Digital Commons Network^™

Investigations Of The Quorum Sensing Repressor Lsrr From Escherichia Coli And Salmonella Typhimurium And The Putative Ai-2 Receptor Lsrb From Clostridium Antoethanogenum, Elijah N. Kissman , '18

Senior Theses, Projects, and Awards

Quorum sensing is a process by which bacteria coordinate community behaviors through the exchange of signal molecules. Both Gram-negative and Gram-positive bacteria use quorum sensing to regulate cell density-dependent activities such as bioluminescence, biofilm formation, and the secretion of virulence factors. Interspecies quorum sensing is mediated by a signal molecule known as autoinducer-2 (AI-2) which is synthesized and recognized by a diverse range of bacterial phyla. The uptake and degradation of AI -2 is accomplished by proteins encoded by the lsr operon, which is regulated by AI-2. Previous research has suggested that dihydroxyacetone phosphate (DHAP), a metabolic product of AI-2 …

Conformation And Directionality Of The Influenza A M2 Protein Domain Essential To Viral Replication, Hayley E. Raymond , '18

Senior Theses, Projects, and Awards

Influenza A causes seasonal epidemics, and the possibility of another worldwide influenza A pandemic remains a public health concern. The influenza A M2 protein is implicated in the virus’s ability to bud and create new infectious virus particles. Specifically, the C-terminal region of the virus is required for viral budding, and this protein domain binds another influenza protein, M1. M2-M1 binding is critical to packaging the viral genome into new virions. To probe the region of M2 involved in viral budding and genome packing, this thesis studied the conformation of residues 60-70 of the C-terminus via site-directed spin label electron …

Investigating Noncanonical Dna Structures As Anti-Cancer Drug Targets, Barrett M. Powell , '18

Senior Theses, Projects, and Awards

This work focuses on the structure and interactions with ligands of noncanonical DNA structures. These noncanonical structures include guanine quadruplexes (GQs), as well as a novel type of quadruple helix. Sequences capable of forming these structures are overrepresented at telomeres and replication perturbed loci, respectively. Better understanding of these structures and ligand interactions will provide an improved platform upon which mechanistic understanding and therapeutic treatments can be designed. Our discussion begins with the development and biophysical characterization of a model for the smallest stable structure formed by the repeat sequence d(CAGAGG)ₙ. This sequence was one of many short purine rich …

Volume 10, Taylor Hogg, Tiffany Carter, Brandyn Johnson, Haleigh James, Josh Baker, Tyler Cernak, Kirsten Bauer, Allie Snavely, Mary Zell Galen, Eric Powell, Thomas Wise, Katie Kinsey, Beth Barbolla, Maeleigh Ferlet, Rebecca Morra, Michala Day, Alexandra Evangelista, Max Flores, Harley Hodges, Clardene Jones, Harrison Samaniego, Jamesha Watson, Abby Gargiulo, Heather Green, Haley Klepatzki, Juan Guevara, Dani Bondurant, Michael Joseph Link Jr., Pamela Dahl, Maeve Losen, Charlotte Murphey

Incite: The Journal of Undergraduate Scholarship

Introduction Dr. Roger A. Byrne

An Analysis of Media Framing in Cases of Violence Against Women by Taylor Hogg

Writing in the Discipline of Nursing by Tiffany Carter

Photography by Brandyn Johnson

The Hidden Life of Beef Cattle: A Study of Cattle Welfare on Traditional Ranches and Industrial Farms by Haleigh James

Bloodworth's by Josh Baker and Tyler Cernak

Prosimians: Little Bodies, Big Significance by Kirsten Bauer

Skinformed by Allie Snavely

Coopertition and Gracious Professionalism: The Effects of First Robotics Folklore and Culture on the Stem Community by Mary Zell Galen

Tilt by Eric Powell And Thomas Wise

The Millennial …

Creation And Use Of Software For Analysis Of Kinetic Proteomic Experiments, Bradley C. Naylor

Theses and Dissertations

In this dissertation, I will review the history and general strategies for performing kinetic proteomics. I will then demonstrate that I have published an open source, user-friendly program for other scientists to use to perform kinetic proteomics data analysis, as well as publishing a novel discovery of key ribosomal subunits being replaced within the lifetime of the ribosome, which was discovered through use of kinetic proteomics. Finally, I will discuss work that is ongoing to improve my software tool for use in human subjects, and work being done to combine kinetic proteomics with other global analysis methods to make novel …

Synthetic Analogues Of The Snail Toxin 6-Bromo-2-Mercaptotryptamine Dimer (Brmt) Reveal That Lipid Bilayer Perturbation Does Not Underlie Its Modulation Of Voltage-Gated Potassium Channels, Chris Dockendorff, Disha M. Gandhi, Ian H. Kimball, Kenneth S. Eum, Radda Rusinova, Helgi I. Ingolfsson, Ruchi Kapoor, Thasin Peyear, Matthew W. Dodge, Stephen F. Martin, Richard W. Aldrich, Olaf S. Andersen, Jon T. Sack

Chemistry Faculty Research and Publications

Drugs do not act solely by canonical ligand–receptor binding interactions. Amphiphilic drugs partition into membranes, thereby perturbing bulk lipid bilayer properties and possibly altering the function of membrane proteins. Distinguishing membrane perturbation from more direct protein–ligand interactions is an ongoing challenge in chemical biology. Herein, we present one strategy for doing so, using dimeric 6-bromo-2-mercaptotryptamine (BrMT) and synthetic analogues. BrMT is a chemically unstable marine snail toxin that has unique effects on voltage-gated K⁺ channel proteins, making it an attractive medicinal chemistry lead. BrMT is amphiphilic and perturbs lipid bilayers, raising the question of whether its action against K …

Using Spectral Methods To Obtain Particle Size Information From Optical Data: Applications To Measurements From Cares 2010, Dean B. Atkinson

Chemistry Faculty Publications and Presentations

Multi-wavelength in situ aerosol extinction, absorption and scattering measurements made at two ground sites during the 2010 Carbonaceous Aerosols and Radiative Effects Study (CARES) are analyzed using a spectral deconvolution method that allows extraction of particle-sizerelated information, including the fraction of extinction produced by the fine-mode particles and the effective radius of the fine mode. The spectral deconvolution method is typically applied to analysis of remote sensing measurements. Here, its application to in situ measurements allows for comparison with more direct measurement methods and validation of the retrieval approach. Overall, the retrieved finemode fraction and effective radius compare well with …

Mxin Differentially Regulates Monomeric And Oligomeric Species Of The Shigella Type Three Secretion System Atpase Spa47, Heather B. Case, Nicholas E. Dickenson

Chemistry and Biochemistry Faculty Publications

Shigella rely entirely on the action of a single type three secretion system (T3SS) to support cellular invasion of colonic epithelial cells and to circumvent host immune responses. The ATPase Spa47 resides at the base of the Shigella needle-like type three secretion apparatus (T3SA), supporting protein secretion through the apparatus and providing a likely means for native virulence regulation by Shigella and a much needed target for non-antibiotic therapeutics to treat Shigella infections. Here, we show that MxiN is a differential regulator of Spa47 and that its regulatory impact is determined by the oligomeric state of the Spa47 ATPase, with …

Progress Toward Synthetically Simplified Natural Anticancer Peptide, David W. Kastner, Steven L. Castle

Library/Life Sciences Undergraduate Poster Competition 2018

Yaku’amide A was isolated in late 2010 from the deep-sea sponge Ceratopsion sp. and exhibits potent inhibitory activity against 39 human cancer cell lines via a potentially novel mode of action. However, the total synthesis requires many steps and produces low yields. In this study, we determined two simpler YA analogues that may retain its anticancer properties and can be synthesized in larger quantities. The analogues replace dehydroisoleucine with either dehydroethylnorvaline or dehydrovaline.

14-3-3zeta Role In Promoting Survival Of Cells To Facilitate Progression Of Cancer, Katie Pennington, Eranga Roshan, Joshua Andersen, Katherine K. Mccormack

Student Works

The regulatory protein 14-3-3z promotes cellular growth and survival, and high expression levels of 14-3-3z are associated with mortality in multiple cancer types. 14-3-3z binds cellular proteins in a phosphorylation-dependent manner to modulate their functions. We have been characterizing the interactome of 14-3-3z which will likely lead to candidates for novel therapies for chemoresistant cancers. Tumor cells must be able to survive in a variety of stresses within the tumor microenvironment, including hypoxia, which occurs when tumors lack adequate blood supply. Previous data from our lab suggested that 14-3-3z promotes the adaptation of tumor cells to hypoxic stress. Our hypothesis …

Higher Energy Gap Control Of Fluorescence In Conjugated Polymers, Chien-Hung Chiang

LSU Doctoral Dissertations

Chemo- and biosensors based on fluorescent conjugated polymer benefit from greater detection sensitivity due to amplification of the electronic perturbations produced by analyte binding. This amplification stems from the exciton-transporting properties of conjugated polymers. A conventional design paradigm relies on the analyte binding events which generate sites of lower energy relative to the polymer energy: either fluorescence quenching sites (turn-off sensors) or bathochromically shifted fluorophores (turn-on sensors). In both type sensors, the excitons migrate to the lower-energy site created by analyte binding.

This dissertation primarily focused the investigation of an alternative paradigm when analyte binding creates higher energy gap sites …

Synthesis, Characterization, And Assessment Of Cationic Polypeptoids Toward Gene Delivery And Development Of Air Stable N-Substituted N-Thiocarboxyanhydrides, Jessica Michelle Simpson

LSU Doctoral Dissertations

Peptoids are a class of peptidomimetic polymers, which have attracted much attention over the years. Due to their structural similarity to peptides, this group of polymers affords good biocompatibility making them of interest for biomedical applications. This dissertation is largely about the design, synthesis, and characterization of cationic polypeptoids for biological applications, particularly nonviral gene delivery. The dissertation will also cover the development, characterization, and polymerization behavior of a new, air stable N-thiocarboxyanhydride (NTA) monomer.

Introducing functionality, such as small biomolecules and organic compounds can provide distinctive properties to the polymers. Chapter 1 introduces gene therapy and concepts pertinent …

Halogen, Chalcogen, And Pnicogen Bonding Involving Hypervalent Atoms, Steve Scheiner, Jia Lu

Chemistry and Biochemistry Faculty Publications

The additional substituents arising from hypervalency present a number of complicating issues for the formation of noncovalent bonds. The XF5 molecule (X=Cl, Br, I) was allowed to form a halogen bond with NH3 as base. Hypervalent chalcogen bonding is examined by way of YF4 and YF6 (Y=S, Se, Te), and ZF5 (Z=P, As, Sb) is used to model pnicogen bonding. Pnicogen bonds are particularly strong, with interaction energies approaching 50 kcal/mol, and also involve wholesale rearrangement from trigonal bipyramidal in the monomer to square pyramidal in the complex, subject to a large deformation energy. YF4 chalcogen bonding is also strong, …

Robust Microplate-Based Methods For Culturing And In Vivo Phenotypic Screening Of Chlamydomonas Reinhardtii, Timothy C. Haire, Cody Bell, Kirstin Cutshaw, Brendan Swiger, Kurt Winkelmann, Andrew G. Palmer

Biomedical Engineering and Sciences Faculty Publications

Chlamydomonas reinhardtii (Cr), a unicellular alga, is routinely utilized to study photosynthetic biochemistry, ciliary motility, and cellular reproduction. Its minimal culture requirements, unicellular morphology, and ease of transformation have made it a popular model system. Despite its relatively slow doubling time, compared with many bacteria, it is an ideal eukaryotic system for microplate-based studies utilizing either, or both, absorbance as well as fluorescence assays. Such microplate assays are powerful tools for researchers in the areas of toxicology, pharmacology, chemical genetics, biotechnology, and more. However, while microplate-based assays are valuable tools for screening biological systems, these methodologies can significantly alter the …

Design, Synthesis, Application Of Biodegradable Polymers, Mussie Gide

USF Tampa Graduate Theses and Dissertations

Bacterial infections have posed a serious threat to the public health due to the significant rise of the infections caused by antibiotic-resistant bacteria. There has been considerable interest in the development of antimicrobial agents which mimic the natural HDPs, and among them biodegradable polymers are newly discovered drug candidates with ease of synthesis and low manufacture cost compared to synthetic host defense peptides. Herein, we present the synthesis of biocompatible and biodegradable polymers including polycarbonate polymers, unimolecular micelle hyperbranched polymers and dendrimers that mimic the antibacterial mechanism of HDPs by compromising bacterial cell membranes. The developed amphiphilic polycarbonates are highly …

De Novo Glycan Sequencing By Electronic Excitation Dissociation And Fixed-Charge Derivatization, Yang Tang, Yi Pu, Jinshan Gao, Pengyu Hong, Catherine E. Costello, Cheng Lin

Department of Chemistry and Biochemistry Faculty Scholarship and Creative Works

Detailed glycan structural characterization is frequently achieved by collisionally activated dissociation (CAD) based sequential tandem mass spectrometry (MS n ) analysis of permethylated glycans. However, it is challenging to implement MS n (n > 2) during online glycan separation, and this has limited its application to analysis of complex glycan mixtures from biological samples. Further, permethylation can reduce liquid chromatographic (LC) resolution of isomeric glycans. Here, we studied the electronic excitation dissociation (EED) fragmentation behavior of native glycans with a reducing-end fixed charge tag and identified key spectral features that are useful for topology and linkage determination. We also developed a …

Investigating The Synthesis Of 1,3,4-Oxadiazoles Via A Novel Two-Step-One-Pot Cyclodehydration Reaction, Brittney Sowers

Undergraduate Honors Thesis Projects

The given research will investigate synthetic strategies and differential functionalization of 1,3,4- oxadiazoles in hopes of obtaining moderate to high yields. Particularly, the effects of electron withdrawing on oxadiazoles will reveal more information about possible mechanistic details and reaction optimization.

The research in this report is a part of a lager research effort being investigated by Dr. Robin Grote. This research is ongoing and has evolved from its start in the Grote Lab. Previously, the Grote Lab has focused on the formation of a patented heterocycle that contained an amino-pyrazine functional group. Currently, our research has shifted focus to the …

Synthesis And Characterization Of Covalent Adaptable Networks Comprised Of Dynamic Imine And Aminal Covalent Bonds, Albert Chao

LSU Doctoral Dissertations

The dissertation is about the design, synthesis and characterization of materials comprised of covalent adaptable networks (CANs). There are three chapters within this dissertation.

Chapter 1 contains a short overview of conventional thermosets and thermoplastics. A new strategy of combining advantages from thermosets and thermoplastics is utilizing dynamic covalent chemistry (DCC) for material design. Dynamic covalent bonds are able to undergo dynamic exchange which allow the material to adapt to a new state when under stimuli such as stress or strain. Material comprised of such reversible networks is called covalent adaptable networks (CANs). These types of reversible covalent bonds followed …

Polymers Course For Small Colleges And Universities, Joseph Furgal

Chemistry Faculty Publications

This article describes the course design and teaching methodology for a polymer chemistry and applications lecture class specifically aimed at small college and university instruction. This intermediate course for advanced undergraduates and masters level graduate students focuses on teaching the basics of polymer history, synthesis and characterization with connections to the core chemistry curriculum in a small class size environment and without a textbook. Furthermore, an extensive overview of the applications of polymeric materials gives students a connection to real life applications. The course includes polymer case studies, informational lessons on real world objects made of polymers, and demonstrations. Student …

A Chimeric Nucleobase - Phenylazo Derivative As An Intrinsic Nucleobase Quencher, Gyeongsu Park, Timothy Martin-Chan, Amer El Samm, Robert H.E. Hudson

Western Research Forum

Molecular beacons are important bioanalytical probes which are most often

constructed from a single-stranded oligonucleotide which has been labeled at

opposite termini with a fluorophore and a quencher. When the fluorophore and

quencher are in close proximity, no fluorescence is observed due to FRET

(Fluorescence Resonance Energy Transfer). DABCYL (4-dimethylaminoazobenzene-

4'-carboxylic acid) has been used as a quencher in the molecular beacon to absorbs

excitation energy from a fluorophore and to dissipate the energy as heat. However,

DABCYL is unable to form a base-pair and is conventionally placed as an overhanging

residue. This produces a derivative wherein the chromophore has …

Preparation, Modification, Characterization, And Biosensing Application Of Nanoporous Gold Using Electrochemical Techniques, Jay Bhattarai, Dharmendra Neupane, Bishal Nepal, Vasilii Mikhaylov, Alexei Demchenko, Keith Stine

Chemistry & Biochemistry Faculty Works

Nanoporous gold (np-Au), because of its high surface area-to-volume ratio, excellent conductivity, chemical inertness, physical stability, biocompatibility, easily tunable pores, and plasmonic properties, has attracted much interested in the field of nanotechnology. It has promising applications in the fields of catalysis, bio/chemical sensing, drug delivery, biomolecules separation and purification, fuel cell development, surface-chemistry-driven actuation, and supercapacitor design. Many chemical and electrochemical procedures are known for the preparation of np-Au. Recently, researchers are focusing on easier and controlled ways to tune the pores and ligaments size of np-Au for its use in different applications. Electrochemical methods have good control over fine-tuning …

Electron Injection From A Carboxylic Anchoring Dye To Tio2 Nanoparticles In Aprotic Solvents, Hui Fang, Yuhao Wu, Danielle L. Kuhn, Brendan G. Delacy, Yi Rao, Hai-Lung Dai

Chemistry and Biochemistry Faculty Publications

Injection of photoexcited electrons in the para-Ethyl Red dye to TiO₂ nanoparticles (Anatase, 40 nm diameter) is characterized by transient absorption on ultrafast time scales. This study focuses on understanding the effect of aprotic solvents on the injection rate. Transient absorption at 1900 cm⁻¹ is probed following a 400 nm pulse which excites the electronic transition of p-ER adsorbed on TiO₂ through its carboxylic group. Measurements conducted in three different solvents show that electron injection lifetimes are in the 250–300 fs range but display a trend in correlation with solvent polarity: the electron injection lifetime is the …

It’S Raining : Remotely Accessible Instruments In Nanotechnology To Promote Student Success, Jared M. Ashcroft, Atilla Ozgur Cakmak, Jillian Blatti, Esteban Bautista, Vanessa Wolf, Felix Monge, Dwaine Davis, M. Josefina Arellano-Jimenez, Raymond Tsui, Richard Hill, Anthony Klejna, James S. Smith, Gabe Glass, Timothy Suchomski, Kristine J. Schroeder, Robert K. Ehrmann

Current Issues in Emerging eLearning

Remotely Accessible Instruments in Nanotechnology (RAIN) is a community of educators that aims to bring advanced technologies into K-12 and college classrooms via remote access. RAIN's mission is to facilitate the study of nanoscale science by lowering barriers for instructors to deliver relevant educational activities for younger students interested in learning about nanotechnology across traditional STEM fields. Additionally, RAIN engages the next generation STEM workforce with a connection to experts, tools and institutions where cutting-edge research is being performed. This resource is particularly vital for underrepresented and minority students, especially those attending institutions that cannot provide on-site access to advanced …

Non-Methane Organic Gas Emissions From Biomass Burning: Identification, Quantification, And Emission Factors From Ptr-Tof During The Firex 2016 Laboratory Experiment, Abigail R. Koss, Kanako Sekimoto, Jessica B. Gilman, Vanessa Selimovic, Matthew M. Coggon, Kyle J. Zarzana, Bin Yuan, Brian M. Lerner, Steven S. Brown, Jose L. Jimenez, Jordan Krechmer, James M. Roberts, Carsten Warneke, Robert J. Yokelson, Joost De Gouw

Chemistry and Biochemistry Faculty Publications

Volatile and intermediate-volatility non-methane organic gases (NMOGs) released from biomass burning were measured during laboratory-simulated wildfires by proton-transfer-reaction time-of-flight mass spectrometry (PTR-ToF). We identified NMOG contributors to more than 150 PTR ion masses using gas chromatography (GC) pre-separation with electron ionization, H3O+ chemical ionization, and NO+ chemical ionization, an extensive literature review, and time series correlation, providing higher certainty for ion identifications than has been previously available. Our interpretation of the PTR-ToF mass spectrum accounts for nearly 90ĝ€-% of NMOG mass detected by PTR-ToF across all fuel types. The relative contributions of different NMOGs to individual exact ion masses are …

Legacy Contaminants In The Northern Gulf Of Mexico Shelf, Jessica N. Landry

LSU Master's Theses

The Mississippi River watershed is the third largest in the world and drains from 31 states in the United States. Due to its route through the U.S., it passes through hundreds of EPA labeled Superfund sites as well as agricultural and suburban watersheds. These sites are known to have historical chemical contamination, and as a result chemicals can be transported by runoff down the Mississippi River into the Gulf of Mexico where their ultimate fate is unknown. Organochlorine chemicals are known to be persistent and are found in agricultural land as well as US EPA Superfund sites, especially DDT, PCBs, …

Chlorination Of 3-Arylsydnones With Iodine Monochloride, Ben Owens

The University Honors Program

An improved method for the chlorination at the 4-position of 3- arylsydnones 1 was developed, using iodine monochloride (ICl) dissolved in DCM. 1,3,4-Oxadiazol-2(3H)-ones 3 were then synthesized from the resultant 4-chloro-3-arylsydnones 2. The scope and limitations will be presented.

Chemotherapeutic Applications Of Rhodamine Based Nanogumbos, Nimisha Bhattarai

LSU Doctoral Dissertations

The work presented in this dissertation employs nanomaterials derived from a group of uniform materials based on organic salts (GUMBOS) for selective chemotherapeutic applications. GUMBOS, similar to ionic liquids, are organic salts consisting of a bulky cationic and anionic moiety. In contrast to ionic liquids, these materials have melting points ranging from 25–250 °C, making them solid phase at room temperature. Similar to ionic liquids, GUMBOS display tunable properties, such as hydrophobicity and solubility, through counter ion variation. These tunable properties provide a variety of applications for these GUMBOS, including selective chemotherapeutics applications. The …

Aerosol Optical Properties And Trace Gas Emissions By Pax And Op-Ftir For Laboratory-Simulated Western Us Wildfires During Firex, Vanessa Selimovic, Robert J. Yokelson, Carsten Warneke, James M. Roberts, Joost De Gouw, James Reardon, David W.T. Griffith

Chemistry and Biochemistry Faculty Publications

Western wildfires have a major impact on air quality in the US. In the fall of 2016, 107 test fires were burned in the large-scale combustion facility at the US Forest Service Missoula Fire Sciences Laboratory as part of the Fire Influence on Regional and Global Environments Experiment (FIREX). Canopy, litter, duff, dead wood, and other fuel components were burned in combinations that represented realistic fuel complexes for several important western US coniferous and chaparral ecosystems including ponderosa pine, Douglas fir, Engelmann spruce, lodgepole pine, subalpine fir, chamise, and manzanita. In addition, dung, Indonesian peat, and individual coniferous ecosystem fuel …

In Vitro Label Free Screening Of Chemotherapeutic Drugs Using Raman Micro-Spectroscopy: Towards A New Paradigm Of Spectralomics., Zeineb Farhane, Haq Nawaz, Franck Bonnier, Hugh Byrne

Articles

This overview groups some of the recent studies highlighting the potential application of Raman micro-spectroscopy as an analytical technique in preclinical development to predict drug mechanism of action and in clinical application as a companion diagnostic and in personalised therapy due to its capacity to predict cellular resistance and therefore to optimise chemotherapeutic treatment efficacy.

Notably, the anthracyclines, Doxorubicin and Actinomycin D, elicit similar spectroscopic signatures of subcellular interaction characteristic of the mode of action of intercalation. Although Cisplatin and Vincristine show markedly different signatures, at low exposure doses, their signatures at higher doses show marked similarities to those elicited …

Comparison Of A Simplified Cupric Oxide Oxidation Hplc Method With The Traditional Gc-Ms Method For Characterization Of Lignin Phenolics In Environmental Samples (Vol 13, Pg 1, 2015), Luni Sun, Robert G. M. Spencer, Peter J. Hernes, Rachael Y. Dyda, Kenneth Mopper

Chemistry & Biochemistry Faculty Publications

In our article entitled “Comparison of a simplified cupric oxide oxidation HPLC method with the traditional GC-MS method for characterization of lignin phenolics in environmental samples” (Limnol. Oceanogr.: Methods 13, 2015, 1–52), doi: 10.1002/lom3.10001, we would like to correct the errors in Fig. 2 and Table 2 as mentioned below. The label to Fig. 2(a) needs to be transposed as indicated in the corrected Fig. 2 image below.