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Undergraduate Research Opportunities Program

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Publication Search Results

Now showing 1 - 10 of 51

Exploration of copper-catalyzed Grignard cross-coupling between 3-halo-4-alkoxybenzoates and bromoisoprenoids

(Georgia Institute of Technology, 2022-05) Lutin, David J.

Allylic functionality, often taking the form of terpenes, is a mainstay of marine natural products. The aryl-allyl connection is particularly common, appearing in several product classes derived from Callophycus serratus, many of which exhibit promising initial biological activities. In pursuit of several total syntheses, which leverage a copper-catalyzed Grignard cross-coupling between a 3-halo-4-alkoxybenzoate and geranylgeranyl bromide, we explored the effects of alkoxybenzoate and halogen substitutions on the coupling. By scrutinizing the constraints and influences of these protecting groups on cross-coupling success, we lay out the potential for downstream deprotection chemistry. Here, we present the results of this investigation, along with a theoretical basis for the observations.
CCSP 2.0: An Open-Source Jupyter Tool for the Prediction of Ion Mobility Collison Cross Sections in Metabolomics

(Georgia Institute of Technology, 2021-05) Watson, Chandler Avery

Tandem mass spectrometric methods revolutionized the chemical identification landscape, allowing serums and molecules to be separated in two or more dimensions. Ion Mobility Mass Spectrometry workflows combined with liquid or gas chromatographic separation have continued to progress chemical identification and further increase the amount and confidence of these identities. Such advancements have also given birth to a new molecular descriptor: the Collision Cross Section, sparking heavy interest in the analytical-computational chemistry to compile these values for known molecules. The main shortcoming has been predicting the CCS value for new molecules such as Poly-Fluorinated Alkyl Sub-stances. Preliminary prediction software has revealed that predicting CCS values for this molecular class is possible, but it can prove temporally, computationally, and financially expensive between different licenses and genetic algorithm. This work combines open-source Python modules (NumPy, Mordred, Pandas, etc.) to construct an alternative workflow that is completely free and capable of running on a mid-specification laptop within a half hour. Using the M-H and combined M+H and M-H datasets taken from the McClean CCS Compendium, median prediction errors of 2.07% and 1.84%, respectively, were found using Support Vector Regression within 5 minutes on a mid-spec laptop, satisfying the 2.50% benchmark. This overall success illustrates the power and versatility of this workflow to produce low errors with datasets as large as 1300+ molecules and as few as 37. This script can be distributed on file-sharing sites like GitHub where other users may customize the free source code to fit their experimental needs.
Discovery of Monoclonal Antibodies for Diagnostics and Therapies Using Conjugate Virus-like Particle Vaccines

(Georgia Institute of Technology, 2021-05) Schroeder, Michelle

Monoclonal antibodies (mAbs) are highly specific antigen binding proteins that are used as biological reagents, therapeutics, and in rapid diagnostics. While mAbs have extensive potential applications, their means production for small molecules and conformationally specific peptides is difficult. Here, we use a method of mAb production in which we pair conjugate virus-like particle (VLP) vaccine with hybridoma technology to produce high-affinity mAbs against three classes of molecules 1) fentanyl derivatives, 2) SARS-CoV-2 peptides, and 3) α-amanitin and microcystin LR cyclic peptide toxins. We successfully produced broad and derivative-selective mAbs against eight fentanyl derivatives. We also showed early signs of success targeting neutralizing and mutant SARS-CoV-2 peptides with conformational specificity using a heterologous prime-boost strategy. Lastly, we produced high affinity mAbs for both α-amanitin and microcystin LR, two highly toxic cyclic peptides. The early success of mAb production against the variety of targets presented in this thesis shows the viability and exceptional versatility of conjugate VLP vaccines as a means to producing mAbs.
Analysis and illustration of primary and secondary structures of ribosomal RNA and ribosomal proteins

(Georgia Institute of Technology, 2020-08) Meade, Caeden Daniel

RiboVision is a collection of applications housed on servers at the Georgia Institute of Technology which serves to facilitate the development of publication-quality diagrams of ribosomal RNA (rRNA) and ribosomal protein (rProtein) structures (Petrov et. al, 2014). In particular, RiboVision seeks to promote analysis of key properties of rRNA and rProteins in primary, secondary, and tertiary structures. As key semantides (ubiquitous macromolecules which carry genetic equivalent to the information intrinsic to DNA molecules and may be used by comparison to inform phylogenetic relationships), comparison of the primary and secondary structures of 16S and 18S RNA allows for the phylogenetic comparison of prokaryotic species and eukaryotic species, respectively (Fuerst, 2001). Sequence alignments are housed on the RiboVision server and stored in a MySQL database. Over the next two semesters, major improvements will be made to the server resulting in the newest edition, RiboVision3, which will feature improvements over the preceding RiboVision2 including the integration of XRNA, a program responsible for the generation of rRNA secondary structures and their exportation of their data into common computer-file formats (CSV, SVG, PDF, etc.) and the PDB Topology Viewer, a program responsible for production of protein secondary structures and their exportation into SVG image files. The core functionality of XRNA - demonstration and editing tools of rRNA secondary structures needs to be iterated upon to allow for a more diverse set of purposes, including processing of high-quality hand-edited images into formats which are compatible with on-server management and conversion into formats native to web browsers.
Synthesis of Degradable Monomers for Ring-Opening Metathesis Polymerization

(Georgia Institute of Technology, 2020-05) Crolais, Alex E.

Ring opening metathesis polymerization (ROMP) is a type of olefin metathesis chain-growth polymerization that has shown great versatility in the field of polymer chemistry. Although it allows polymerization of monomers containing a variety of functional groups, how effective it is in polymerizing degradable monomers is largely unknown. In this report, we demonstrate a novel synthetic pathway to synthesize an acetal-containing degradable monomer that is compatible with ROMP and the Grubbs 3 (G3) catalyst. Polymers made from this monomer were characterized by GPC analysis and underwent degradation studies. Acetals generally undergo hydrolysis in mildly acid conditions and even in biologically relevant pH ranges, so this new monomer will have potential applications in drug delivery systems. The monomer also has the capacity to have its functional groups modified, changing its functionality which will be further studied.
Effects of Nuclear-Targeted Nanoparticles on the Cell Function in Human Oral Squamous Cell Carcinoma Cells During Cisplatin Treatment

(Georgia Institute of Technology, 2020-05) Mann, Breanna E.

This project focuses on evaluating the effects of nanoparticles on the cellular responses in human oral squamous cell carcinoma (HSC) cells during the administration of cisplatin. Cisplatin is an effective chemotherapeutic drug used to treat numerous forms of human cancer. It is, however, also highly susceptible to creating drug resistance in cancer cells. Restriction of the mobility of HSC cells reduces its ability to spread resistant cells throughout the body. In this study, we investigated the cellular mobility of HSC cells in the presence of a combination of cisplatin and nuclear-targeted gold nanocubes. The HSC cells were treated with cisplatin with and without nanocubes to study their effects on the mobility. Trends were assessed for changes in position and velocity over time. It was found that, the presence of nanoparticles alone restricts the displacement of the HSC cells. As an extension, the effects of nanoparticles on drug resistant HCS cells was studied. HSC cells were systematically treated with cisplatin to create cisplatin-resistant cell lines. The viability of these cell lines were then tested at different levels of drug resistance. Furthermore, the effect of nuclear-targeted nanoparticles on bypassing drug resistance in cisplatin-resistant HSC cells were evaluated. Trends amongst cell resistance and nanoparticle presence were assessed. Furthermore, the radius and surface charge were analyzed to understand characteristics that lead to optimal uptake. Additionally, the growth and changes in uptake experienced by cisplatin resistant cells were analyzed to gain insight into how these changes effected uptake of the nanoparticles.
Enrichment and Isolation of Iron-Oxidizing Bacteria from an Ancient Earth Analogue

(Georgia Institute of Technology, 2019-08) Ghazi, Layla

Fe2+ was an abundant component of ancient anoxic oceans and could have acted as a respiratory electron donor. The overall goals of this study were to test whether anaerobic microbial growth could occur with Fe2+ as the electron donor in Fe2+-rich sediments from an ancient ocean analogue (Lake Matano, Indonesia) and to determine the taxonomic identity of the bacteria. Sediments were incubated with Fe2+ sulfide as the electron donor in a nitrogen:carbon dioxide (90/10%) atmosphere. Manganese (III), nitrate, nitrite, and oxygen were provided as electron acceptors. With Mn3+ as the electron acceptor, cultures showed some evidence of growth near the middle of the gradient tube. However, orange Fe3+ oxides were absent, suggesting that anaerobic Fe2+ oxidation had not occurred. Ferric oxides were also absent in tubes containing nitrate and nitrite. A white precipitate was present in cultures with Mn3+, which indicated that the microbes reduced Mn3+ to Mn2+. The precipitate was not present in uninoculated controls. With oxygen as the electron donor, a layer of orange Fe3+ oxide minerals formed near the water-air interface, indicative of growth of microaerophilic Fe2+-oxidizing bacteria. This layer did not form in uninoculated controls. Our preliminary results suggest that anaerobic Lake Matano enrichments are capable of Fe2+ oxidation using oxygen but not alternative electron acceptors. After subsequent transfers of the enrichments that showed growth of microaerophilic Fe2+-oxidizing bacteria, the bacteria were isolated and their 16S rRNA gene was sequenced. Sequences were most similar to the Betaproteobacteria genus Comamonas and the Alphaproteobacteria genus Skermanella. Some species of Comamonas are known to oxidize Fe2+, while the exact mechanism of the metabolism of Skermanella are not well known. The presence of microaerophilic Fe2+ oxidizing bacteria from Lake Matano, Indonesia serves as a link between understanding the transition from an anoxic to an oxic world.
Expansion of Mitochondrial and Nuclear Heme Sensor Library

(Georgia Institute of Technology, 2019-05) Atuluru, Pranusha

The long-term objective of the work in the lab is to determine the mechanisms by which cells sense and respond to the utilization of heme, an essential nutrient. Heme is an iron-containing compound of the porphyrin class that enables proteins to carry out an array of functions. Heme-dependent processes require that heme be dynamically mobilized to hemoproteins in almost every subcellular compartment. Although it is understood that the cytotoxicity and hydrophobicity of heme requires heme be tightly regulated by the cell, the method by which this is done is unknown [1]. The primary factor that limits the understanding of heme mobilization and trafficking is the lack of tools available to sense heme, more specifically labile heme. The Reddi lab is working to develop ratiometric fluorescent sensors to offer better insight into subcellular labile heme pools relevant for heme trafficking and signaling. HS1 (Heme Sensor 1) is mutated at either the His or Met in the heme-binding coordinating bundle of cytochrome to create sensors of different affinity. Ten new mutant sensors were created from the original HS1 and HS1-M7A, and it is seen that two sensors, H102C and H102C-M7H, are the most suitable sensors to be used in the mitochondria, nucleus and cytosol. With the use of these sensors, different pathways of heme trafficking and signaling can be studied in the cell.
Probing Heme Trafficking Factors via Organellar Contact Points Using Genetically Encoded Fluorescent Heme Sensors

(Georgia Institute of Technology, 2019-05) Saini, Arushi

Heme is an important protein cofactor and signaling molecule that plays diverse roles in biological systems. The hydrophobicity and cytotoxicity of heme necessitates that it is transported and trafficked in a regulated manner. However, the molecules and mechanisms responsible for mediating heme trafficking remain poorly understood. Until recently, the tools to study heme in vivo did not exist, but the emergence of genetically encoded fluorescent sensors has enabled comprehensive real time analysis of heme in model organisms such as Saccharomyces cerevisiae. This study showcases a new a protocol that allows investigation of heme trafficking from its site of synthesis in the matrix side of the mitochondrial inner membrane to the outer matrix, cytosol, and nucleus over time. The method allows for the simultaneous examination of heme re-population in three cellular compartments after chemically depleting it. The study revealed that mitochondrial contact points play central roles in regulating heme availability and illuminates novel approaches to heme trafficking. These methods have the potential to be adapted to more inclusive compartmental analyses and enable a better understanding of heme trafficking which can empower innovative approaches to study infectious diseases, neurodegenerative disorders, and anemias associated with perturbations in heme cellular dynamics.
Carrier protein and halogenase selectivity in the biosynthesis of halogenated pyrroles

(Georgia Institute of Technology, 2019-05) Lail, Andrew J.

Natural product biosynthetic pathways often share similar architecture even when they lead to different final products. In polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) enzymatic pathways, the substrate is attached to a carrier protein (CP) while the tailoring enzymes make modifications to yield a final product. The CP may therefore have a role in determining what enzymes act on the substrate, influencing the final product’s chemistry. In this study, pyrrole halogenases from several different bacterial species were characterized in vitro to test their ability to halogenate pyrrolyl CPs from four different natural product biosynthetic pathways. The reactions were analyzed via mass spectrometry to determine the halogenation state of the products formed. This study concludes that only some halogenases can act promiscuously on CPs from other pathways. Additionally, there is some modulation in the number of halogenation events between certain CP and halogenase pairs. The selectivity of these halogenase and CP interactions is likely caused by protein-protein interactions, and the structure of the CP/halogenase complex may provide new insights into such interaction.