Training Faculty / Research Projects

Vanderbilt Summer Undergraduate Research
in Chemical Biology

Students will work in the lab for one or both mentors on the research team.
For more information about faculty research interests, visit their websites via the links below or by visiting: http://www.vanderbilt.edu/vicb/members.htm


	"Molecular Trolling for Point of Care Viral Detection" Mentors: David Wright (Chemistry) and Rick Haselton (Biomedical Engineering) Description: This work will focus on the design of a new diagnostic device for the multiplexed detections of respiratory viruses. Molecular hooks (capture stem-loop hairpin DNA constructs) are directly coordinated at known locations on a gold clad polyester filament. Filament motion is used to troll for and entrain viral RNA present in a test solution. Subsequent to capture, any necessary processing steps are carried-out using pull-through processing and fluorescence reporting. Researcher Skills and Interests: This project is ideally suited for the student interested in multiple aspects of chemistry including inorganic chemistry, analytical chemistry, biochemistry and nanotechnology.


	“Structural Mass Spectrometry Strategies for Natural Product Discovery” Mentors: John McLean (Chemistry) and Brian Bachmann (Chemistry)


	“Mass Spectrometry Directed Phosphoproteomics in Cancer Biology" Mentors: John McLean (Chemistry) and Donna Webb (Biological Sciences)


	“Lipidomics Characterization in Migrating Cells” Mentors: John McLean (Chemistry) and Chris Janetopoulos (Biological Sciences)


	"Oxidative Stress in Neuronal Cells: the Chemistry and Biology of Neural Degeneration" Mentors: Ned A. Porter (Chemistry) and Zeljka Korade (Biochemistry) Description: Smith-Lemli-Opitz syndrome is a devastating developmental disorder that effects about 1 in 10,000 individuals. It results in mental retardation, seizures, failure to thrive. Mortality in the first few years of life is 25-50%. Our hypothesis is that one of the underlying causes of the syndrome is a genetic defect that leads to the formation of toxic metabolites that result in altered neuronal development. The project focuses on the mechanism of formation of the toxic metabolites and the biological activities of those compounds. Researcher Skills and Interests: This project is suited for students with a background in organic chemistry and an interest in biological processes.


	"Molecular Basis for Carbohydrate Selectivity by Streptococcal Adhesins" Mentors: Gary Sulikowski (Chemistry) and Tina Iverson(Pharmacology) Description: This project involves the chemical synthesis of a cell-surface carbohydrate (glycopeptide) recognized by an infectious bacterium (S. gordonii). A second aspect of this program is to understand the molecular basis of the recognition of this carbohydrate by the bacterium binding protein (carbohydrate binding site). Finally, inhibition of this interaction could lead to the development of new antibiotics. Researcher Skills and Interests: This project is best suited for those students who have taken organic chemistry including lab. Students should possess an interest in learning the following techniques: interpreting NMR spectra, organic synthesis and structural biology.


	"Synthesis of Chiral Amines for Medicinal Chemistry" Mentors: Jeff Johnston (Chemistry) and Alex Waterson (Chemistry) Description: Many potential therapeutics are chiral nonracemic small molecules. Racemic small molecules contain an equal mixture of an organic compound present as two enantiomers: non-superimposable mirror images of one another. We have developed new reactions that produce only one of the two enantiomers, and this project entails the preparation of important single enantiomer amines for use in fragment-based screening and medicinal chemistry studies. Researcher Skills and Interests: This project is best suited for those students that have completed a full year of organic chemistry and its laboratory - additional laboratory experience in synthetic organic chemistry is advantageous. Students should be interested in synthetic organic chemistry, and the use of separation/purification techniques (chromatography) and analysis (NMR spectroscopy).


	"Chemistry and Screening of Novel Natural Products" Mentors: Gary Sulikowski (Chemistray), Larry Marnett (Biochemistry), and Brian Bachmann (Chemistry)
	Description: This project involves the isolation and identification of natural products produced by soil microorganisms. Phases of this project involve culture and fermentation of microorganisms (primarily soil bacteria), isolation of natural products, structure elucidation and evaluation of cytotoxicity against cancer cells and/or bacteria. Researcher Skills and Interests: This project is best suited for those students who have taken organic chemistry including lab. Students should possess and interest in learning the following techniques: fermentaion, isolation of organic compounds using HPLC, and interpreting NMR spectra including two-dimensional NMR.


	"High-Throughput Mass Spectrometric Analysis of Lipid Signaling in Inflammatory Cells" Mentors: Larry Marnett (Biochemistry) and Alex Brown (Pharmacology)


	"Structure and Engineering of Biosynthetic Enzymes" Mentors: Brian Bachmann (Chemistry) and Tina Iverson(Pharmacology) Description: We are engineering new biocatalysts for the production of clinically important pharmaceuticals. Using a combination of protein structure guided mutagenesis and "directed evolution" methodologies, we are attempting to find biological replacements for important chemical processes. Ultimately these catalysts may offer "green" and less expensive ways to manufacture life saving drugs. Researcher Skills and Interests: This project is best suited for those students who have taken a biochemistry course and have a background understanding and/or direct experience in basic biomolecular methods such as PCR, cloning, protein expression and purification and bioassay.


	*"Exploring Neutralization of S. Aureus* Infections via Trace Metal Binding by Calprotectin" Mentors: Walter Chazin (Biochemistry) and Eric Skaar (Microbiology/Immunology) Description: Calprotectin is an integral part of the innate immune response. In tissues infected by bacterial pathogens such as Staphylococcus aureus, calprotectin acts to suppress the growth of the invading organism. We have obtained evidence that the mechanism for the growth suppressing activities of calprotectin involves the binding of essential trace metals such as zinc and manganese that are critical for the organism's cellular metabolism. This project involves testing this hypothesis through the design, production and evaluation of calprotectin mutants that reduce its capacity for binding these essential metals. Researcher Skills and Interests:** This project is best suited to students that have taken a biochemistry course and who may have knowledge of site-directed mutagenesis by PCR and protein purification. Students should possess an interest in learning state of the art multi-disciplinary research and a combination of the following techniques: bacterial expression and purification of proteins, biophysical analysis using NMR and isothermal titration calorimetry, and cell growth assays.


	"Investigation of Multifunctional Nanoparticle Systems for Imaging and Treatment of Cancer" Mentors: Eva Harth (Chemistry) and Andries Zijlstra (Pathology) Description: The conversion of new cancer drug treatments into clinical practice is delayed by the lack of suitable systems to deliver drug treatment to the cancer location. We propose to develop multifunctional nanoparticles optimized for the simultaneous delivery and imaging of anti-cancer therapy. The project will involve the synthesis of increasingly advanced iterations of multifunctional nanoparticles (Dr. Harth’s lab), which will be tested and validated by in vitro and in vivo models in the Zijlstra Lab. The models will enable the quantitiation of the therapeutic effect by measuring tumor growth, vascularization, tumor cell migration and distant metastasis. Researcher Skills and Interests: Students should have attended classes in Organic chemistry and Biology.


	"Protein Adducts Resulting from Lipid Peroxidation" Mentors: Ned Porter (Chemistry) and Daniel Liebler (Pharmacology) Description:Polyunsaturated lipids undergo reaction with molecular oxygen in vivo and form reactive byproducts that modify proteins. The project focuses on the development of methods to identify these modified proteins and assess the consequences of such modifications. We are particularly interested in how such modifications may impact plasma lipids such as LDL (bad cholesterol) and HDL (good cholesterol). Researcher Skills and Interests: This project is suited for students have taken organic chemistry and one year of biological sciences.


	"Novel Schizophrenia Therapeutics Through Cheminformatics in Drug Discovery" Mentors: Jens Meiler (Chemistry) and Jeff Conn (Pharmacology) Description: The student will use computational methods to analyze the interaction of chemicals with metabotropic glutamate receptors (mGluR). The objective of these studies is to identify features of the chemical structure that are critical for allosteric regulation of mGluRs and therefore key for a therapeutic activity. The student will use computational docking techniques as well as machine learning approaches (artificial intelligence) to study these structure-activity relations (SAR). Through collaboration with the Conn laboratory results will verified through experimental studies such as mutagenesis of mGluRs. Researcher Skills and Interests: This project is best suited for those students for have taken general chemistry, organic chemistry, physical chemistry, and mathematics. Knowledge in computer science is advantageous. Students should possess an interest in learning one or more of the following techniques: machine learning, small molecule docking, pharmacophore mapping, computer programming.

	"Chemistry and Biology of Endogenous DNA Damage by Lipid Peroxidation" Mentors: Carmelo Rizzo (Chemistry) and Larry Marnett (Biochemistry)


	"Natural Product Synthesis and Biology" Mentors: Gary Sulikowski (Chemistry) and Craig Lindsley (Pharmacology) Description: REU students will engage in the multi-step synthesis of small molecule natural products of modest complexity. The natural products of interest have demonstrated biological activity and the synthetic scheme will allow access to structural modifications providing analogs for further biological evaluation. Researcher Skills and Interests: This project is best suited for those students who have taken organic chemistry including lab. Students should possess and interest in learning the following techniques: interpreting NMR spectra, and organic synthesis.


	"Quantum Dot Nanoconjugate Imaging of Neural Receptors" Mentors: Sandra Rosenthal (Chemistry) and Randy Blakely (Pharmacology) Description: In our research we synthesize derivatives of drugs such that they can be attached to fluorescent quantum dots, thereby creating nanoconjugates. These nanoconjugates are then used to image individual nerotransmitter transporter porteins. In this way we can obtain movies of the dynamics of these proteins, which are important in a wide range of mental disorders. Researcher Skills and Interests: This project is best suited for a student interedted in synthetic organic chemistry and an interest in biological problems. Student must have completed two semesters of organic chemistry laboratory.


	"Determination of Absolute Stereochemistry of Pharmacologically Significant Small Molecules" Mentors: Prasad Polavarapu (Chemistry), Craig Lindsley (Pharmacology) Description: Several drugs are derived from chiral organic molecules and the enantiomers of these chiral drugs have significantly different biological properties. At Vanderbilt several small chiral molecules have been discovered where one enantiomer has favorable biological effects, while the second shows little or weak bioactivity. Unfortunately the absolute stereochemistry of these organic compounds is not yet known. The research group of Polavarapu uses a combination of chiroptical spectroscopic and computational methods to determine the absolute stereochemistry of chiral molecules. Students working in this program will actively engage in the experimental and computational studies to determine the absolute configurations. Researcher Skills and Interests: This project is best suited for those students who have taken at least organic chemistry. Interest and background in physical chemistry would be useful. Students will collect experimental chiroptical spectroscopic data, including optical rotation and CD spectra, and analyze these data in conjunction with computational predictions.


	"Discovery and Synthesis of New Antibiotics" Mentors: Gary Sulikowski (Chemistry), Eric Skaar (Microbiology & Immunology) Description: REU students who contribute to this project will focus on the multi-step synthesis of small molecules. Students will learn to design and synthesize molecules to improve biological potency within a chemical series. Our goal is to establish structure activity relationships (SAR) across several series and discover a tool compound for biological target identification of a new class of antibiotics. Researcher Skills and Interests: This project is best suited for those students who have taken organic chemistry including lab. Students should be interested in synthetic organic chemistry, the use of separation/purification techniques (chromatography), analysis (NMR spectroscopy) and medicinal chemistry.

	Copyright © 2009 Vanderbilt University