Department of Chemistry
DEPARTMENTS of BIOLOGICAL SCIENCES and CHEMISTRY
invite applications for
MERCK/AAAS UNDERGRADUATE SCIENCE
Period of activity is a block of eight weeks beginning May 14, 2007 or as arranged between you and your project mentors.
Application Deadline: Monday, March 26, 2007 at 4:00 pm.
The Departments of Biological Sciences and of Chemistry at
SUNY Brockport have been awarded a Merck/AAAS Undergraduate Science Research Program (USRP) grant, sponsored
by the Merck Institute for Science Education (MISE) and the American Association for the Advancement of
Science (AAAS). This award is designed to
We invite you apply to join with chemistry and biological sciences faculty for an exciting and stimulating eight weeks of full time (40 hour/week) research at the interface of chemistry and biology. Projects are described on the following pages.
Four stipends of $3200 will be available, one for each project. Participants will need to make their own arrangements for room and board during this period.
Eligibility. each student must:
Read the project descriptions to see which additional courses are required or recommended for each project. (Applicants may be currently enrolled in some of these courses.)
Exceptions: If your GPA in these courses is less than 2.8 (A = 4.0), then you should be sure that strong evidence of your suitability for research participation is present in your application and faculty recommendations. If you might wish to be considered but do not meet all of these criteria, (for example, you have not had all these courses) feel free to discuss your case with the project mentors.
Preference will be given to Biological Sciences and Chemistry majors who intend to pursue graduate education in chemistry and life sciences.
Applications. A complete application will consist of:
All applications materials, including your faculty recommendations, must be received in Rm 125 Smith Hall by Monday, March 26, 2007 at 4:00 pm.
A committee of the participating biological sciences and chemistry faculty will evaluate the applications. The committee will announce its decisions as soon as possible (within two weeks of the submission deadline). The committee will offer a research fellowship, place an applicant on an alternates list, or not accept an applicant. A successful applicant will be expected to accept or reject the fellowship offer within a week of the announcement of the offer.
Before submitting an application, you should discuss the research projects that interest you with the faculty mentors. The research projects are described on the next two pages. All are projects that are interdisciplinary across chemistry and biology, with one faculty member from each department collaborating on the project. Make an appointment to speak with the asterisked faculty member about the project. In the case of project #2, both faculty members are asterisked, and you may speak with either one.
Participating student researchers will have the opportunity to make progress toward scientific goals at the interface of chemistry and biology, while learning about the process of research: 1) Understanding a field of science and how their research fits in; 2) designing and executing experiments; 3) critically evaluating the data and results from experiments and deciding how to proceed; 4) documenting experiments and their results; and 5) presenting research results both orally and in written form.
During the summer research periods, all of the participating students and faculty will participate in events that will take place on Friday afternoons. Events will consist of 1) students presenting their research progress and challenges; 2) informal talks by invited speakers from nearby academic institutions who do interdisciplinary research in chemistry and biology, and 3) at least one trip to visit an area institution where interdisciplinary research is performed. The students will also serve as hosts to interdisciplinary speakers during the 2006-2007 academic year.
Fellowship recipients will write a research report and present the results of their work at SUNY Brockport’s Scholars Day, as well as at regional or national conferences, such as the National Conference on Undergraduate Research or professional conferences in biology, chemistry, or both. They may also be eligible for nomination as an associate member of Sigma Xi, The Scientific Research Society (an international society devoted to promoting research in all the sciences).
Have questions??? Please contact Dr. Maggie Logan (firstname.lastname@example.org, 395-5594) or any of the project mentors.
Project # 1. Evaluating the Effects of Dilute Aqueous Solutions of Ionic Liquids on Freshwater Biofilms: Tracey Householder* (Biology) and Markus Hoffmann (Chemistry) Additional recommended courses: BIO 323 (Microbiology) and CHM 305-306 (Organic Chemistry I and II)
Ionic liquids are a relatively new class of designer solvents for chemical synthesis that have been touted as environmentally benign. However, as recently reviewed(1), environmental toxicology and biodegradability studies of ionic liquids have only been performed in the past 3-4 years, and only one of these investigations included phosphonium-based ionic liquids (2). More importantly, the effects of dilute ionic liquids have not been studied on microorganisms grown from actual ecological systems. While single species ecotoxicology test systems are useful when comparing the toxicity of chemicals, they are not good models for measuring effects on multi-species ecosystems. Because of the dynamic nature of biofilm-based ecosystems, we hypothesize that toxicity of ionic liquids on biofilms may differ significantly from that seen in the usual test systems.
To explore our hypothesis, we will use a biofilm continuous flow stirred reactor in which locally-obtained freshwater is the only source of microorganisms and nutrients. Biofilms will be grown on glass slides or other appropriate substrates, and the flow rate, stir rate, and temperature will be adjusted to simulate the body of water that was sampled. We will test the effects of ionic liquids in two ways: a) the effect on established biofilms, and b) biofilm development in the presence of ionic liquids. Thus, the effect of the anion and the functional groups of the organic cation on the observed toxicity will be elucidated using imidazolium and phosphonium-based ionic liquids that are currently used in M. Hoffmann’s research program. Our Opti-Grid confocal microscope will be used to examine the architecture of the biofilms and the location of viable cells within that structure. To quantify the effects on viability, we will utilize the Molecular Probes LIVE/DEAD BacLight Bacterial Viability Kit. By staining the microorganisms with fluorescent molecules, we can easily utilize fluorescence microscopy to perform direct counts on disrupted biofilms to quantify viable and non-viable cells.
A student involved in this project will become familiar with the structures and properties of ionic liquids as well as determining whether there is a structure-activity relationship in their toxicity, and become proficient with fluorescence microscopy, digital image acquisition, and multi-species biofilms.
1. Scammells, P. J. et al. Aust. J. Chem. 2005, 58, 155-169.
2. Stock, F. et al. Green Chem. 2004, 6, 286-290.
Project #2. Cationic Telluride Antioxidants for the Determination of the Genes Responsible for Repair of Oxidative Damage to Mitochondrial DNA: Rey Antonio Sia* (Biology) and Maggie Logan* (Chemistry) Additional required courses: BIO 302(Genetics) and 306 (Cellular and Genetics Lab) and CHM 305-306 (Organic Chemistry I and II)
Mitochondria are responsible for cellular respiration and the generation of most cellular ATP. Their function can be lost through mutations of mitochondrial genes that arise during DNA replication or recombination, or during exposure to mutagens such as reactive oxygen species generated in the production of ATP (1). Mutations in the mitochondrial genome are associated with neuromuscular diseases, cancers, and aging (2). In R. Sia's previous work, 22 genes believed to be involved in various aspects of mitochondrial maintenance were isolated from the budding yeast, Saccharomyces cerevisiae. The focus of this project is to identify which of the 22 genes are specifically involved in the repair of oxidative damage to mitochondrial DNA. The hypothesis is that deletion of a gene involved in reducing/repairing oxidative damage to mitochondrial DNA will result in an increased loss of mitochondrial function. Deletion strains exposed to hydrogen peroxide will be assayed for increased loss of mitochondrial function compared to untreated deletion strains. In a parallel experiment, these deletion strains will be treated with antioxidants as well as hydrogen peroxide. A reduction in the loss of mitochondrial function in the presence of an antioxidant is expected in deletion strains whose product is involved in repairing/ reducing oxidative damage. Candidate antioxidants will be cationic, electron-rich alkylaryltellurides, where the positive charge facilitates transport into mitochondria. They will be synthesized using methodology developed by M. Logan and have “tunable” oxidation potentials. The tellurides also protect against both 1-electron and 2-electron oxidation (3), complementing previous mitochondria studies performed with cationic vitamin E derivatives (4).The student will participate in both the chemical and biological aspects of the research project, first preparing and/or evaluating the properties of cationic tellurides, then using them as probes in a genetic assay to screen the 22 genes for a role in the repair/reduction of oxidative damage.
1. Scheffler, I.E. (1999) Mitochondria, Wiley-Liss, Inc., New York
2. Wallace, D.C. Science 1999, 283, 1482-1488.
3. Kanda, T.; Engman, L.; Cotgreave, I. A.; Powis, G. J. Org. Chem., 1999, 64, 8161-8169.
4. Smith, R.A.J., et al. Eur. J. Biochem. 1999, 263, 709-716.
Project #3. The Relationship of Protein Denaturation and Protein-Surface Interactions: Mark Heitz* (Chemistry) and Rey Antonio Sia (Biology) Additional recommended courses: CHM 303 (Analytical Chemistry I) or CHM 305-6 (Organic Chemistry I and II)
The effect that protein conformational changes can have on protein-surface interactions is both important and not well understood. For example, conformational change in the protein lysozyme (a predominant eye protein) results in denaturation. In the presence of contact lens materials lysozyme can irreversibly denature, bind strongly to the polymer surface and become irremovable. However, the strength of binding is proportional to the extent of denaturation(1). Fluorescence spectroscopy is used in the study of protein conformation(2,3), and emission from intrinsic moieties (e.g., tryptophan, Trp) are often measured since there is no perturbation of the protein conformation. However, lysozyme contains six Trp residues in varying microenvironments, which complicates data analysis. Our hypothesis is that the analysis will be greatly simplified if we can control the source of the fluorescence emission. To enhance our ability to understand the correlation between lysozyme denaturation and binding with polymer surfaces, we propose two different approaches to the modification of lysozyme.
In the first approach, we will covalently attach a fluorophore, acrylodan, to a known location in the protein(4). By chemically attaching a probe to the protein we will know its location, and can link observed spectral changes to domain-specific conformational changes. In the second approach, site-directed mutagenesis at the DNA level will modify specific Trp residues such that the observed signal is correlated to a domain-specific location in the protein. Several of the Trp codons will be altered to code for another amino acid such as phenylalanine. We anticipate that such conservative amino acid changes will not significantly alter the tertiary structure of lysozyme. In the process of creating these mutant lysozyme proteins, the student will learn techniques in both chemical synthesis and molecular biology.
Once chemical modifications to the protein are complete, we will characterize the solution spectroscopy of native and modified lysozyme, with the ultimate goal of determining how lysozyme adsorption to a polymer substrate influences the sorption/desorption equilibrium and surface binding of the protein. Current reagents for the mutagenesis approach include a lysozyme gene cloned into a yeast expression vector. The student researcher will be involved in the mutagenesis of the lysozyme gene and the purification of the products from yeast for spectroscopic analysis.
1. Maziarz, E. P.; private communication.
2. Edelman, G. M.; McClure, W. O. Acct. Chem. Res. 1968, 1, 65
3. Hansen, S. B., et al. J. Biol. Chem. 2002, 277, 41299.
4. Lundgren, J. S.; Heitz, M. P.; Bright, F. V. Anal. Chem. 1995, 67, 3775.
Project #4. Development of a New Gastrointestinal Motility Assay in the Zebrafish: Adam Rich* (Biology), Mark Heitz (Chemistry). Additional recommended courses: BIO 301 (Cell Biology) and 302 (Genetics)
Motility disorders of the GI tract are common, with one in five Americans experiencing dyspepsia, irritable bowel syndrome, constipation, or reflux. Few drug treatments are available for motility disorders due to the limited understanding of GI physiology at the molecular level. Zebrafish larvae are transparent, thus allowing direct observation of GI motility in intact organisms. 1 Despite these advantages, the zebrafish has not been utilized for GI motility studies. One cell type, the interstitial cell of Cajal (ICC) sets GI contraction frequency and coordinates motility in the mammalian GI track. The Rich group has identified this cell type in the zebrafish GI tract 1 but has not fully examined its role in GI motility. A mutant zebrafish lacking ICC, Sparse, is available and is currently being characterized in the lab. This proposal will test the hypothesis that mutant zebrafish lacking ICC display aberrant GI contractions, leading to motility dysfunction.The proposal will require refinement of an assay to determine overall GI function, "time for food to pass", which reflects coordination of GI contractions. Zebrafish larvae will be incubated in a dye solution, then removed, washed, and returned to a dye-free medium. Excretion of dye into the bath media will be used to determine time for food to pass. These data will be compared to contraction efficiency measured in age-matched larvae using spatio-temporal mapping techniques, a type of motion analysis using digital imaging. The role of the kita and kitb genes will be examined using the Sparse mutant zebrafish which lacks a functional kita gene. The role of ICC will be examined by blocking the kita and kitb genes using Gleevec, a tyrosine kinase inhibitor. Kit function is necessary for ICC development. Finally, compounds that act as prokinetics in humans, such as erythromycin and serotonin, will be examined for effects on zebrafish GI motility. Spectroscopic studies using fluorescent dyes as reporters of chemical environment will be directed by Dr. Mark Heitz. GI physiology, spatio-temporal mapping, and zebrafish care will be directed by Dr. Adam Rich. Participating students will become proficient with microscopy, fluorescence spectroscopy, quantitative data analysis, and gastrointestinal physiology. The project will contribute a new zebrafish-based GI motility model, and may enable identification of mutants with aberrant GI motility, and/or pharmacological screens of GI motility to facilitate identification of novel drug targets.
1. Kit-Like Immunoreactivity in the Zebrafish Gastrointestinal Tract Reveals Putative ICC
Rich, S.A. Leddon, S.L. Hess, S.J. Gibbons, S. Miller, X. Xu, and G. Farrugia Developmental Dynamics, March, 2007
2. Goldsmith, P. Current Opinion in Pharmacology. 4: 1-9, 2004.