UNDERGRADUATE RESEARCH -- Summer 2005

Student: Craig Betchart ’06  

Home Town: Concord, NH
in the Mehta lab    
Project: X-ray Diffraction and NMR Studies of Peptide-Solvent Interactions
 
  Research Description
  Short peptides are strings of a few amino acids. They serve as stringent tests for our understanding of protein folding. Our goal is to experimentally understand the role of the solvent in determining peptide
secondary structure. Our aim is to study several alanine- and glycine-rich model peptides using x-ray diffraction and nuclear magnetic resonance (NMR). Both solid-state and liquid-state NMR will be used to acquire information about the conformation of these molecules in forms ranging from crystalline to ideally dilute solutions. Specifically, we are interested in changes in the peptide backbone torsion angles.
X-ray diffraction data will also be taken to assess crystalline order for partially solvated states and results from the two sets of experiments compared.
 
 
 
 
 
 
 
    Other interests: Swimming, skiing, baseball, Linux.

 

Student: Chris Boyd ’07  

Home Town: Ithaca, NY
in the Matlin lab    
Project: Organic Synthesis and Investigative Photochemistry of Oxyallyl Diradicals as Reactive Intermediates
 
  Research Description
  Oxyallyl diradicals, resonance-stabilized species with two unpaired electrons, have been invoked by chemists as intermediates in certain reactions. However, there is currently a lack of firm evidence for the existence of these radicals, especially since such radicals could tautomerize to form substituted cyclopropanones, species with considerable Baeyer strain but without unpaired electrons. We aim to synthesize compounds that could give rise to oxyallyl radicals theoretically predicted to be more stable, and that could give rise to novel and interesting polycyclic systems. The molecules will be bombarded with light to induce the formation of reactive intermediates, and the bonding in such intermediates will be studied via infrared spectroscopy. Currently, we are working to confirm a procedure for inducing a regiospecific unsaturation in ketones, which we plan to use on a cyclooctanone derive with a long alkenyl sidechain.
 
 
 
 
 
 
 
    Other interests: Physics, biology, Elizabethan and Jacobean drama, left-wing politics, playing board games and video games with my friends, The X-Files, Law & Order

 

Student: Michael Brenner ’07  

Home Town: Northville, MI
in the Thompson lab    
Project: Isolation of Individual Capsaicinoids from Chili Peppers
 
  Research Description
  Capsaicinoids, N-vanillyl acyl amides, are the “hot” components of chili peppers (genus Capsicum), many spicy foods, some topical pain-relief creams, and most defense sprays. More than twenty naturally-occurring capsaicinoids are known with small, but significant differences in structure. Only four of the compounds are available commercially in pure form. The goal of this research is to develop a method for the isolation of milligram quantities of individual capsaicinoids from chili pepper.
The first stage of the process involves argentation solid phase extraction that provides very good separation of the capsaicins (the group of capsaicinoids that contain a double bond in the acyl portion of the molecule) from the non-capsaicins (no double bond). Silver ion complexes with alkenes, and, thereby, the capsaicins are retained more strongly on a silver-loaded strong cation exchange resin. The non-capsaicins elute with moderately polar solvents, while only polar solvents can remove the capsaicins. Work this summer will improve and optimize this initial separation step.
The second stage of the process will employ semi-preparative liquid chromatography to separate the individual capsaicins from each other and also the individual non-capsaicins from each other. The effectiveness of a C30 phase to provide the necessary chromatographic resolution of the two mixtures will be tested this summer. Individual capsaicinoids will be isolated by collection of the chromatographic eluate at specific retention times and then evaporation of the solvent. The purity of the separated materials will be assessed by NMR and comparison to reference NMR spectra obtained earlier in our laboratory.
 
 
 
 
 
 
 
    Other interests: Roller hockey, Rollerblading, Computers, Computer games, Reading, lying in the grass looking at the stars.

 

Student: Ye Lin Choi ’06  

Home Town: Old Tappan, NJ
in the Fuchsman lab    
Project: A Method for Determining the Concentration of Hydrogen Peroxide in the Presence of NADH or NADPH
 
  Research Description
  Hemoglobin and myoglobin are the proteins in red blood and muscle cells that function by reversibly binding oxygen. In addition, hemoglobin and myoglobin both catalyze a reaction between NADH or NADPH (two-electron reducing agents important in many biological reactions) and dissolved oxygen, producing NAD+ and hydrogen peroxide. We are trying to measure the relative amounts of NADH (or NADPH) consumed and hydrogen peroxide produced. We h
ave observed that NADH interferes with known assays for hydrogen peroxide, and are using spectroscopic, inorganic, and enzymatic methods to develop a means to eliminate this interference. Our final goal is to use our new assay to determine relative amounts of NADH (or NADPH) consumed and hydrogen peroxide produced.
The reaction between NADH or NADPH and oxygen to produce hydrogen peroxide may be involved with reperfusion injuries, which result from the return of oxygen after prolonged oxygen deprivation in living tissue.
 
 
 
 
 
 
 
    Other interests: Traveling, movies, swimming, languages, cooking, music, violin/viola

 

Student: Mae Gackstetter ’06  

Home Town: Inver Grove Heights, MN
in the Thompson lab    
Project: Testing of Devices for the Determination of Ethanol in Oral Fluid
 
  Research Description
  Roadside testing for ethanol in suspected drunk driving cases is becoming more common, and the body fluid most easily obtained from the suspect at the roadside is saliva or, more generally, oral fluid. Consequently, a number of devices that purportedly make an accurate measurement of ethanol concentration in oral fluid are now offered for sale to law enforcement and the general public.
The goal of the research, sponsored by the National Institute of Standards and Technology (NIST), is to test the effectiveness of some of the available testing devices and compare their technical merits with a standard gas chromatographic (laboratory) method for ethanol. NIST has an interest in setting standards for measurements that intersect with manufactured goods and services, particularly in the law enforcement area (NIST Office of Law Enforcement Standards).
The project, with a completion deadline at the end of the summer, involves validation of the gas chromatographic method, learning how to collect, process, and store oral fluid, measuring the specificity, precision, and accuracy of the testing devices, and checking the claims of the manufacturers. Full written and oral reports will be presented to NIST upon completion of the project.
 
 
 
 
 
 
 
    Other interests: Fencing, medicine, forensic pathology, Latin, belly dancing, wood-carving, the outdoors, music.

 

Student: Amelia Hadler ’08  

Home Town: Atlanta, GA
in the Mehta lab    
Project: Synthesis and Purification of Carbon-13 Labeled Peptides
 
  Research Description
  Our project deals with peptides, which are short chains of amino acids. We study tripeptides to determine their structure and bond angles at different levels of hydration and in different solvents using NMR and x-ray diffraction. Later we may turn our attention to slightly longer peptides. Specifically, we synthesize peptides composed of alanine and glycine, the two simplest amino acids, using solid phase synthesis. This involves attaching an Fmoc protected amino acid to a resin bead before loading it into an automated peptide synthesizer. Then the amino acid is deprotected and the second amino acid is attached. The final step in the synthesis is to cleave the resin from the peptide using methylamine solution. This results in a crude product that must be purified using high performance liquid chromatography (HPLC). We first analyze a small amount to produce a chromatogram of our sample. Using this information, we can then purify the entire sample using preparative HPLC. We are beginning to synthesize carbon-13 labeled peptides for use in later NMR experiments.
 
 
 
 
 
 
 
    Other interests: Playing French horn, cooking, backpacking, baseball, the Civil War, old movies, history, and religion.

 

Student: Emily Magorian ’07  

Home Town: Baltimore, MD
in the Whelan lab    
Project: Selection of an Aptamer that Recognizes CA 125
 
  Research Description
  The selective detection of biomolecules in serum is an important tool for basic research and clinical applications. Traditionally, such assays have relied on antibody molecules as the basis of detection. In this project we will explore a relatively new class of affinity molecules—aptamers—and develop analytical assays that exploit their unique advantages. Aptamers are single-stranded nucleic acid molecules with recognition ability comparable to antibodies. The process of aptamer selection begins with a large random pool of oligonucleotides. The oligos are allowed to interact with the target protein of interest, and those that bind well to the target are separated from those that do not. Good binders are amplified by polymerase chain reaction, and the cycle of selection and amplification continues until the pool converges on a small number of excellent binders. This summer, we will select a DNA aptamer that recognizes CA 125, a protein that is widely used as an ovarian cancer biomarker.
 
 
 
 
 
 
 
    Other interests: Singing, tae kwon do, cooking, poetry, languages and hiking.

 

Student: Amie Patchen ’06  

Home Town: Ithaca, NY
in the Craig lab    
Project: Structural Studies of the cis and trans Isomers of Hexatriene by Rotation and Vibration-Rotation Spectroscopy
 
  Research Description
  DFT calculations of the structures of the two isomers of hexatriene suggest that the structural consequences of pi-electron delocalization are greater than for butadiene. In addition, hexatriene is the next member in the series of polyenes, which are important structures in molecules of the vision apparatus and in photosynthesis. Thus, complete structures, preferably equilibrium ones, are being sought for the two isomers of hexatriene. Pure rotational transitions from microwave spectroscopy are being used for the slightly polar cis isomer. The rotational structure in high-resolution infrared spectroscopy is being used for the nonpolar trans isomer. Various carbon and deuterium isotopomers must be synthesized. This project is being done in cooperation with other laboratories where high-resolution spectrometers are available.
 
 
 
 
 
 
 
    Other interests: Swing dancing, swimming, languages, religion, writing, traveling, cooking, rock climbing and teaching.

 

Student: Anita Ofori-Addo ’06  

Home Town: Accura, Ghana
in the Whelan lab    
Project: Selection of an Aptamer that Recognizes CA 125
 
  Research Description
  Aptamers are single stranded oligonucleotides—DNA or RNA—that are selected out of a large, random pool on the basis of a particular function. Often aptamers function as high-affinity binders to biological molecules. The process of selecting aptamers relies on repeated cycles of selection and amplification until a small number of oligos with the desired binding property dominate the pool. Selection can occur in one of two formats, on a stationary phase or in free solution. My contribution to this project is the development and optimization of a selection process that will identify candidate oligos that bind to the ovarian cancer biomarker CA 125. It is hoped that such aptamers may form the basis of new detection methods for ovarian cancer.
 
 
 
 
 
 
 
    Other interests: Meeting people, dancing, languages, traveling, volunteering, eating food from different parts of the world.

 

Student: Nolan Pearson ’06  

Home Town: Bedford, TX

in the Whelan lab    
Project: Development of an Antibody-based Affinity-probe Capillary Electrophoresis Assay for CA125
 
  Research Description
  Capillary electrophoresis (CE) separates biomolecules with excellent efficiency on the basis of their mobility in an applied electric field. The separation is accomplished in a glass capillary with an inner diameter on the order of tens of microns. When coupled with laser-induced fluorescence detection (LIF), CE can detect attomoles of protein or other biological analytes. In situations when the analyte of interest is non-fluorescent, it is possible to involve the analyte in a non-covalent affinity complex with another molecule—called an affinity probe—that is fluorescent. The resulting combination of affinity interaction and CE separation is called an affinity probe CE assay (APCE). In this project, an APCE assay for the ovarian cancer biomarker CA 125 will be developed. It is expected that very small amounts of this important biomarker may be detected via an APCE-LIF assay.
 
 
 
 
 
 
 
    Other interests: Piano, tennis, German, movies, Scrabble and Proust

 

Student: Lynn Shen ’07  

Home Town: Philadelphia, PA
in the Craig lab    
Project: Structural Studies of the trans,trans and cis,cis Isomers of 1,4-Difluorobutadiene by Vibration-Rotation Spectroscopy
 
  Research Description
  A surprising energy relationship exists between the three isomers of 1,4-difluorobutadiene. The cis,cis isomer has the lowest energy; the trans,trans isomer has the highest energy. This project seeks detailed structural information that should correlate with the energy differences. An equilibrium structure of the polar cis,trans isomer has been found from the joint application of microwave spectroscopy and quantum chemical calculations. For the nonpolar trans,trans and cis,cis isomers the rotational structure in high-resolution infrared spectra is analyzed and related quantum chemical calculations are done. The spectra of various carbon and deuterium isotopomers, which must be synthesized, are needed for this project. This work is being done in cooperation with other laboratories where high-resolution spectrometers are available.
 
 
 
 
 
 
 
    Other interests: Piano, running, basketball, soccer, reading, traveling, biking, listening to music.

 

Student: Yuka Shiheido ’06  

Home Town: Chiba, Japan
in the Fuchsman lab    
Project: A Method for Determining the Concentration of Hydrogen Peroxide in the Presence of NADH or NADPH
 
  Research Description
  Hemoglobin and myoglobin are the proteins in red blood and
muscle cells that function by reversibly binding oxygen. In addition,
hemoglobin and myoglobin both catalyze a reaction between NADH
or NADPH (two-electron reducing agents important in many biological reactions) and dissolved oxygen, producing NAD+ and hydrogen
peroxide. We are trying to measure the relative amounts of NADH (or NADPH) consumed and hydrogen peroxide produced. We have observed that NADH interferes with known assays for hydrogen peroxide, and are using spectroscopic, inorganic, and enzymatic methods to develop a means
to eliminate this interference. Our final goal is to use our new assay
to determine relative amounts of NADH (or NADPH) consumed and
hydrogen peroxide produced.
The reaction between NADH or NADPH and oxygen to produce
hydrogen peroxide may be involved with reperfusion injuries,
which result from the return of oxygen after prolonged oxygen
deprivation in living tissue.
 
 
 
 
 
 
 
    Other interests: Traveling, tea, Chinese, Chinese medicine,
seeing movies, cooking, shopping

 

Student: David Smith ‘06  

Home Town: Cleveland, OK
in the Romberg lab    
Project: Determining the Effects of FtsZ-interacting Proteins on FtsZ GTP Hydrolysis Rate
 
  Research Description
  FtsZ is bacterial tubulin homolog essential to prokaryotic cell division. In vivo FtsZ forms a ring structure that constricts during cytokinesis. In vitro, the FtsZ protein forms polymers that hydrolyze GTP. The stability of FtsZ polymer depends on the extent of nucleotide hydrolysis within the polymer. The cell controls polymerization through regulatory proteins that directly bind FtsZ to affect nucleotide hydrolysis and/or polymer stability. This study will quantify the effects on the FtsZ-GTP hydrolysis rate of two polymer stabilizing proteins, ZipA and ZapA, and one destabilizing protein, EzrA. The extent of hydrolysis will be quantified using HPLC analysis. FtsZ is bacterial tubulin homolog essential to prokaryotic cell division. In vivo FtsZ forms a ring structure that constricts during cytokinesis. In vitro, the FtsZ protein forms polymers that hydrolyze GTP. The stability of FtsZ polymer depends on the extent of nucleotide hydrolysis within the polymer. The cell controls polymerization through regulatory proteins that directly bind FtsZ to affect nucleotide hydrolysis and/or polymer stability. This study will quantify the effects on the FtsZ-GTP hydrolysis rate of two polymer stabilizing proteins, ZipA and ZapA, and one destabilizing protein, EzrA. The extent of hydrolysis will be quantified using HPLC analysis.
 
 
 
 
 
 
 
    Other interests: Flip-flops, finger paint, Mighty Morphin Power Rangers, Oklahoma, tornadoes, homegrown tomatoes, Star Trek, the Great State Fair of Oklahoma, 4-wheelin’, history of science, country music, Doris Day movies, computer science, science fiction novels, snickerdoodle cookies, antidisestabilishmentarianism

 

Student: Matthew Thayer ’08  

Home Town: Livonia, MI
in the Whelan lab    
Project: Development of an Antibody-based SPR Assay for CA 125
 
  Research Description
  Surface Plasmon Resonance Spectroscopy (SPR) provides a means of detecting protein-protein interactions in real time and without the need for labels. One important application of SPR is in the context of assays to detect proteins that are biomarkers of disease. In this project, an antibody molecule that recognizes the ovarian cancer biomarker CA125 will be immobilized onto the sensing surface of an SPR instrument, creating a specific test for CA125. The SPR instrument we will be using is the miniaturized Spreeta sensor. Using this sensor, which about as large as a quarter, may enable this sensitive and selective assay to be transportable, for eventual use in clinical settings or field hospitals.
 
 
 
 
 
 
 
    Other interests: Chilling with friends, reading, eating, and sleeping.

 

Student: Kiri Ulmschneider ’08  

Home Town: Midland, TX
in the Mehta lab    
Project: Synthesis and Purification of Carbon-13 Labeled Peptides
 
  Research Description
  Our project deals with peptides, which are short chains of amino acids. We study tripeptides to determine their structure and bond angles at different levels of hydration and in different solvents using NMR and x-ray diffraction. Later we may turn our attention to slightly longer peptides. Specifically, we synthesize peptides composed of alanine and glycine, the two simplest amino acids, using solid phase synthesis. This involves attaching an Fmoc protected amino acid to a resin bead before loading it into an automated peptide synthesizer. Then the amino acid is deprotected and the second amino acid is attached. The final step in the synthesis is to cleave the resin from the peptide using methylamine solution. This results in a crude product that must be purified using high performance liquid chromatography (HPLC). We first analyze a small amount to produce a chromatogram of our sample. Using this information, we can then purify the entire sample using preparative HPLC. We are beginning to synthesize carbon-13 labeled peptides for use in later NMR experiments.
 
 
 
 
 
 
 
    Other Interests: swimming, reading, knitting, taking naps in the sun, camping and hiking.

 

Student: David Wilson, ’06  

Home Town: Beaver, PA
in the Matlin lab    
Project: Synthesis of Dendrimer-based Metalloenzyme Mimics
 
  Research Description
  Zinc metalloenzymes bind water or hydroxyls to zinc in their active sites, and the presence of this metal is essential to these enzymes’ catalytic activity. Two well-studied examples are carbonic anhydrase, which catalyzes the reaction of carbon dioxide and water and alkaline phosphatase, which catalyzes the hydrolysis of phosphate monoesters. Both of these enzymes use an active-site zinc to activate a water molecule for nucleophilic attack. The complex between zinc and water lowers the pKa of water-bound hydrogen, resulting in activated hydroxyls at reduced pH (7-8).
Our research focuses on creating dendrimer-based mimics of these metalloeznymes. Dendrimers are hyperbranched polymers with a three-dimensional globular structures. They show promise as metalloenzyme mimics because these globular structures are similar to those of naturally occurring enzymes. Our target molecule is based around a nitrogen-substituted dodecane ring that is a reasonably good metalloenzyme mimic on its own. This core creates a hydrophobic catalytic center like those seen in enzymes. Our molecule will also have polyether chains on its exterior; these will make the molecule water soluble. Once our target dendrimer has been synthesized, we’ll add zinc and examine the ability of our molecule to catalyze the hydrolysis of phosphate monoesters.
 
 
 
 
 
 
 
    Other Interests: soccer, basketball, squash, chess, card games (poker, bridge, spades, hearts, etc.)Other Interests: soccer, basketball, squash, chess, card games (poker, bridge, spades, hearts, etc.)