REU Publications and Presentations
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This collection contains publications with REU student co-authors from their summer at Boston University, from the "Fundamental Chemical Research Addressing Problems in Biology". Also included in this collection are the summer's end poster presentations by the REU students, held annually at our "Summer's End REU Research Celebration". Some posters have not been uploaded pending publication of results.
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Item 2014 REU Poster: Synthesis of Novel Beta-Amyloid Oligomer Inhibitors for the Treatment of Alzheimer's Disease(2014-08) Colon, GerardoAlzheimer's disease is a condition which affects over five million Americans, making it the sixth leading cause of death in the United States. This, combined with the fact that Alzheimer’s currently had no known cure, makes it a particularly expensive drain on the medical industry. In the 2013 fiscal year alone, caregivers provided a total of 17.7 billion unpaid care hours, which amounts to over $220 billion. A certain ligand (DS-26) , which has been previously proven to be effective against Alzheimer’s in in silico studies was synthesized and tested via Surface Plasmon Resonance (SPR). In addition, variations of this ligand ( DS-207 through DS-307) were synthesized and tested via SPR as well.Item 2014 REU Poster: Measuring Tryptophan Metabolism Using Analogs of Tryptophan(2014-08) Diallo, ThiernoItem 2015 REU Poster: Exploring the Chemical Mechanisms of Fungal Succession(2015-08) Ford, VanessaDecomposition of dead organic matter (i.e. litter) is driven by diverse communities of decomposer fungi that turn over regularly and frequently during the course of decay. The mechanisms by which decomposer communities assemble, and how the assembly process influences eco-system-level biogeochemistry, are unclear. Our objective was to determine the processes that give rise to consistent patterns of dominance during succession in diverse decomposer communities.Item 2014 REU Poster: Quantifying Lipid Contents In Liposomes with Enveloped Plasmonic Nanoparticles(2014-08) Seytono, BeatrixPhosphatidylserine(PS) and monosialotetrahexosylganglioside(GM1) are examples of two host-derived lipids in the membrane of enveloped virus particles that are known to contribute to virus attachment, uptake, and ultimately dissemination. We learn the binding infinity of PS and GM1 lipid by using gold nanoparticle (GNP) since it is stable and conductive. Besides, changing concentration of lipid on the virus can control how the virus infective. The performed studies can use identify unknown concentration of lipid.Item 2013 REU Poster: Investigating the Surface Charge of HIV-1 Virus-like Particles Using Plasmonic Nanoparticles(2013-08) Edmonds, EthanIn metals, the quanta of oscillations of electrons is referred to as a plasmon. In a situation where two plasmons are nearby, oscillations can occur between the spheres in a process called plasmon coupling. The closer the spheres are to each other, the stronger this force will be. This is the main idea used in plasmon coupling microscopy. A clear correlation between surface charge of gold nanoparticles and their interactions with virus particles was found. The Reinhard lab plans to continue to research this and eventually map the surface charge of the virus particles, which is an important factor in virus-cell interactions.Item 2013 REU Poster: Modulation of Indolic Plant Defense compound Synthesis by Tryptophan Analogs(2013-08) Sanon, Marie PriscaLike bacteria and fungi, plants are able to synthesize aromatic amino acids Tyrosine (Tyr), Phenylalanine (Phe) and Tryptophan (Trp). Those amino acids are used in plants not only for protein synthesis, but also for a variety of compounds that control development and defense. Arabidopsis thaliana uses Trp to produce distinct secondary metabolites that function as deterrents to herbivory (indole glucosinolates), as defense against microbial pathogens (camalexin) and as growth regulators(indole-3-acetic acid). To better understand the relationship between Trp biosynthesis and indole glucosinolate (IGs) production, we have tested different analogs of Trp on Columbia, a wild-type Arabidopsis accession. We have found that alpha-methyl tryptophan cannot be incorporated into IGs and in fact inhibits IG synthesis.Item 2013 REU Poster: Proposed Synthesis for Electron-Rich Nanohoops(2013-08) Pantelopulos, GeorgeCarbon Nanotubes (CNTs) are nano-scale tubes composed of fused benzene rings. The electronic and optical properties of CNTs are determined by chirality and diameter. CNTS are of great interest in developing a multitude of revolutionary technologies due to these properties. A general synthesis was developed which is used to create CPPs with diameters of 7-12 benzenes ([7]-[12] Cycloparaphenylene). It hinges upon the syn conformation of a masked benzene ring which has two rings off para positions with aryl substituents.Item 2015 REU Poster: Cloning, Expression and Purification of HisSumoMet18TevStrep, and Chemical Crosslinking of Proteins in the targeting Complex of Cytosolic Iron Sulfur Cluster Pathway(2015-08) Hassan, ZanubIron sulfurs play an important role in many biological functions such as: DNA replication, and repair, amino acid metabolism, and respiration. In yeast, the 4Fe-4S cluster needed by proteins located in the nucleus and in the cytosol are assembled and inserted by the Cytosolic Iron Sulfur Cluster Assembly (CIA) pathway. These clusters are assembled by the scaffold and sent to inactive Apo proteins (without clusters) by the targeting complex. In the cytosol, there is a three protein complex called the CIA targeting complex that identifies apo-targets in order to assemble them to their cofactor. This targeting complex comprised of the protein Cia 1, Cia 2, and met18 which are yeast proteins. However, the mechanism by which this occurs has not been established. One thing that has limited our ability to understand apo-enzyme recognitions has been problems that has to do with purification of the individual components of the CIA targeting complex. Previous work has shown that purification of Met18 is challenging due to purification of many undesired truncated products. To optimize purification of the full length protein, I designed a construct with a C-terminal Strep tag. Another challenge faced is the weak and dynamic interaction that exists between the CIA targeting components and apo-proteins. To stabilize these interactions so they can be characterized, I developed a method to covalently crosslink Cia1 to Cia 2 The pure full length Met18 was purified using the new construct that was purified using the new construct, and using a streptavidin affinity resin. Also, the mixture of both Cia 1 and Cia 2 formed what looks like a dimer and a monomer. Cia 2 alone also crosslinked, while Cia 1 alone did not have any crosslinked product which was what we expected because of the prior knowledge we have about how they exist. Now with sufficient amounts of each component of the targeting complex at our disposal, the interactions between these proteins can now be defined, and to help with biochemical characterization, crosslinking Cia1 and Cia2 using DSS crosslinker shows that the dynamic interactions that exists between the trafficking complex components can be stabilized using DSS crosslinker.Item 2014 REU Poster: Purification and Enzymatic Activity of Cfd1 and Nbp35(2014-08) Mushajiang, MierzhatiThe Cytosolic Iron-Sulfur Cluster Assembly (CIA) pathway consists of eight proteins responsible for Iron-Sulfur cluster assembly and transfer to extramitochondrial apo-protein targets. Cfd1 and Nbp35 are two of these proteins that are responsible for assembling and transferring Iron-Sulfur clusters. Unlike other CIA proteins they also possess the ability to hydrolyze ATP. When both of them were purified in our lab, there are co-purified contaminants. It is unclear that if these co-purified contaminants contribute background activity to ATP hydrolysis. Therefore it has been my job to purify these proteins further and asses the affect of increased purity on ATPase activity by using an enzymatic readout of ATP hydrolysis. We found that most effective method for removing contaminants from Cfd1 and Nbp35 is using Co resin. Our results also suggest that co-purified contaminants are not ATPases.Item 2014 REU Poster: Expression and Characterization of WT BMUL4434 from Burkholderia multivorans(2014-08) Johnson, Santina C.Bacterial cytochrome c peroxidases (bCcPs) are di-heme enzymes that protect the cell from peroxide by reducing it to water. Alternatively, MauG is a di-heme enzyme that is similar in structure to bCcPs, yet is a poor peroxidase. Instead, MauG catalyzes the formation of tryptophan tryptophyl quinone (TTQ) the catalytic cofactor required for MADH. Previous work in the Elliott lab used bioinformatics to investigate how sequence divergence within peroxidase superfamily reflects functionality. The bioinformatics analysis led to the discovery of unreported di-heme enzymes found in all strains of Burkholderia. BMUL4434 from Burkholderia multivorans was gene synthesized and codon optimized for expression in E. coli. We expressed and purified WT BMUL4434 and obtained initial optical characterization to understand where it falls in the peroxidase superfamily.Item 2013 REU Poster: Purification and Characterization of a Ferredoxin from Mycobacterium tuberculosis(2013-08) de Oliveira, Jonas A.M. tuberculosis possesses a sulfite reductase (MtsirA) that is over-expressed when the bacteria is in its dormant stage of infection. MtSirA catalyzes the six-electron reduction of sulfite to sulfide. Previous kinetic studies of MtsirA have used methyl viologen (MV), a chemical reductant, as an electron donor. The goal of this work is to purify and characterize a ferredoxin from M. tuberculosis (MtFd) and determine if MtFd can act as an electron donor to mtSirA, with the ultimate goal of using it as a more physiologically relevant electron donor in kinetic studies of mtSirA. We have found that that MtFd purifies without a cluster and must be chemically reconstituted. MtFd likely contains a [4Fe-4S] cluster, and may be able to donate electrons to mtSirA.Item 2013 REU Poster: Small Molecule Evolution: A Biomimetic Approach to Small Molecule Lead Generation and Optimization(2013-08) Bloodworth, Tiara L.The goal of my project was to determine the standard calibration curves of compounds in the small molecule evolution library. Solutions of several small molecules were prepared at various concentrations and analyzed using the nanoAcquity UPLC instrument. Diode array traces were collected for each solution, in which UV-active compounds showed up as a single peak in the chromatogram. These peaks were extracted at a single wavelength (usually max) to produce new traces, and peak area was determined. Plots of peak area against concentration were obtained for each small molecule, and the results showed a linear relationship between concentration and peak area at a single wavelength. Equations of the line were found and this data will be used to determine unknown concentrations of small molecules in solution after chemical reactions are performed. The information will be vital for the biological assessment of new compounds formed by chemical modification.Item 2015 REU Poster: Body Fluid Analysis by Surface Enhanced Raman Spectroscopy for Medical and Forensic Applications(2015-08) Mei, ZheSurface Enhanced Raman Specroscopy(SERS) of human erythrocytes on Au nanoparticle SiO2 substrates excited by 785 nm laser radiation in a Raman microscope were reported. It was determined that the signal of Red Blood Cells originates entirely from hemoglobin. Preliminary analysis of the forensics applications of SERS determined that SERS offers a single, rapid, highly sensitive analytical tool for the identification of human body fluids and species origin of blood samples. SERS detection limits for body fluid detection one or two orders of magnitude greater than current forensic techniques.Item 2013 REU Poster: Development of SERS-Based Metabolic Profiling Method for Leukemia Cells(2013-08) Ansah, MaureenMetabolic profiling, or the study of low molecular weight intermediates, as a result of activation of tu-morigenesis pathways; has been found to be an important and successful measurement for the pathological state of cells, i.e. leukemia cell. SERS-based method provides us an alternative, ultra-sensitive label-free method to study the cancer cells metabolites. Abnormal metabolite molecules can be identified with comparison to the spectra of non-cancerous cells. The identity of these molecules can be confirmed by comparison with modeling compounds.Item 2014 REU Poster: Determining the Efficiency of Surface-Enhanced Raman Spectroscopy Substrates in Body Fluid Identification(2014-08) Hatfield, MarsellaA forensic scientist has many goals at a crime scene, including identifying unknown stains (possibly containing body fluids) and collecting evidence for further DNA testing. Body fluid identification is important to understand the nature of the crime and the possible perpetrators. The current methods of body fluid identification include alternate light sources, phenolphthalein, and luminol tests, which can give yield false positive results. A method for overcoming these current limitations is to utilize Raman and surface-enhanced Raman spectroscopy to identify the substance.Item 2014 REU Poster: Total Synthesis of Myxopyronin(2014-08) Lim, LinusMyxopyronin A and B was first isolated in the early 1980s from the bacteria Myxococcus fulvus. These molecules possess a single stereocenter with a (R) – configuration. The ability to inhibit the growth of several Gram-positive and Gram-negative bacteria and to selectively target bacteria RNA polymerase over human polymerase makes Myxopyronin a molecule worth studying. This project approaches the total synthesis of Myxopyronin via racemic and asymmetric routes.Item 2014 REU Poster: Synthesizing Antiviral Agents Effective Against Hepatitis C Virus(2014-08) Steck, EmelieChronic Hepatitis C Virus, or HCV, affects 120-150 million people worldwide. HCV causes liver disease and there is not a vaccine or an effective treatment. Previous research indicated that two compounds, SL209 and SL205, inhibited the dimerization of core, the capsid protein of HCV responsible for assembling and releasing the infectious particle2. Current research is focused on testing the effect that the structure of these compounds has on their bioactivities, so analogues with similar structures to SL209 and SL205 are being synthesized.Item 2013 REU Poster: Synthetic Utilization and Exploration of Gallium(2013-08) Landreth, Adrian J.Pursuit of naturally occurring compounds or those resembling natural products is a major interest to organic chemistry. These compounds can contribute to humanity in multiple applications. Many compounds used in society are known as heterocyclic compounds. In this work, we described the gallium (III) catalyzed cyclization of bis-alkynes to produce new heterocylic scaffolds that can be used for diversification and subsequent screening for biological activities.Item 2015 REU Poster: Synthesis of New Scaffolds via Bisalkyne Cyclizations Catalyzed by Triflic Acid(2015-08) Duque, Jaime Alvarez; ;The need for novel synthesis methods for the creation of unique molecular scaffolds is a present-day topic in medicinal chemistry. Current methods of drug discovery rely largely on an economical approach, biasing the efforts of synthesis to the creation of facile or pre-explored scaffolds. Diversity-oriented synthesis seeks to reverse this trend by facilitating the preparation of complex molecules. Building on a diversity-oriented approach, the synthesis of Indenopyridene scaffolds from 1,6 N-tethered diynes was explored. The construction of the scaffold is achieved through a novel acid-catalyzed cycloisomerization/Friedel-Crafts mechanism, leading to a heterocyclic three-ring system. The effect of substituents on the bisalkyne precursors, as well as reaction conditions such as temperature and concentration, were analyzed. Findings suggest that electron-withdrawing substituents tend to facilitate product formation, while electron-donating groups hinder the reaction. A trend in concentration and temperature also seems to be present, indicating that decreasing these parameters results in increased product yield. The reaction provides an easily diversifiable heterocyclic scaffold, and may prove to be a useful tool in both synthetic organic chemistry and medicinal chemistry.Item 2015 REU Poster: Cyathane Inspired Scaffold Synthesis in Flow(2015-08) Reinhardt, BenjaminCyathane natural products were proven biologically relevant molecules as they stimulate the expression of NGF. As such some cyathanes are potential therapeutic agents for Alzheimer’s disease. A preliminary pharmacophore model was produced which consists of a simplified seven-six bicyclic molecular scaffold. A synthetic route could utilize the Buchner reaction, but until this time only unsubstituted, carbonyl stabilized diazo compounds have been used due to the explosive nature of other diazo species. Such a bicyclic compound would require further modification to remove the carbonyl functional group. Flow chemistry was utilized to overcome these restrictions with the Buchner Reaction. 1-(4-diazopentyl)-2-methoxybenzene was used as the model substrate, and numerous electronic and substitution analogs were synthesized to further expand the scope of the Buchner Reaction in flow. Optimizing the flow reaction to use unprotected hydrazine to form a free hydrazone intermediate in situ was also explored. The (5-(2-methoxyphenyl)pentan-2-yl) hydrazone was successfully formed, while further results are yet pending.