Life Sciences Commons^™

Quantifying The Role Of Water Quality On Nitrogen Cycling In A Trophic Estuary, Kayla Gonzalez-Boy

Symposium of Student Scholars

Jobos Bay Estuary is an intertidal, tropical estuary located in southern Puerto Rico. The estuary covers about 12 km² and has a variety of habitats, such as seagrass beds, mangroves, mud flats, and coral reefs, which play important roles in sediment trapping and water quality maintenance. Seagrasses also serve as nursery and feeding grounds and provide shelter for macrofauna. Currently, the role of seagrasses and water quality on nitrogen (N) cycling in trophic estuaries is not well constrained. Understanding variations in sediment-based effects on N cycling rates and transformations, and how they are associated with water quality, is an …

Investigating The Activity Of Alternative Warheads For Targeted Covalent Inhibition Of The Inhibitor Vertebrate Lysozyme Protein From Pseudomonas Aeruginosa, Katie Hambrick

Master of Science in Chemical Sciences Theses

Pseudomonas aeruginosa (P. aeruginosa) is a Gram-negative bacterium that causes blood and lung infections in hospital environments due to its ability to survive on improperly sterilized medical equipment. P. aeruginosa has developed several multi-drug resistance mechanisms that make it very difficult to treat with current antibiotics.¹ This presents the need for a new class of antibiotics that cannot be overcome by P. aeruginosa’s mechanisms of resistance.

The primary goal of this project was to develop a small library of inhibitors that could later be incorporated into lead compounds for novel antibiotic drug discovery. One of P. …

Designing And Synthesizing A Warhead-Fragment Inhibitory Ligand For Ivyp1 Through Fragment-Based Drug Discovery, Samuel Moore

Symposium of Student Scholars

Fragment-based drug discovery (FBDD) is a powerful tool for developing anticancer and antimicrobial agents. Within this, magnetic resonance spectroscopy (NMR) provides a comprehensive qualitative and quantitative approach to screening and validating weak and robust binders with targeted proteins, making NMR among the most attractive strategies in FBDD. Inhibitor of vertebrate lysozyme (Ivyp1) of P. aeruginosa serves as an excellent target because of its active cellular location and implications in clinical prognosis for cystic fibrosis and immunocompromised patients. This study uses current NMR and biophysical techniques to develop a covalent, fragment-linked warhead inhibitor for Ivyp1 through synthetic methods, warhead linking, and …

Growth Outcomes Of Pseudomonas Aeruginosa Inhibitor Of Vertebrate Lysozyme Knockouts In Conditions Mimicking The Cystic Fibrosis Lung Environment, Amani Gaddy

Master of Science in Chemical Sciences Theses

Pseudomonas aeruginosa (PA) is a Gram-negative bacterium, often found in cystic fibrosis (CF) patients and can lead to the decline of lung functioning and premature death in 80% of infected patients when microcolonies form within the mucin of the lung. Due to its major capacity for antibiotic resistance, an alternative strategy towards defending against the bacterial invasion of PA is by the antibacterial activity of our own innate immune system with use of elements such as lysozyme. Pseudomonas aeruginosa inhibitor of vertebrate lysozyme class 1 (Ivyp1) is a periplasmic protein produced by gram-negative bacteria that inhibits the enzymatic activity of …

Synthesis And Characterization Of A Novel Reaction-Based Azaborine Fluorescent Probe Capable Of Selectively Detect Carbon Monoxide Based On Palladium-Mediated Carbonylation Chemistry, Samuel Moore, Carl Jacky Saint-Louis

Symposium of Student Scholars

Azaborines are fascinating compounds because they possess valuable properties such as photochemical stability, have high molar absorption coefficient and high fluorescent quantum yields, as well as large Stokes shifts and tunable absorption/emission spectra. Here, we designed, synthesized, and will examine a novel reaction-based azaborine fluorescent probe capable of selectively detect carbon monoxide (CO) based on palladium-mediated carbonylation chemistry. This novel azaborine fluorescent probe will exhibit high selectivity for CO and display a robust turn-on fluorescent response in the presence of CO in aqueous buffer solution.

Ketal-Azaborine Versus Ketal-Azaborine With A Spacer: Structural Effects On The Photophysical Properties Of Tunable Heteroaromatic Polycyclic Chromophores, Albert Campbell, Janiyah Riley, Samuel Moore, Albert Campbell

Symposium of Student Scholars

Flat-structured heteroaromatic polycyclic compounds with extended conjugated π-systems such as azaborines are in high demand in the material and imaging technology markets because of their unique features such as simultaneous tunability of fluorescence color and intensity. We have designed, synthesized, and investigated a series of novel conjugated thermally stable ketal-azaborine chromophores that contain a phenyl ring as a spacer between electronic moieties and the ketal-azaborine core as easily tunable high-luminescent organic materials. We investigated the impact of the phenyl spacer on the ketal-azaborine unit. We examined the structural effects on their photophysical properties by incorporating electron –donating and –withdrawing substituents …

Azaborine Versus Azaborine With A Spacer: Structural Effects On The Photophysical Properties Of Tunable Azaborine Chromophores, Kaia Ellis, Janiyah Riley, Lyric Gordon, Janiyah Riley

Symposium of Student Scholars

Azaborines are fascinating compounds because of their valuable and interesting optical properties making them suitable to be utilized in many optoelectronic devices. We have designed, synthesized, and investigated a series of novel conjugated thermally stable azaborine chromophores by incorporating a phenyl ring as a spacer linking the chromophore to different electronic moieties as easily tunable high-luminescent organic materials. We investigated the effect of the phenyl spacer on the azaborine unit. The substituent effects of different electronic moieties were investigated by the insertion of electron –withdrawing and –donating moieties to the phenyl spacer. We examined the role of the electron –donating …

Microbial Diversity And Community Structure In Sediments Associated With The Seagrass (Thallassia Testudinum) In Apalachicola Bay, Florida, Rahma Ahmed, Thomas Mcelroy, Troy Mutchler

Symposium of Student Scholars

Seagrass is an angiosperm which provides many ecosystem services in coastal areas, such as providing food, shelter and nurseries for many species, and decreasing the impact of waves on shorelines. A global assessment reported that 29% of known seagrass meadows are in a state of decline due to the effects of human activity. Seagrass is commonly found in shallow marine waters where they form meadows containing a microbiome that plays an important role in providing nutrients for seagrass growth, though little is known about the microorganisms within the seagrass meadow sediments. Our project collected sediments from seagrass meadows and adjacent …

Snake Venom Peptides And Toxin Targeting The Main Protease Of Sars-Cov-2, Breauna Strawder, James Stewart, Mohammad A. Halim

Symposium of Student Scholars

The corona virus began to spread in Wuhan, China which caused it to spread worldwide creating a global pandemic in the beginning of 2020, infecting over 243 million and killing over 4.5 million people worldwide. Significant efforts were made to produce vaccines against the virus, which led the recognition of a few vaccines that has been approved by FDA. These vaccines, Pfizer-BioNTech, Moderna and Johnson & Johnson, which all have efficacy against Covid-19. Despite having vaccines, COVID-19 is still present and infecting millions and killing thousands of people every day. Multiple therapeutic options would allow us to slow down or …

Binding Affinity And Interaction Of Sars-Cov-2 Epitopes With Major Histocompatibility Complex, Sareena Kandavalli, James Stewart, Mohammed A. Halim

Symposium of Student Scholars

SARS CoV-2 has been affecting the world since 2019. It caused 245 million cases of infection and around 5 million deaths worldwide. The most important strategies for the development of vaccines against SARS-CoV-2 are inactivated or weakened virus, replicating or non-replicating viral vector-based approaches, DNA, RNA, virus particle like approaches and epitope-based approaches. The epitope-based approach is rapid, accurate, cost-effective, and reliable against pathogens. By presenting epitopes (antigen peptides) on antigen-presenting cells (APCs), the major histocompatibility complex (MHC), also recognized as the human leukocyte antigen (HLA) system in humans, plays an essential role in triggering T-cell immune responses. The focus …

Cell Penetrating Peptide Inhibiting The Main Protease Of Sars-Cov-2, Adam Ashley, James Stewart, Mohammad Halim

Symposium of Student Scholars

As of October 2021, SARS-CoV-2 has infected over 244 million people and killed about 5 million people. The current FDA approved vaccines are effective; however, they lose their effectiveness after a few months of receiving both doses of the vaccine, and it is recommended to get a booster shot six months after receiving the second dose of the vaccine. Therefore, new highly effective, long lasting antiviral agents and strategies are needed to create an alternative treatment for SARS-CoV-2 and the different variants. Previous studies have shown that cell penetrating peptides (CPPs) have led to greater efficiency of intracellular delivery. However, …

Effects Of Exogenous Application Of Plant Growth Regulators (Snp And Ga3) On Phytoextraction By Switchgrass (Panicum Virgatum L.) Grown In Lead (Pb) Contaminated Soil, Adrianne Beavers, Marina Koether, Thomas C. Mcelroy, Sigurdur Greipsson

Faculty Articles

Soil lead (Pb) contamination is a major environmental and public health risk. Switch-grass (Panicum virgatum), a second-generation biofuel crop, is potentially useful for the long-term phytoremediation and phytoextraction of Pb contaminated soils. We evaluated the efficacy of a coor-dinated foliar application of plant growth regulators and soil fungicide and a chelator in order to optimize phytoextraction. Plants were grown in soil culture under controlled conditions. First, three exogenous nitric oxide (NO) donors were evaluated at multiple concentrations: (1) S-nitroso-N-acetylpenicillamine (SNAP); (2) sodium nitroprusside (SNP); and (3) S-nitrosoglutathione (GSNO). Second, the effect of SNP (0.5 µM) was examined further with the …

The Veiled Lady Fungus, Nick Parbhoo

Symposium of Student Scholars

This semester I studied the Stinkhorn mushroom Phallus Indusiatus. The plan of this research is to develop a protocol for growing this fungus and using it in collaboration with research on it’s web-like properties of the unique veil produced by the fruiting body. This will be distributed to teams of engineers as well as NASA for Dr. Penick’s research. Due to logistics of receiving spores from across the world, we still have not been able to begin growing these mushrooms. However, I have described a protocol that we will follow in order to grow. The protocol contains detailed descriptions …

Conserved Regions Mediate Interactions Between Canonical Nox Domains, Akua Acheampong

Symposium of Student Scholars

NAPDH oxidase (NOXes) are membrane-bound enzymes that generate reactive oxygen species (ROS) that play a role in immune response and signaling. Misregulation of NOXes is implicated in various human pathologies. NOXes contain a catalytic core comprised of a heme-containing transmembrane (TM) domain and a cytoplasmic dehydrogenase (DH) domain that binds FAD and NADPH. Several conserved regions at the interface of the TM and DH domains in eukaryotic NOXes have been suggested to mediate enzyme function and activity. In 2017, researchers successfully purified SpNox, a bona fide NOX homolog from Streptococcus pneumoniae and verified its NOX properties. SpNox’s robust activity in …

Binding Affinity Of Flavins To The Dehydrogenase Domain Of Spnox, Quinesha Williams

Master of Science in Chemical Sciences Theses

NADPH oxidases (NOX’s) are enzymes that catalyze the production of superoxide through single electron transfer. This superoxide production leads to the production of other reactive oxygen species (ROS). ROS affect many metabolic processes throughout the body that can cause several different diseases, making this an ideal target for drug discovery. The general structure of NOX contains a transmembrane (TM) domain and a dehydrogenase (DH) domain connected by a linker. The DH domain contains binding sites for FAD and NADPH/NADH that both participate in the electron transfer necessary for producing superoxide. Structural information of NOX’s is still relatively new to the …

Creating A Protein Chimera To Study Regulation Of Muscle Diversity, Shannon Scarboro

Symposium of Student Scholars

Creating a protein chimera to study regulation of muscle diversity.

Body muscles are made of many individual super-cells, called muscle fibers, that have distinct properties and determine every individual’s strength and endurance. Initially all muscle fibers have identical characteristics, but become differentiated into specific types in adults. The mechanism of such transition is not well understood, despite its obvious importance for shaping human physicality.

Remarkable conservation of the muscle tissue enables us to use fruit flies to study the mechanisms of muscle fiber diversity. We hypothesized that the transcription factor Mef2 acts as a molecular switch that activates structural genes …

Expression And Purification Of Proteins For A Structural Determination: Orf8, Paivy1, Paivy2, Sarah Fashinasi, Avery Moss

Symposium of Student Scholars

Protein purification is a crucial procedure in order to analyze the behavior, structure, and function of a select protein. The Orf8 protein is an increasingly mutable accessory protein found within the SARS-CoV2 virus, however the complex and unpredictable nature of this protein has been met by its inability to be purified thus far. By purifying the model proteins, PaIVY1 and PaIVY2, we believe that we can denote a sound purification method to apply to the Orf8 protein. In our procedure, we transformed BL21(DE3)pLysS cells and inoculated them in LB media. The cells were then placed into a centrifuge to isolate …

Investigating The Sars-Cov-2 Orf 8 Accessory Protein: Expression, Purification, And Structural Determination, Laney Hedgeman, Caroline Salha

Symposium of Student Scholars

Abstract

In order to provide insight into potential therapeutic breakthroughs for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), more research must be done to understand the structure and function of its proteins. The open reading frame 8 (ORF 8) accessory protein is particularly unstable on its own outside of the viral envelope but can be stabilized when bound to the small ubiquitin-related modifier (SUMO) protein. The stable ORF 8-SUMO protein complex can be expressed and purified using familiar techniques and later characterized with nuclear magnetic resonance (NMR) spectroscopy, thus allowing us to gain knowledge about the role it plays …

Bioanalytical Determination Of Glucose Concentration In Sports Drinks Using Uv/Vis Spectroscopy, Laney Hedgeman, Brianna Bond

Symposium of Student Scholars

Abstract

The purpose of our project is to indirectly monitor the enzymatic activity of glucose oxidase as it reacts with the glucose present in sports drinks through the quantitative analysis of the generated ferricyanide. As glucose oxidase catalyzes the oxidation of beta-D-glucose in the presence of oxygen, D-glucono-1,5-lactone is produced along with hydrogen peroxide. The hydrogen peroxide is used in a subsequent reaction with ferrocyanide catalyzed by horse radish peroxidase to produce water and the chromophore ferricyanide. This compound absorbs in the ultraviolet/visible spectrum at 420 nm, which can be quickly measured using Ultraviolet/Visible Spectroscopy. Since the molar ratio of …

Designing A Reactive Warhead To Bind And Inhibit Pseudomonas Aeruginosa’S Periplasmic Protein, Inhibitor Of Vertebrate Lysozyme, Leah Greinke

Master of Science in Chemical Sciences Theses

Pseudomonas aeruginosa is a Gram-negative bacterium commonly found throughout the environment. It is a significant cause of disease and mortality in immunodeficient patients such as those suffering from cystic fibrosis (CF). Due to the emerging antibiotic resistance of P. aeruginosa, it is becoming increasingly more challenging to treat an infection by traditional means. Further complicating treatment, P. aeruginosa secretes a protein known as Inhibitor of Vertebrate Lysozyme (PaIVY) that binds to and inhibits C-type lysozyme, thus preventing the degradation of the bacterium. A reactive chemical warhead was synthesized from a rhenium(I) tricarbonyl derivative inorder to bind to and irreversibly …

Analysis Of Foki Cleavage Resistance Observed In Dna Sequences Generated Via The Combinatorial Selection Method, Repsa, Andre Berry

Master of Science in Chemical Sciences Theses

FokI is a thoroughly investigated and highly utilized restriction endonuclease that recognizes the DNA sequence, 5’-GGATG-3’, and cleaves outside of this site 9 and 13 base-pairs downstream. The shifted cleavage function possessed by this kind of endonuclease is utilized in many applications including the combinatorial selection method, REPSA. FokI employment in the REPSA procedure has demonstrated the tendency to select for an unmodified sequence that possesses the recognition site yet is refractory to cleavage by the enzyme. Sequencing of the cleavage resistant DNA has revealed the inhibitory event to be induced by the presence of an additional inversely oriented recognition …

Probing Interactions Between Canonical Nox Domains, Akua Acheampong

Master of Science in Integrative Biology Theses

NAPDH oxidase enzymes (NOXes) reduce molecular oxygen to superoxide and other ROS. NOXes contain a catalytic core comprising a heme-containing transmembrane (TM) domain and a cytoplasmic dehydrogenase (DH) domain that binds the substrate NADPH and the cofactor. Previously, NOXes were only characterized in eukaryotes, but have recently been identified in prokaryotes, namely bacteria. Due to their constitutive activity and solubility in detergent, bacterial NOXes, such as Streptococcus Pneumoniae NOX, have emerged as a model for studying NOXes. Past research studies in NOXes have identified conserved, putative interacting regions at the interface of the TM and DH domains: the TM B-loop, …

Determination And Dissection Of Dna-Binding Specificity For The Thermus Thermophilus Hb8 Transcriptional Regulator Tthb099, Kristi Moncja

Master of Science in Chemical Sciences Theses

Transcription factors (TFs) have been extensively researched in certain well-studied organisms but far less so in others. Following the whole-genome sequencing of a new organism, TFs are typically identified through their homology with related proteins in other organisms. However, recent findings demonstrate that structurally similar TFs from distantly related bacteria are not usually evolutionary orthologs. Here we explore TTHB099, a cAMP receptor protein (CRP)-family TF from the extremophile Thermus thermophilus HB8. Using the in vitro iterative selection method Restriction Endonuclease Protection, Selection and Amplification (REPSA), we identified the preferred DNA-binding motif for TTHB099, 5'-TGT(A/g)n(t/c)c(t/c)(a/g)g(a/g)n(T/c)ACA-3', and mapped potential binding sites, and …

Differential Analysis Of Individual Centruroides Vittatus Venom

Symposium of Student Scholars

Scorpions are well known, venomous arthropods (Class: Arachnida, Order: Scorpiones). Their venom is composed of neurotoxins, proteases and cytotoxic peptides which plays a major role in toxic components such as inflammatory, antimicrobial and hemolytic activity. Venom is key for the survival of scorpions as it is involved in defense against prey and in feeding on predators. Centruroides vittatus (bark scorpion) is commonly found in North America, with habitat ranges from Nebraska to southern Texas. For this study, scorpions were harvested from Laredo, Texas (27˚57’ N, 99˚43’ W), held in captivity for 4 months and fed a consistent diet of Acheta …

Characterization Of Endothelial Nitric Oxide Synthase Serine-600 Phosphorylation, Kevin Patel

Master of Science in Chemical Sciences Theses

Endothelial nitric oxide synthase (eNOS) is part of a family of three nitric oxide synthase (NOS) enzymes that catalyze the production of nitric oxide (NO). NO is a gaseous, free-radical signaling molecule that has a variety of cellular and physiological functions that range from maintaining cardiovascular homeostasis to neurotransmission. The function of NO greatly depends on the concentration and is cell type specific. eNOS is the most regulated of the three NOS isoforms and the mechanisms of regulation can be through protein-protein interactions and posttranslational modifications. A connection with eNOS and the cell cycle has begun to form with recent …

Identification And Characterization Of Preferred Dna-Binding Sites For The Thermus Thermophilus Hb8 Transcriptional Regulator Ttha0973, James Shell Cox, Kristi Moncja, Mykala Mckinnes, Michael W. Van Dyke

Faculty Articles

Advances in genomic sequencing have allowed the identification of a multitude of genes encoding putative transcriptional regulatory proteins. Lacking, often, is a fuller understanding of the biological roles played by these proteins, the genes they regulate or regulon. Conventionally this is achieved through a genetic approach involving putative transcription factor gene manipulation and observations of changes in an organism’s transcriptome. However, such an approach is not always feasible or can yield misleading findings. Here, we describe a biochemistry-centric approach, involving identification of preferred DNA-binding sequences for the Thermus thermophilus HB8 transcriptional repressor TTHA0973 using the selection method Restriction Endonuclease Protection, …

Genistein Has Antiviral Activity Against Herpes B Virus And Acts Synergistically With Antiviral Treatments To Reduce Effective Dose, Julia C. Lecher, Nga Diep, Peter W. Krug, Julia K. Hilliard

Faculty Articles

Herpes B virus is a deadly zoonotic agent that can be transmitted to humans from the macaque monkey, an animal widely used in biomedical research. Currently, there is no cure for human B virus infection and treatments require a life-long daily regimen of antivirals, namely acyclovir and ganciclovir. Long-term antiviral treatments have been associated with significant debilitating side effects, thus, there is an ongoing search for alternative efficacious antiviral treatment. In this study, the antiviral activity of genistein was quantified against B virus in a primary cell culture model system. Genistein prevented plaque formation of B virus and reduced virus …

Understanding How Map Kinases Influence Endothelial Nitric-Oxide Synthase Activity, Xzaviar Solone

Master of Science in Integrative Biology Theses

Mitogen activated protein kinases (MAPK) p38 and ERK have both been reported to bind endothelial nitric oxide synthase (eNOS) with submicromolar affinity via proposed interactions with a pentabasic non-canonical MAPK binding sequence in the autoinhibitory insertion of eNOS. The neuronal isoform, which lacks the pentabasic motif, did not bind either MAPK significantly. In the present study, the pentabasic motif was validated using predictive modeling programming, and eNOS phosphorylation by MAPKs (P38, ERK and JNK) was examined using in vitro kinase assays and immunoblotting. JNK phosphorylation at Ser¹¹⁴ contrasts with ERK, which phosphorylated Ser⁶⁰⁰, and p38, which phosphorylated …

Five Decades Of Research On Mitochondrial Nadh-Quinone Oxidoreductase (Complex I), Tomoko Ohnishi, S. Tsuyoshi Ohnishi, John C. Salerno

Faculty Articles

NADH-quinone oxidoreductase (complex I) is the largest and most complicated enzyme complex of the mitochondrial respiratory chain. It is the entry site into the respiratory chain for most of the reducing equivalents generated during metabolism, coupling electron transfer from NADH to quinone to proton translocation, which in turn drives ATP synthesis. Dysfunction of complex I is associated with neurodegenerative diseases such as Parkinson’s and Alzheimer’s, and it is proposed to be involved in aging. Complex I has one non-covalently bound FMN, eight to 10 iron-sulfur clusters, and protein-associated quinone molecules as electron transport components. Electron paramagnetic resonance (EPR) has previously …

Sumo Targeting Of A Stress-Tolerant Ulp1 Sumo Protease, Jennifer Peek, Catherine Harvey, Dreux Gray, Danny Rosenberg, Likhitha Kolla, Reuben Levy-Myers, Rui Yin, Oliver Kerscher, Jonathan L. Mcmurry

Faculty Articles

SUMO proteases of the SENP/Ulp family are master regulators of both sumoylation and desumoylation and regulate SUMO homeostasis in eukaryotic cells. SUMO conjugates rapidly increase in response to cellular stress, including nutrient starvation, hypoxia, osmotic stress, DNA damage, heat shock, and other proteotoxic stressors. Nevertheless, little is known about the regulation and targeting of SUMO proteases during stress. To this end we have undertaken a detailed comparison of the SUMO-binding activity of the budding yeast protein Ulp1 (ScUlp1) and its ortholog in the thermotolerant yeast Kluyveromyces marxianus, KmUlp1. We find that the catalytic UD domains of both ScUlp1 and KmUlp1 …