient in the metabolism and cellular response to exogenous fatty acids. Characterization of the mutants has identified several gene products and pathways that are involved in response to exogenous fatty acids, including MGA2 and PDR16. These two gene products are not directly concerned with fatty acid uptake, but seem to be
involved in cellular response to fatty acid supplementation. We have found that cells harboring a mutation in pdr16 are not only growth defective on medium chain fatty acids, but also contain elevated amounts of sterols and fatty acids, have an altered fatty acid composition, and are deficient in the esterification of fed fatty acids. Mutants mga2 expression results in some, but not all, of the same defects. Using both molecular genetic and biochemical approaches, we are currently investigating the precise roles of the PDR16- and MGA2- encoded proteins in regulating lipid metabolism and traffic, and the interaction/overlap between these separate pathways. Students in my laboratory assist with hypothesis formation, experimental design, and data acquisition and analysis. Students also routinely read and discuss scientific literature and develop skills for writing and presenting their data.

Bacteriophage biology, genomics, and genome evolution
Principle Investigator

Dr. Joseph Stukey

A bacteriophage, or more simply, phage, is a virus that infects bacterial cells.  They are the most numerous “biological” entities in our world and collectively carry the largest group of novel genetic information.  Mycobacteriophages are phages that infect the bacterial genus, Mycobacterium.  More than 30 genetically distinct types have been described, all of which are capable of infecting the same host, M. smegmatis MC2155.  My research interests are mycobacteriophage biology and their interaction with host cells and the evolution of their genomes.

mycobacteriophage scout Initiation of phage infection starts with the phage recognizing and attaching to a receptive host cell.  The phage genomic DNA is then transferred into the cell where phage genes are expressed that direct the infection down one of two developmental pathways ending in lysis (cell death with release of new phage particles) or lysogeny (cell survival with integration of phage genome into host genome).  The whole process, from initiation through subsequent lysis or lysogeny, requires multiple molecular interactions between specific phage and host cell components.  One area of my research seeks to identify and characterize these phage-host cell interactions at the molecular level.  This research project employs a combination of microbiological, molecular, biochemical and bioinformatic methods of analyses.

 A second area of interest is mycobacteriophage genomics and genome evolution.  My project seeks to better understand the similarities and differences in genome structure and gene content across the known mycobacteriophages, and to address questions on the nature and function of the evolutionary mechanisms that generate the observed genetic diversity.  This research project primarily uses bioinformatics in the comparative analyses of mycobacteriophage genomes but may also require using methods of microbiology, molecular biology, and biochemistry to directly test the specific hypotheses generated by these analyses. 

 Our research findings will provide new and important information on the identity and molecular biology of phage-host cell interactions at work during mycobacteriophage infection and a better understanding of the evolution of mycobacteriophage genomes.

mycobacteriophage pumpkin

Mycobacteriophage Pumpkin (left) isolated by Caitlin Peirce at Hope College, 2008, and “getting to the heart of the matter” with a plaque produced by Pumpkin on a lawn of M. smegmatis (right).
Interactions of soil microbes and pioneer plant seeds
Principle Investigators

Dr. Kathy Winnett-Murray and Dr. Greg Murray

Forests are among the most exuberant expressions of life on our planet, both for the diversity of organisms themselves and for the complexity of interactions among them. Chief among these are interactions between plants and their pollinators, seed dispersers, and seed predators and pathogens. The roles of animals in these interactions have received much attention, but the ways in which plant reproduction is affected by microbes remains poorly explored. Microbes are generally thought to act as seed pathogens, but their interactions with seeds are likely to be both more diverse and nuanced. Microbial degradation of seed coats may actually facilitate germination long before it exposes the interior of the seed to decay, for example, and microbes may interact with one another in ways that protect seeds from the pathogenic effects of some of them. “Pioneer” plants — those that specialize on colonizing recently disturbed patches of forest — constitute a model system in which to study such interactions. Many pioneer seeds include an extended period of dormancy in the soil, but the interactions between seeds and the soil microbial community, and those among the microbial species themselves, remains virtually unknown. Our research group is exploring these interactions with a common North American pioneer plant, Phytolacca americana, the seeds of which can survive in the soil for at least 40 years. Using a series of soil exposure and germination experiments, we will quantify the consequences of microbial action for seed viability and germination rate. We will also attempt to correlate these consequences with the physical effects of microbial action on the seed coat, via both scanning electron microscopy (for surface features) and light microscopy (for thickness). Genomic analyses of the microbial communities (i.e., the “microbiome”) associated with seeds will shed light on the identities of the microbes present, and whether the microbial associations with seeds that survive and those that are killed are different. We also hope to assess microbial effects on the seed coats of several tropical pioneer species, and students who participate in this research may have the option to accompany the faculty mentors to Costa Rica to participate in the field component of this project. This project is a collaboration between K. Greg Murray, Kathy Winnett-Murray, and Aaron Best, all in the Department of Biology.

Vollbrecht Students talking about their research