Biochemistry, Biophysics, and Structural Biology Commons^™

Novel Strategies In Near Infrared Spectroscopy (Nirs) And Multivariate Analysis (Mva) For Detecting And Profiling Pathogens And Diseases Of Agricultural Importance., Johjan Mariana Santos Rivera

Theses and Dissertations

The time required for the identification of pathogens is an important determinant of infection-related mortality rates and disease spread for species of relevance in agriculture. Conventional identification methods require a processing time of at least one to twenty days. Therefore, inaccurate empirical treatments are often provided while awaiting further identification, such that most cases progress with further aggravation of symptoms, contamination of other animals or plants, generating economic loss from decreased yield, and increased mitigation costs. Thus, there is a need for innovative, non-destructive, and rapid analytical techniques that provide reagent-free, portable, reliable, and holistic approaches to detect diseases in …

Optimized Selenium Status, Gut Microbiota, And Type 2 Diabetes, Ying-Chen Huang

Theses and Dissertations

We have previously demonstrated that long-term dietary Se deficiency in old Terc^-/- mice with humanized telomeres induces type-2 diabetes and exacerbates age-dependent increases in the abundance of A. muciniphila and Lachnospiraceae, which are related to obesity and metabolic syndromes. The objectives of this dissertation are: 1) to determine the minimum intake of Se required for type 2 diabetes prevention in middle-aged mice; 2) to evaluate the efficacy of A. muciniphila and R. torques (a Lachnospiraceae family member) to intervene dietary Se deficiency-induced type 2 diabetes and the underlying mechanisms; 3) to assess sex differences in the responses to …

Zinc-Mediated Regulatory Function Of Psd-95 On Nmdar At Post-Synapses, Luis F. Acosta

Theses and Dissertations

Postsynaptic density-95 (PSD-95) is a membrane-associated guanylate kinase that mediates localization of receptors in the excitatory postsynaptic density. It has been reported that PSD-95 mediates postsynaptic localization of NMDA receptors and anchors postsynaptic AMPAR receptors mainly through its postsynaptic membrane targeting by its N-terminal palmitoylation. Recent studies have shown that Ca2+/calmodulin blocks palmitoylation of PSD-95 by binding at the N-terminus of PSD-95, which promotes dissociation of PSD-95 from the postsynaptic membrane and causes loss of surface AMPARs in cultured neurons. Another metal ion zinc is found in various areas of the brain. As an endogenous neuromodulator, zinc plays a role …

Targeting Protein Synthesis In Clostridioides Difficile To Develop Antimicrobial Candidate, Elvira L. Alanis

Theses and Dissertations

Clostridioides difficile is a gram positive, spore forming, obligate anaerobic bacterium that causes Clostridioides difficile infection (CDI) which can result in pseudomembranous colitis and toxic megacolon. In the case of this research a focus on Protein synthesis is made since it is an essential metabolic process and is a validated target for antibiotics. Protein synthesis begins with Initiation which includes the three translation initiation factors. Through the NMR chemical shift assignments, the IF1 structure was determined, and it was found to be composed of a short α helix and five β helixes. A peptide was designed after the short α …

Nanostructured Materials For Biomedical Applications, Silverio Lopez

Theses and Dissertations

Nanotechnology has been used in an increasing number of applications in biochemistry and molecular biology. Compared to bulk materials, nanoscale materials offer a variety of advantages in applications due to an increased surface-to-volume ratio of the reactants. The unique properties of nanostructured materials and their properties such as stability, reactivity, magnetic response, pressure discharge performance and biocompatibility depend on particle size and shape. This work focuses on a nanoenergetic material composed of Aluminum (Al), Copper II oxide (CuO), and Iodine (I) pentoxide (I2O5), and the biomedical application of nanoscale dextran-coated magnetite (Fe3O4), which was produced using microfluidics to tune particle …

Assessing The Effects Of Levonorgestrel (Lng) On Neural Differentiation In The Developing Hypothalamus Using The Zebrafish (Danio Rerio) As A Model, Gabriella Hinojosa

Theses and Dissertations

Neurogenesis is a critical component of fetal neurodevelopment consisting of: migration, proliferation and differentiation. Health concerns from anxiety to reproductive issues have been linked to alterations of neurogenesis processes. Endocrine disrupting chemicals (EDCs) can mimic hormones vital to this process, potentially adversely affecting the susceptible fetal brain. One EDC, Levonorgestrel (LNG), is a testosterone-like progestin used in birth control methods that has a high bioavailability and long half-life. Using zebrafish embryos as a model, this lab previously discovered that an environmentally relevant LNG dose (5 ng/L) significantly increased anxiety behaviors. The hypothalamus is responsible for the development …

Exploring Dna Compaction Via Bacillus Subtilis Parb Protein By Single Molecule Investigation, Miranda L. Molina

Theses and Dissertations

Faithful chromosome segregation involves ParB, a DNA-binding and compacting protein that specifically recognizes parS DNA sites near the replication origin. ParB spreads 10-20 kb from parS sites, which recruitments additional ParB molecules to neighboring DNA, forming higher-order nucleoprotein complexes. ParB is also a novel CTPase enzyme and hydrolyses CTP to self-dimerization and create a clamp that slides along DNA. To understand the roles of CTP in Bacillus subtilis ParB (BsParB), we purified wild type ParB (BsParB (WT)) and recombinant ParB (BsParB(R80A)) mutant. BsParB(R80A) was known to prevent CTP binding and not compact DNA. Proteins N- and C-terminally appended with a …

Structures And Regulations Of Translation Initiation Factors In Pseudomonas Aeruginosa Protein Biosynthesis To Develop New Potential Antimicrobial Agents, Nicolette Valdez

Theses and Dissertations

Pseudomonas aeruginosa is a Gram-negative, multidrug resistant bacterium that has been recognized as the prominent cause of nosocomial infections. Untreated acute and chronic infections associated with P. aeruginosa can develop into other diseases such as pneumonia, otitis externa, and osteomyelitis. P. aeruginosa infections commonly affect immunocompromised individuals such as cystic fibrosis, cancer, and burn patients. The misuse and overuse of antibiotics has contributed to the increased antibiotic resistance in P. aeruginosa and thus has led to an unmet need for discovery of novel antibiotic candidates. Protein biosynthesis is an essential metabolic process occurring in all bacteria and a validated target …

Eukaryotic Initiation Factor 4e (Eif4e) In Complex With Eif4e Binding Protein 1 (4e-Bp1) Binds With Higher Affinity To M7gpppn Cap Of A Subset Of Human Mrnas, Izza F. Nawaz

Theses and Dissertations

Fluorescence anisotropy binding assays were used to analyze the binding of eIF4E in complex with 4E-BP1 onto the 5’ m7G cap of a subset of mRNA that are known to carry cap-independent translation. These studies suggest that 4E-BP1 increases eIF4E binding affinity to 5’cap of both FGF-9 and HIF-1𝝰.

Repurposing Metformin And Antifolates For The Treatment Of Hepatocellular Carcinoma, Sherouk Mohamed Tawfik

Theses and Dissertations

Hepatocellular carcinoma (HCC), one of the most prevalent types of cancers worldwide, continues to maintain high levels of resistance to standard therapy. As clinical data revealed poor response rates, the need for developing new methods has increased to improve the overall wellbeing of patients with HCC. Due to its safety, wide availability and previously reported anti-cancer effects, metformin (MET) serves to be a possible therapeutic agent when combined with other well-known anti-cancer agents. The aim of this study was to investigate the potential anti-cancer effects of MET, an anti-diabetic agent, when combined with two antifolate drugs: trimethoprim (TMP) or methotrexate …

Identification Of Novel Phosphorylation Sites In Sars-Cov-2 Nucleocapsid Protein, Josie Daldegan Rezende

Theses and Dissertations

COVID-19, the 2019 disease outbreak, continues to cause severe mortality worldwide. Fast and reliable tests that identify the SARS-CoV-2 virus, which is responsible for causing the COVID-19 disease, are crucial for controlling the spread of the virus. Antigen tests are ideal for the rapid diagnosis of COVID-19. Current antigen tests for COVID-19 detect the SARS-CoV-2 nucleocapsid (N) protein. The nucleocapsid is the most abundant protein produced by the virus upon infection, which makes it a superior target for detection by an antigen test. Nucleocapsid proteins from several coronaviruses, including SARS, have previously been shown to be modified by posttranslational modification …

The Role Of Irf-1 In Spontaneous Mouse Glioma, Aakash B. Vaidya

Theses and Dissertations

Glioblastoma Multiforme has been shown to be one of the deadliest primary brain cancers. One of the reasons why GBM is so deadly, is a unique immunosuppressive tumor microenvironment that promotes GBM growth and progression. Both astrocyte and microglia have been implicated in immunosuppression. In this study, we explored the role of Interferon Regulatory Factor 1 (IRF-1) in astrocytes and glioma cells on the growth of spontaneous glioma tumors. IRF-1 is regulated by the JAK/STAT pathway and induces expression of Programmed death ligand 1 (PD-L1). PD-L1 downregulates immune responses to glioma. We found that IRF-1 had no effect on spontaneous …

Targeting Bcl-2 Family Proteins In Therapy Induced Senescent Cancer Cell Models, Wade Cook

Theses and Dissertations

Non-small Cell Lung Cancer (NSCLC) originates from numerous different cell types in the lungs and is among the deadliest of cancers. Head and Neck Squamous Cell Carcinomas (HNSCC) are derived from the mucosal membranes of the oral cavity, pharynx, and larynx. Both NSCLC and HNSCC are predominately caused by tobacco smoke inhalation and as such mutations in the tumor suppressor gene TP53 are common. Since similarities exist in the root cause of NSCLC and HNSCC, they may also share similarities in treatment methods. Cisplatin is a platinum-based DNA damaging agent that has been used as a cancer chemotherapy for decades. …

Structure-Based Drug Discovery And Development Of Protein Structure Prediction Tools Using An Empirical Force Field, Noah B. Herrington

Theses and Dissertations

Traditional drug discovery has rapidly accelerated thanks to development of computational molecular modeling. The crucial component that these computational studies hinge upon is having a well-defined, and energetically favorable structure. Structures of proteins and ligands that meet these criteria are important for accurately simulating models used to study drug binding. To demonstrate the role of accurate structure simulation in the study of these events, this thesis presents, first, a story examining the problem of accurate structure modeling of ionizable residues within protein structures, specifically aspartic acid, glutamic acid, and histidine. I present our method, which uses the HINT force field …

Protein Structure And Interaction: The Role Of Aromatic Residues In Protein Structure And Interactions Between Pyridoxine 5'-Phosphate Oxidase/Dopa Decarboxylase, Mohammed H. Al Mughram

Theses and Dissertations

Naturally developed proteins are capable of carrying out a wide variety of molecular functions due to their highly precise three-dimensional structures, which are determined by their genetically encoded sequences of amino acids. A thorough knowledge of protein structures and interactions at the atomic level will enable researchers to get a deep foundational understanding of the molecular interactions and enzymatic processes required for cells, resulting in more effective therapeutic interventions. This dissertation intends to use structural knowledge from solved protein structures for two distinct objectives.

In the first project, we conducted a bioinformatics structural analysis of experimental protein structures using our …

The Utilization Of Enzymes And Enzyme Products For Antimicrobial Effects, Brandon Edward Burdette

Theses and Dissertations

Bacterial resistance is outpacing the discovery of novel antimicrobials. Therefore, it is essential to look at antimicrobials using novel methods. MTAN is a crucial enzyme for some bacteria such as Helicobacter pylori. Transition state analog inhibitor design and fragment-based drug design are drug design approaches typically used independently, but combining these techniques yields inhibitors that bind tightly and are effective in pM concentrations. We demonstrate the efficacy of the combined techniques by investigating the inhibition of HpMTAN, which is an essential enzyme. Enzyme byproducts can also be effective for causing bacterial cell death, hydrolyzing GsdmD by caspases-1/4/5/11 results in an …

Dissection Of The Genetic Architecture Of Grain Quality In Rice, Shuai Liu

Theses and Dissertations

Rice is an important human staple food for over half of the world’s population. Amylose content (AC), gelatinization temperature (GT), grain protein content (GPC), percentage grain chalkiness (PGC), and mineral content are important parameters for evaluating rice quality, which attracts customers and breeders. Only limited genes or QTLs (OsAAP6, OsGluA2, OsASN1, Chalk5, OsHMA3, etc.) are reported regulating rice GPC, PGC, and mineral content due to the lack of genetic knowledge and molecular markers. To dissect the genetic architecture of rice grain quality regulation, genome wide association studies (GWAS) were performed using two populations …

A Review Of Calcineurin Biophysics With Implications For Cardiac Physiology, Ryan B. Williams

Theses and Dissertations

Calmodulin is a prevalent calcium sensing protein found in all cells. Three genes exist for calmodulin and all three of these genes encode for the exact same protein sequence. Recently mutations in the amino acid sequence of calmodulin have been identified in living human patients. Thus far, patients harboring these mutations in the calmodulin sequence have only displayed an altered cardiac related phenotype. Calcineurin is involved in many key physiological processes and its activity is regulated by calcium and calmodulin. In order to assess whether or not calcineurin contributes to calmodulinopathy (a pathological state arising from dysfunctional calmodulin), a comprehensive …

Initial Characterization Of Prna From Burkholderia Ambifaria: Developing An Nadph-Dependent Activity Assay For Tryptophan Halogenation, Mahmuda Akter

Theses and Dissertations

Some bacteria produce a potent antifungal agent (pyrrolnitrin) from tryptophan using four dioxygen dependent steps to outcompete other microbes. Each step of this process is catalyzed by an oxygenase encoded by the prnABCD cassette. The first enzymatic step in pyrrolnitrin biosynthesis is the regioselective chlorination of tryptophan to form 7-chlorotryptophan. This halogenation is catalyzed by PrnA, a Flavin dependent oxygenase, which has been isolated and characterized from P. fluorescens. The pyrrolnitrin biosynthesis pathway (prnABCD) has been also observed in the Burkholderia genus. This thesis comprises my studies on the expression, purification, and characterization of PrnA from Burkholderia ambifaria. Beyond the …

Characterization Of Biomarkers For Alzheimer’S Disease And Hiv-1 Associated Neurocognitive Disorders, Armando Garces Iii

Theses and Dissertations

Alzheimer’s disease is a neurodegenerative disorder that is characterized by progressive cognitive decline and the accumulation of amyloid beta and neurofibrillary tangles in regions of the brain. These protein deposits are known to generate multiple effects on the brain that lead to neurodegeneration. It has been established that (Human Immunodeficiency Virus) HIV-1 accelerates the aging process of people living with HIV-1. Moreover, there is significant clinical evidence indicating a potential link between the neurodegeneration developed by those with an HIV-1 infection and AD. HIV-1 viral infection causes cognitive impairment known as …

Evolutionary Development Study Of Firebrat (Thermobia Domestica), Luis Cantu Jr.

Theses and Dissertations

As most evolutionary development studies regarding wing origin take place using insects taxonomically closer to model organism, Drosophila melanogaster, there is a need of expanding studies to lower clades. While D. melanogaster is higher phylogenetically, basal clades would allow for a historical perspective of what occurs within the gene flow of conservative biomarkers. Further understanding of wings and flight would allow for a clearer understanding of how the migration of insects from sea to land has allowed them to become one of the most speciose taxa. Through the study of Thermobia Domestica, part of the Zygentoma, we expand on comprehension …

Development Of A Novel Strategy To Improve Checkpoint Immune Response In Pancreatic Cancer, Poornima Devi Shaji

Theses and Dissertations

Pancreatic Cancer is the 3rd lethal causing cancers in United States with a survival rate less than 5-7%. In advanced unresectable pancreatic cancer, treatment options are restrained to surgery because of its extreme aggressiveness. Immunotherapy, one of the current advanced treatments has shown promising response in other cancers. However, this therapy is limited in pancreatic cancer due to desmoplasia and fibrotic tumor microenvironment (TME).

Our superparamagnetic iron oxide nanoparticles (SPIONS) of curcumin (Curcuma longa, principal curcuminoid of turmeric) have potential ability to inhibit desmoplasia and tumor stroma with an increased bioavailability. This would soften up the tumors for …

Insights Into Halophilic Microbial Adaptation: Analysis Of Integrons And Associated Genomic Structures And Characterization Of A Nitrilase In Hypersaline Environments, Sarah Sonbol

Theses and Dissertations

Hypersaline environments are extreme habitats that can be exploited as biotechnological resources. Here, we characterized a nitrilase (NitraS-ATII) isolated from Atlantis II Deep brine pool. It showed higher thermal stability and heavy metal tolerance compared to a closely related nitrilase.

We also studied integrons in halophiles and hypersaline environments. Integrons are genetic platforms in which an integron integrase (IntI) mediates the excision and integration of gene cassettes at specific recombination sites. In order to search for integrons in halophiles and hypersaline metagenomes, we used a PCR-based approach, in addition to different bioinformatics tools, mainly IntegronFinder.

We found that integrons and …

Mucinomics: A Bioinformatic Analysis Of Snail Mucins, And Their Function, Maxwell B. Mcdermott

Theses and Dissertations

This thesis outlines the current research on secreted snail mucus, highlighting the potential of this biopolymer, and also demonstrates a research strategy to fulfill the unmet need of examining the hierarchical structures that lead to the enormous biological and chemical diversity of snail mucus genes.

Investigation Of Techniques And Their Application For The Cryopreservation Of Algal Species, Jazmine Leija

Theses and Dissertations

An alternative source for petroleum-based crude oils are algae derived biofuels. Fossil fuels are harmful for the environment, expensive and becoming scarce. There has been an increase in research on environmentally sustainable energy, using lipids derived from microalgae, which can be converted into biofuel. The use of microalgae as a source for biofuels has a lot of benefits including decreasing greenhouse gas emissions, rapid fuel production, absorption of carbon dioxide, and production of a renewable source of energy.

Algae cryopreservation aids in the maintenance of the best algae strains selected for producing lipids for biofuels. Cryopreservation will help minimize genetic …

Divergent Regulatory Roles Of Nurd Chromatin Remodeling Complex Subunits Gatad2 And Chd4 In Caenorhabditis Elegans, Nicole Lynn Golden

Theses and Dissertations

During stress, a protective cellular network known as the heat shock response (HSR) is induced to maintain protein-folding homeostasis, or proteostasis. While the HSR is essential for stress resistance, its misregulation is associated with neurodegenerative disease and cancer. Using the nematode model organism Caenorhabditis elegans, we have identified the chromatin remodeling complex NuRD (nucleosome remodeling and deacetylase) as a novel regulator of the HSR. Here, we begin with a brief introduction of the HSR and chromatin remodeling complexes in C. elegans, prior to presenting our findings in a series of two chapters. In chapter one, we outline a set of …

Distinct Spatiotemporal Regulation Of The Cytoprotective Heat Shock Response In Caenorhabditis Elegans, Rosemary Nadine Plagens

Theses and Dissertations

Every organism studied to-date utilizes the heat shock response (HSR) to maintain protein-folding homeostasis (proteostasis) during temperature or other protein-folding stress. The HSR has been well characterized using acute heat stress (HS) in single-celled models, but less is known about how distinct cell types and tissues respond to HS. Furthermore, how metazoans respond to prolonged HS at the molecular level remains relatively unexplored. The model organism C. elegans, with its genetic tractability and distinct tissues and behaviors, has been used extensively in the field to characterize the acute HSR, but with considerable variability across labs regarding HS temperature and duration. …

Survival Kinetics And Antimicrobial Interventions To Mitigate Foodborne Pathogen Contamination Of Low-Moisture Foods, Rajat Sharma

Theses and Dissertations

Contamination of low-moisture foods (LMFs) with foodborne pathogens such as Salmonella and Shiga-toxin producing Escherichia coli (STEC) has been rising over the last couple of years. Commodity groups such as peanuts, tree nuts, and their products are frequently recalled when associated with illness outbreaks resulting from these pathogens. In this project, two major challenges related to understanding the survival kinetics of pathogens and the efficacy of novel antimicrobial treatments in mitigating their risk in LMFs were systematically investigated. Studies were conducted for determining the survival kinetics of three Salmonella spp. strains in three different tree nut flours (i.e., almond, chestnut, …

Characterization Of Ph – Responsive Nanocage Based On The Ferritin Iron Storage Protein, Satyam Singh

Theses and Dissertations

The iron-storage protein ferritin (Ftn) assembles into a protein cage structure with 24 subunits and octahedral (4-fold, 3-fold, 2-fold) symmetry. Each monomeric subunit contains a robust four-helix bundle fold. The fully assembled Ftn structure has a high degree of thermal stability (up to 100°C), a mono dispersed size (12 nm in diameter), and a large central cavity (7-8 nm in diameter). The central cavity stores ferric iron in phylogenetically diverse group of organisms, including humans. The central cavity has been used for encapsulation of cargoes such as other metals, contrast agents for imaging, small molecule drugs for therapy, …

Uncovering Potential Biofilm Modulators, Liliana Margent

Theses and Dissertations

Biofilms have negative and positive impacts depending on the context they develop. In this work, I optimized a biofilm assay to evaluate the effect of three different types of compounds indole derivatives, 2,5 Diketopiperazines, and 12-hydroxystearic acid on the biofilm formation of E. coli.