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2008 Trainees

2008 group photo

 

     
   

2008 Student Testimonials

   

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2008 REU Students

   

Reid Barnett, King University
2009: Reid graduated from King College in May 2009. He is completing research on his senior thesis project: "Mitochondrial effects in C.elegans after exposure to the glyphosate-containing pesticide Touchdown and attenuation with adjuvant phytotherapy of aqueous extract of the Chinese herb Huang qin." He will continue to work with his professor throughout the summer with her NIH funded research on other pesticides containing glyphosate as well as pesticides containing Mn-Zn EBDTCs. In 2010 he hopes to find work in a lab in the Pacific Northwest for a year or two before applying to graduate school.
Mentor:  Brian Bachmann

Research Abstract: Many natural products are derived from specific clades of bacteria known as Actinomycetes and Myxobacteria.  Due to the diverse and abundant secondary metabolites of these two groups of bacteria, they provide the greatest hope for isolation of novel bioactive compounds.  A variety of Actinomyetes and Myxobacteria have been isolated from soil samples from all over the world.  In the search for superior pharmacologically active compounds, cave dwelling bacteria are being investigated for potentially active chemicals. Caves act as natural incubators in that they maintain a constant humidity and temperature throughout the year.  In theory, any indigenous bacteria would have evolved to live and reproduce optimally in the conditions of each specific cave.  The question exists, however, whether changes in temperature will allow for greater variety of bacteria to be isolated. Actinomycete bacteria were present in a number of soil samples.  The samples incubated at 30º yielded the most isolated strains.  At 15º, only one strain of bacteria was isolated.  Table 1 details the soil samples from which each strain was isolated.  At the conclusion of the experiment, colonies from each strain were placed in a 65% glycerol solution and into a -20º freezer to await DNA and bioactivity assessments. It is unknown what the atmospheric conditions are in the caves from which these soil samples were collected.  Due to the lack, also, of DNA analysis on the strains, it is currently not able to be known whether each individual strain is merely a clone of another strain or even a currently identified strain.  Further testing will need to be done to assess any bioactive properties the secondary metabolites of these bacteria may possess. 
     
 

Matthew Bryant
University of Central Florida

2009: Matthew graduated from Central Florida University in May 2009. He has chosen to attend graduate school at Vanderbilt University.
Mentors: David Cliffel & David Wright

Research Abstract:  Near-infrared fluorescence enhancement was observed upon direct coupling of gold monolayer-protected clusters (Au-MPC’s) to platinum monolayer protected clusters (Pt-MPCs) through a peptide linker.  Au-MPCs are known to have intrinsic fluorescence in the near-IR region (em 950-1050 nm), while we report little to no fluorescence for similar Pt-MPCs.  Mixing these nanoparticles in solution, each having oppositely charged ligands, leads to overall decreased fluorescence.  Directly coupling the nanoparticles through a peptide linker causes an increase in fluorescence  intensity randing from 1.5 to 4.5 fold when compared to Au-MPCs , or 12 to 15 fold when compared to quenched Au-MPC/Pt-MPC mixtures.  Reaction of the coupled MPCs with the well known protease trypsin yields decreased fluorescence due to cleavage of the peptide linker, and liberation of Pt-MPCs.   The current work on these MPCs involves a small molecule linker, preferably a thiol with amine functionality to be used as a linker similar to the peptide to see if a larger increase will be observed in the near-IR.  Au-MPC to Au-MPC linkage will also be attempted to see if the fluorescence is due to the Au/Pt interaction.  

     
 

Dain Beezer
Fisk University

2009: Dain is participating in a REU program at Alabama A&M University this summer studying the sun’s corona. Dain is in a dual Fisk/Vanderbilt 3-2 Dual Degree Program in Chemical Engineering. He has just completed three years at Fisk, and will be at Vanderbilt full time to finish the final two years of his degree program. He will graduate with a BS in Chemistry and BE in Chemical Engineering.
Mentors: Ned Porter & Daniel Liebler

Research Abstract:   HNE (4-hydroxynonenal) is a secondary oxidation product of polyunsaturated fatty acids.  This alpha beta unsaturated aldehyde, is very reactive toward nucleophiles such as DNA and proteins. It has been shown to modify proteins that trigger cell signals and alter gene expression pathways responsible for pathogens of some oxidative stress related diseases.  In order to better understand the damaging effects of HNE, identification of HNE target proteins is necessary.  The selective capture and release of HNE protein adducts using click chemistry and affinity purification have been utilized to identify protein adducts followed by LC-MS/MS.  In this study, we develop methods to selectively catch either modified proteins or modified peptides in order to enrich adducts for LC-MS/MS analysis. Alkynylated HNE (aHNE) was added to human plasma and incubated at 37 degrees followed by reduction using sodium borohydride. The reaction mixture was filtered with MWCO=10kd to remove small molecules.  The Adducts were then clicked with biotin-azide in the presence of ascorbate, copper sulphate, and ligand.  The biotinylated proteins were either immobilized onto streptavidin beads overnight in  a cold room then washed with various solutions to remove nonspecific binding proteins (protein catch) or trypsinized in solution followed by streptavidin purification (peptide catch).  The washed streptavidin beads were suspended in PBS buffer and exposed briefly to UV light (365nm) to release the adducted proteins or peptides.  In the case of protein catch, the photo eluate from the streptavidin beads was resolved by SDS-PAGE.  The gel bands were excised and digested with trypsin in gel.  The adducts that were prepared from both protein catch and peptide catch were analyzed using LC-MS/MS.  The data were searched against a human protein database in Sequest and identified the adducted proteins using ID Picker.  Thirty-nine protein groups were identified.  Among them human serum albumin (HSA) and Apolipoproteins (ApoA1) were identified to be highly modified with aHNE.  In the case of HSA, Michael adducts have been found on H67, H146, and K199.  In the case of ApoA1, HNE has been adducted on H162, H193, and H199.  Based on this observation, it would be interesting to pursuit further studies of these proteins to explore possible link to oxidative stress related diseases. 

   

 

   

Charles Johnson
Rockhurst
Mentor:  Michael Stone

     
 

 

David Lonie
Austin Peay University
David graduated from Austin Peay University in May 2009 and will be going to SUNY-Buffalo (Dr. Eva Zurek) to do computational chemistry work on solids under extreme pressures. He has been working with developers from across the US and Europe recently on Avogadro (http://avogadro.openmolecules.net/). Between that work and the computational modeling he did for Dr.Bornhop, he's become very interested in computational work. As a result of the work David did last summer in the Bornhop group, he has a patent pending.

Mentor: Daryl Bornhop

 

     
   

Tomi Oluwatola
Howard University
2009: Tomi graduated from Howard University in May 2009. She will begin Medical School at Howard University in the fall.

Mentors: Gary Sulikowski & Craig Lindsley

Research Abstract:  Advances in the Development of Positive Allosteric Modulators of Metabotropic Glutamate Receptor Subtype 5 (mGluR5).  ADX-47273, [(S) - (4-fluorophenyl) (3-(3-(4-fluorophenyl)-1, 2, 4-oxadiazol-5-yl) piperidin-1-yl) methanone], a recent compound of Addex Pharmaceuticals selectively modulates mGluR5 in the presence of an endogenous agonist and thus represents a potential antipsychotic treatment. Over 50 analogues have been synthesized and are being examined for their response to glutamate using fluorometric Ca2+ assays.  The analogues were prepared by diversifying aryl groups at two points about an (R) or (S)-3-oxadiazolyl-piperidine scaffold. The compounds were synthesized by EDC amide coupling and subsequent dehydration. Our assay shows that there is a ~10 fold difference in potencies between the R and S enantiomers with the S-enantiomer being consistently more active. We have also noticed that while some of the compounds are solely potentiatiors others show agonist activities in addition to potentiation. Two leads with similar efficacies to the patent compound were discovered, one of which will likely be examined on an animal model.

Publications
D. W. Engers, A. L. Rodriguez, R. Williams, A. S. Hammond, D. Venable, O. Oluwatola, G. A. Sulikowski, J. Conn, C. W. Linsdley, "Synthesis, SAR and Unanticipated Pharmacological Profiles of Analogues of the mGluR5 Ago-potentiator ADX-47273," ChemMedChem, 2009, Volume 4, Issue 4, Pages 505-511

 
     
   

Felicia Udoji
Tennessee State University
2009: Felicia, a senior at Tennessee State University, is participating in a REU program under a NIH grant in the Cliffel group at Vanderbilt University.
Mentors: Eva Harth & Heidi Hamm

Research Abstract:  Recently, there has been a significant demand for novel delivery and imaging agents to meet requirements of specific biological environments.  In this realm, we have utilized a water-soluble star polymer, synthesized from RAFT polymerization techniques with and without fluorescent cores. The introduction of suitable functionalities allowed the post-modification within inorganic imaging reagents, peptidic structures and dendritic molecular transporters through mild thiol-ene chemistries and chelating entities. Molecular transporters are vital due to their exceptional ability to transfer molecules into subcellular locations. Overall, we have created unique water-soluble macromolecular systems in a size regime of 20-30 nm with the opportunity to further investigate challenging tissues and cells towards the early detection, imaging and treatment of inflammatory tissues and diseases.  This type of system could prove to be invaluable in the area of medical research.

 
     
   

Emily Wang
Vanderbilt University
2009: Emily, a senior at Vanderbilt University, is at Rice University in Houston, TX this summer participating in the Rice Quantum Institute REU Program.

Mentors: Gary Sulikowski & Craig Lindsley

Research Abstract:   Recognized as a valuable resource for biologically active metabolites, actinomycete bacteria are a significant source of new cytotoxic compounds against certain types of cancer. Lucentamycins A-D were recently isolated from the actinomycete Nocardiopsis lucentensis by Cho and co-workers, and two of these peptides demonstrated high cytotoxicity against HCT-116 human colon carcinoma. A key step in the total synthesis of lucentamycins A-D is the formation of the ethylideneproline core. An efficient synthetic scheme has been devised to form this core fragment starting with commercially-available chiral sources. The scheme employs a four-step conversion of D-serine to Garner’s aldehyde, which is then further elaborated to provide an enyne suitable for ethylideneproline ring formation. Metal-catalyzed enyne cyclization using zirconocene, titanium, or palladium is predicted to give rise to the desired ethylideneproline core.

Publications:
Progress toward the Total Synthesis of Lucentamycin A: Total Synthesis and Biological Evaluation of
8-epi-Lucentamycin
AJ. Org. Chem. 2009, 74, 8852–8855

 
     
   

Sophie (Ruoxi) Zhao
University of Pennsylvania
2009: Ruoxi is a senior at the University of Pennsylvania with a double major in Chemistry and Economics. This summer she will be doing research for two sets of professors at Wharton Business School at U. Penn. One of her jobs (for two Accounting professors) involves the characterization of fraud cases using a database of about 5,000 cases, the goal being to assess what kind of fraud cases tend to occur at certain lifetimes of a firm, if they can be forecasted, and when they do occur, how much they tend to cost the firm. Her second job (for four professors in the Business and Public Policy department) involves a series of projects including characterizing firm sizes/lifetime by industry, profiling banks to investigate how access to regular financial institutions affects the impact of payday loans, and building a database on court cases involving eviction from rental apartments and houses. After graduation she will apply to Ph.D. programs in Applied Economic Policy/Strategic Management.

Mentor: John McLean

Research Abstract:   Gas-phase studies of oligonucleotides, combined with theoretical modeling, offer insights into the intrinsic structural and energetic conformations of oligonucleotides that are otherwise unobtainable (or very challenging to obtain) through conventional methods such as X-ray crystallography and NMR due to instrumental resolution and solvent effects. Based on differences in intramolecular interactions and packing conformations of isobaric oligonucleotides, ion-mobility mass spectrometry (IM-MS) provides two- dimensional separations based on mass-to-charge ratio (m/z) and drift time (td, which can be linearly related to molecular structure through calculation of collision cross sections). Single-stranded oligonucleotides of 4 bases of the same molecular weight were studied with positive ionization mode MALDI-IM-MS and their collision cross sections were calculated. The results indicate that isobaric oligonucleotides with a minimal drift time difference of 18 μs can be successfully separated on the 2D IM-MS plot. This leads to the potential application of IM-MS for the characterization of conformational isomers and post transcriptional modifications of oligonucleotides, DNA, and RNA.

Publications
L. S. Fenn, M. Kliman, A. Mahsut, S. R. Zhao, and J. A. McLean, "Characterizing Ion Mobility-Mass Spectrometry Conformation Space for the analysis of Complex Biological Samples," Anal. Bioanal. Chem.,2009, May;394(1):235-44