Biochemistry, Biophysics, and Structural Biology Commons^™

Molecular Characterization Of Nitrogenase Regulation In Methanosarcina Acetivorans, Melissa Chanderban

Graduate Theses and Dissertations

Nitrogenase is the metalloenzyme only found in bacteria and archaea that is essential for biological nitrogen fixation (diazotrophy), but it can also serve as a catalyst in biofuel production. All diazotrophs contain a molybdenum (Mo) nitrogenase, while some species contain additional alternative nitrogenases where either vanadium (V) or iron (Fe) replace Mo in the active site cofactor. Nitrogen fixation by bacteria has been extensively studied. The limited investigation of nitrogen fixation in methanogenic archaea (methanogens) indicates production of nitrogenase is simpler than in bacteria and methanogen nitrogenase has different biochemical properties. Thus, methanogen nitrogenases provide a promising alternative for genetic …

The Binding Of The Micronutrient Transition Metals To The Alkylation Products Of Chemical Warfare Agent, Sulfur Mustard, And Thiols, Potentially Giving New Understanding To Physiological Effects Of Exposure And Increased Toxicity, Colin O'Donnell

Graduate Theses and Dissertations

Model compounds, 3,6,9-trithaiundecane-1,11-dicarboxylic acid (TTDPA), 2,5,8-trithianonane-1,9-dicarboxylic acid (TTDAA), and 1,11-diamide-3,6,9-trithiaundecane (TTDAce), closely related to the adducts formed by cysteine alkylation of the chemical weapon, sulfur mustard, were synthesized. It is shown that TTDPA forms complexes with key metal micronutrients: copper, nickel, cobalt, manganese, and zinc. Though the strength of binding to TTDPA varies, the complexes in many cases precipitate from solution. All metals produced a visible precipitate upon interaction with TTDPA under the conditions tested, however only Cu2+, Mn2+, and Zn2+ produced enough to be measured. The mass of formed precipitate seemed to peak at an equimolar ratio of TTDPA …

Comparative Analysis Of Conformational Transition Pathways In Homologous Proteins, Dylan Sebastien Ogden

Graduate Theses and Dissertations

Molecular dynamics (MD) simulations are routinely used to study the dynamics of proteins. However, conventional MD limited to the sampling of local conformational changes as the functionally important conformational transitions of proteins often extend beyond the timescales of the simulations employed, for example, membrane transport proteins. We have determined the combination of multiple MD based techniques that allows for a rigorous characterization of energetics and kinetics of large-scale conformational changes in membrane proteins. The methodology is based on biased, nonequilibrium collective variable based simulations including nonequilibrium pulling, string method with swarms of trajectories, bias-exchange umbrella sampling, and rate estimation techniques. …

An Analytical Method To Detect And Quantify Ll-37 In An In Vitro Co-Culture Of Activated Thp-1 Cells And Staphylococcus Aureus, Staphylococcus Epidermidis, And Pseudomonas Aeruginosa, Victoria Hunter

Graduate Theses and Dissertations

Healthcare-associated infections (HCAIs) affect 1.7 million hospitalized patients each year, resulting in over 98,000 deaths and anywhere from $28.4 to $45 billion in treatment costs. Furthermore, it has been established that more than 80% of these infections are caused by biofilms While HCAIs can be bacterial, viral, fungal, or parasitic, there are between 12 and 17 species cause 80 to 87% of all HCAIs. Among the most commonly isolated microorganisms are Pseudomonas aeruginosa (P. aeruginosa) and Staphylococcus aureus (S. aureus). Thus, biofilms are of importance not only due to their prevalence in HCAIs but also due to the increased antibiotic …

Examining The Expression Patterns Of Desulfotalea Psychrophila Dsrab Operon And Pit At Subfreezing Temperatures And Different Concentrations Of Sulfate Salts As A Model For Mars And Icy Worlds Survival And Colonization, Sergio Luis Mosquera Mora

Graduate Theses and Dissertations

Since ancient times, Humanity has been fascinated with the idea of what lies beyond the borders of our planet. Fortunately, the combined efforts of many nations have made it possible to send unmanned spacecraft to orbit planets located close to Earth. These missions have the principal goal to collect data that could help us understand the basic environmental conditions that persist on those planets, or for evidence of past or present life. Equally important, landers and rovers have been successfully deployed to start the in-situ exploration of many planets of the Solar System. Among them, Mars has been extensively studied …

Validation Of Whole Genome Resequencing For Mapping The Genetics Of Ascites In Broilers And Viral Susceptibility In Layers, Katherine Pepper Lee

Graduate Theses and Dissertations

This dissertation focused on the efficacy and validity of whole genome resequencing (WGR) for fine mapping genetic determinants of particular traits in a given organism. Previously, our research group used WGR to identify haplotype blocks of single nucleotide polymorphisms associated with ascites resistance with some as strong candidates for use in marker-assisted selection (MAS). Chapter 2 discusses the completion of a MAS project through evaluation of ascites incidence as well as production traits of economic value to poultry producers. Thus, the MAS project also covered viability of this methodology in the industry. The MAS significantly reduced ascites incidence in broilers …

Characterization Of Genetic Pathways Involved In Resistance To A Novel Antifungal Peptide, Kayla L. Haberman

Graduate Theses and Dissertations

Antibiotic resistance is increasing prevalence, particularly in Candida glabrata. This opportunistic pathogen is closely phylogenetically related to Saccharomyces cerevisiae; however, its characterization is limited. C. glabrata is only second to Candida albicans as a fungal pathogen in immunocompromised patients. Commonly resistant to azoles, the most common fungal therapy, it has become costly and challenging to treat. A histatin 5 derived antifungal peptide, KM29, has a high degree of efficacy in Candida species and S. cerevisiae. The objective of this work is to advance our understanding of the mechanism of action of KM29 against C. glabrata. Previous work in the lab …

Habitability, And Evolution Of Microorganisms Under Extreme Conditions, Azarin Yazdani

Graduate Theses and Dissertations

The choice of a solvent determines the possible biochemistry of life. Life on Earth is based on carbon biochemistry and has evolved in an environment with water as a solvent. As a polar solvent abundant on Earth, water has unique physical properties, including a large range of liquidity and low viscosity, making it a very good solvent for terrestrial life. Liquids other than water are abundant in the universe, and the chemical nature of these liquids might lead to different chemistries of life. In the first chapter, we review the main characteristics of a good solvent, and then we use …

Identification Of Genomic, Proteomic, And Metabolomic Signatures Associated With Pulmonary Hypertension Syndrome In Broilers, Duaa Almansaf

Graduate Theses and Dissertations

The present dissertation contains a collection of studies that examine the genomic, proteomic, and metabolomic association to pulmonary hypertension or ascites phenotype in fast-growing broilers. Pulmonary hypertension is a multifactorial metabolic disease influenced by physiological, environmental, and nutritional factors. It is characterized by a number of structural changes including, thrombosis and adverse pulmonary vascular remodeling. Thus, the atrial pressure is increased, and the right ventricle becomes hypertrophied, resulting in heart failure and the death of the bird. Pulmonary hypertension or ascites is a global problem that has negatively impacted the economy. The increased mortality rate of broilers (25%) is estimated …

The Role Of Temperature Variation On Macrophage Physiology And Function In Vitro In Mice, Chicken, And Fish, Intisar Abdullah Hassan

Graduate Theses and Dissertations

Fever is an essential component of the immune response. Baseline body temperatures vary in different species, and fever represents increased temperature over baseline. Fever initiates and enhances immune responses as well as creates an environment in which the body has advantages over pathogens. Macrophages are often the first line of cells that come in contact with pathogens, asthey reside in and traffic through tissues. They are important for their engulfment of pathogens that results in the digestion of the pathogen, and they also produce nitric oxide and cytokines that contribute to immune responses in a variety of ways, including initiating …

Chondronecrosis With Osteomyelitis In Broilers: Bacterial Species Involvement And Influence Of Probiotics And Synbiotics, Amer Abdullah Hasan

Graduate Theses and Dissertations

Since 1945, the market for broiler production has evolved from a collection of smallholder poultry farms into an industry worth billions of dollars. Poultry production has not gone without challenges. Lameness in young broilers is presently a serious issue in the poultry industry for reasons of animal health and welfare, as well as significant lost production and revenue. Bacterial chondronecrosis with osteomyelitis (BCO) is a major form of lameness in broilers. This dissertation contains information about (i) the influence of Staphylococcus agnetis, Staphylococcus saprophyticus, Staphylococcus epidermidis and Enterococcus faecalis on inducing BCO lameness, (ii) evaluation of of probiotics for reducing …

Bacterial Chondronecrosis With Osteomyelitis In Broilers: Genomics, Phylogenomics, And Methods To Detect Specific Pathogens During Outbreaks., Abdulkarim Abdulaziz A. Shwani

Graduate Theses and Dissertations

Lameness is a major issue in animal welfare and the broiler industry. Bacterial chondronecrosis with osteomyelitis (BCO) is one of the main causes of lameness. Many staphylococcal species, including Staphylococcus agnetis isolate 908, have been isolated from the bones and blood of lame broilers at the University of Arkansas. Staphylococcus agnetis is a coagulase-variable, Gram-positive bacterial species that has been previously associated with subclinical or mild clinical cases of mastitis in dairy cattle. The annotated complete genome of hypervirulent strain 908 was published at NCBI. In this study, it has been compared to nine genomes we assembled for hypervirulent isolates …

Investigating Molecular Mechanisms Behind Bacterial Chondronecrosis With Osteomyelitis (Bco) Pathogenesis In Modern Broilers, Alison Ramser

Graduate Theses and Dissertations

Bacterial chondronecrosis with osteomyelitis (BCO), a leading cause of lameness in broiler chickens, is characterized by infection, inflammation, and bone attrition. There are currently no effective treatments and positive diagnosis is only possible through necropsy evaluations. Lameness is also a rising animal welfare and economic concern, making prevention and detection of BCO all the more critical. These challenges are exacerbated by a lack of mechanistic understanding of BCO’s etiology. The question I asked during my dissertation was how bacteria induce bone attrition in BCO pathology. My research has shown that mitochondrial dysfunction is characteristic of BCO conditions along with autophagy …

Studying Acetylation Of Aconitase Isozymes By Genetic Code Expansion, Jessica Araujo

Graduate Theses and Dissertations

The tricarboxylic acid (TCA) cycle is a very important, centrally located, energy-producing pathway that connects numerous other metabolic and regulatory pathways. Enzymes of this cycle have been more recently implicated in various cancers and neurometabolic disorders, however, the exact mechanism by which this happens becomes quite complex when considering the potential modification of these enzymes and the presence of multiple forms of the enzymes and therefore there is much to be studied in this area.

Aconitase has become a recent enzyme of interest as its substrate, citrate, has been found to play a major role in many vital processes within …

Essential Amino Acid (Eaa) Regulation Of Skeletal Muscle Protein Turnover With Age, Mary Komp

Graduate Theses and Dissertations

Skeletal muscle (SM) is vital for both long term health and quality of life. Recent research suggests an increase in catabolic signals with age triggers pathologic conditions, such as sarcopenia. Although results from in vitro studies model how EAA can regulate muscle protein synthesis (MPS), the relevance of these models to muscle protein breakdown (MPB) and the presence of physiological EAA concentrations remains to be established. Therefore, the objective of this study was to determine the effects of a low, normal, and supra physiological dose of EAA (0.2, 1.0, and 3.0 x EAA) in a young (passages 2-10) and aging …

Macronutrient Availability Shapes Host Response To Infection And Feeding Behavior, Weston Gerald Perrine

Graduate Theses and Dissertations

Macronutrients in the diet are vital to the physiological processes necessary for an organism to effectively clear a pathogen. Diet can be important to a host’s susceptibility to infection and severity of pathology, though results can vary across host-pathogen systems (Sen et al. 2016). Manipulating the ratio of specific macronutrients in the diet is an effective method to begin understanding how individual macronutrients, rather than food types, have on immune responses. Using an avian host-pathogen system, I explored the effects of dietary macronutrient composition, specifically lipid and protein content, on disease pathology and behavior of canaries (Serinus canaria) infected with …

Characterization Of The Influence Of A Small Molecule Inhibitor On Ras-Related Proteins Interactions, Emilio Duverna

Graduate Theses and Dissertations

The Ras superfamily of small G proteins are involved in cell-signaling processes that, if not regulated, may lead to cell multiplication, apoptosis inhibition, and tumorigenesis. They function as molecular switches, which through GTP/GDP exchange cycle, switch on or off cellular activities. Overexpression and/or hyperactivity of these proteins have been linked to many diseases including various cancers. CDC42, a member of the Rho subfamily of the Ras superfamily of small G proteins, participates in the regulation of many cellular processes including cell adhesion, mitosis, and cytoskeletal rearrangements. CDC42 binds to and activates many effector proteins including CDC42-activated kinase (ACK). Abnormal activities …

Preparation Of Proteins And Peptides From Heat-Stabilized Defatted Rice Bran Via Solid State Fermentation And Investigating For Skin Health, Ali A. Bisly

Graduate Theses and Dissertations

Heat-stabilized defatted rice bran (HDRB) is an abundant and inexpensive agro-industrial by-product of rice milling and rice oil extraction process. Furthermore, HDRB is a potential source of proteins. However, the direct protein extraction has low yield of protein due to the impact of heat stabilization and oil extraction process which made the HDRB proteins bound and interact with other components. This research is based on using solid-state fermentation (SSF), which is a natural and cost-effective approach to facilitate protein extraction from HDRB using Bacillus subtilis (natto) Takahashi as a microorganism.

Response surface methodology (RSM) analysis was used with Box-Behnken design …

Diffusive Dynamics Of Biological Macromolecules In The Cytoplasm Of Live Bacteria, Asmaa Ali Sadoon

Graduate Theses and Dissertations

Bacteria are small organisms that play important roles in our bodies and in maintaining our surrounding environment. However, bacterial infections are considered as one of the health diseases that threatens the lives of humans. Resistance of bacteria to antibiotics has made treating bacterial infections more challenging. With the emergence of many developed optical techniques, it has become possible to study various biological mechanisms of molecules inside these small organisms with high resolution and precise localization. In this research, single particle tracking photoactivation localization microscopy (sptPALM) technique was used to investigate the dynamics of fluorescent histonelike nucleoid-structuring proteins (H-NS) in live …

The Role Of Ccaat Binding Factor In The Regulation Of Catalase Gene Expression In Candida Albicans, Zahra Al-Rumaih

Graduate Theses and Dissertations

Candida albicans is a fungal opportunistic human pathogen. Its infections range from surficial infections like skin rash to fatal systemic infections. Filamentation growth mode is associated with C. albicans virulence because it helps penetration of the host’s epithelial cells. The CCAAT-binding factor (CBF) is a conserved heterooligomeric transcription factor found in 30% of eukaryotes genes. In C. albicans it is composed of 4 major subunits, including Hap2, Hap3, Hap4, and Hap5. Hap2 and Hap5 are essential for DNA binding and function. Hap4 has 3 homologous subunits: Hap41 and Hap42 are putative subunits of CBP. Hap43 is the only Hap4 subunit …

Site-Specific Effects Of Lysine Acetylation On Aminoacyl-Trna Synthetase, Hao Chen

Graduate Theses and Dissertations

Aminoacyl-tRNA synthetases (AARSs) are an ancient and highly conserved family of enzymes which can catalyze a two-steps aminoacylation reaction to charge tRNAs with their cognate amino acids, thus playing crucial roles in ribosomal protein synthesis. Naturally, the accurate amino acids and tRNA recognition of these synthetases are essential to the fidelity of translation process. To assure the correct recognition, some of these synthetases have evolved with an editing function to help remove the mischarged tRNAs. In addition to these functions, AARSs are also involved in various biological processes ranging from transcription to translation. Currently, a series of proteomic studies have …

Engineering Fluorescently Labeled Human Fibroblast Growth Factor One Mutants And Characterizing Their Photophysics Properties Towards Designing Fret Assays, Mamello Mohale

Graduate Theses and Dissertations

Human fibroblast growth factor one (hFGF1) belongs to a family of 22 FGF members produced by fibroblast cells. Cell signaling during physiological processes of angiogenesis and wound healing occurs when hFGF1 binds to its receptor (FGFR). However, when heterogenous homeostasis is not maintained, fibroblast cells exhibit excessive proliferation which can lead to a myriad of cancers. smFRET is an ultrasensitive distant dependent (1-10 nm) technique capable of resolving such heterogeneity in structural dynamics and binding affinities (Kd). Therefore, we successfully designed and characterized fluorescently labeled hFGF1 tracers which span the visible light region of the electromagnetic spectrum for use in …

Enzymatic Degradation Of Microcystin-Lr By Microcystinase (Mlra), Faisal Alqhtani

Graduate Theses and Dissertations

Microcystin-LR (MC-LR) is affecting the water supply worldwide. Hence, a way to eliminate this toxin is an essential target. In this study, successful cloning of the mlrA gene and producing MlrA enzyme that can degrade the cyclic MC-LR to linearized MC-LR was done. MlrA protein was expressed in Escherichia coli BL-21 (E. coli). Also, enhancing the MlrA yield by adding nickel to LB media was a success in producing more MlrA enzyme from the same volume. Even though the enzyme showed no activity after adding Ni, the enzyme was expressed at a higher yield. Furthermore, it was to investigate adding …

Deciphering Chemomechanical Couplings In Proteins Using Microsecond-Level Molecular Dynamics Simulations, Vivek Govind Kumar

Graduate Theses and Dissertations

All-atom molecular dynamics (MD) simulations combine the high temporal resolution of experimental methods like smFRET and spatial resolution of methods like x-ray crystallography, to provide a detailed dynamic picture of biomolecular processes. Here, microsecond-level atomistic MD simulations have been used to characterize chemomechanical couplings in human fibroblast growth factor 1 (hFGF1) and the spike proteins of SARS CoV-1 and SARS-CoV-2. hFGF1 is a globular signaling protein that is involved in several physiological processes ranging from cell proliferation to wound healing. Experimental studies have previously described the low proteolytic and thermal stability of hFGF1, in addition to the stabilizing role of …

Effects Of Localized Oxygen Production By Electrolysis On The First-Generation Glucose Sensor Response, Nandita Halder

Graduate Theses and Dissertations

Glucose sensors are very important for detecting blood glucose both in vitro and in vivo. First-generation glucose biosensors were based on the glucose oxidase (GOx) enzyme using molecular oxygen as the electron acceptor and therefore oxygen dependent. Unfortunately for in-vivo work, oxygen in the body is variable and limited. Alternative approaches to overcome the oxygen dependency came with their own limitations. The widely used and commercially available ex-vivo glucose test strip uses a mediator in place of oxygen to free it from oxygen dependency. The mediator-based technology, in most cases cannot be transferred to in vivo applications due to the …

Investigating Effects Of Microenvironmental Stress On Cell Metabolism Using Multiphoton Imaging, Lisa Rebello

Graduate Theses and Dissertations

Resistance to therapy in cancer is a major cause of poor prognosis in patients. Tumor hypoxia plays an active role in mediating treatment resistance and has been linked to metastases and metastatic potential in cancer. Our research focused on three objectives: i) To understand metabolic effects of chronic and intermittent hypoxia in murine breast cancer cells and its affiliation with metastatic potential ii) To identify the metabolic changes associated with radiation therapy in a panel of radiosensitive and radioresistant human head and neck cancer cells and iii) to monitor the changes in cell metabolism associated with gain of treatment resistance. …

Host-Parasite Interactions Within Food Webs, Adam Zvanut Hasik

Graduate Theses and Dissertations

Parasitism is one of the most common life history strategies employed in nature, yet the effects of parasites are often thought to be minimal, and the vast majority of studies fail to consider parasites and their effects on host organisms. This is likely a problem, as the magnitude of parasite-mediated effects on their hosts can be quite large. Additionally, the effects of parasites are known to extend beyond the host to affect other species interactions. I used a series of approaches to gain a more integral understanding of host-parasite interactions by studying (1) the effects of parasites on biotic interactions …

Characterization Of Iron-Sulfur Cluster Biogenesis In Methanogenic Archaea, Thomas Modlin Deere

Graduate Theses and Dissertations

Iron-sulfur (Fe-S) clusters are among the oldest cofactors on the planet, used by proteins in almost all forms of life on Earth to carry out processes ranging from energy transfer to DNA replication. Among the organisms believed to use these Fe-S proteins more extensively than almost any others are the methanogens, an ancient lineage of archaeal microbes that produce methane as a required product of their metabolism. Methane, the primary component of commercial natural gas, is both a potent greenhouse gas and an important fossil fuel. It can also be renewably produced as a biofuel. Biogenic methane is almost entirely …

The Characterization Of Angiopoietin-Like Protein 4 Overexpression In Triple Negative Breast Cancer, Jodi Simeon

Graduate Theses and Dissertations

Triple Negative Breast Cancer (TNBC) is highly invasive and metastatic with approximately 15% of patients developing liver metastases. The primary treatment of metastatic TNBC is chemotherapy, however, there is an increased chance of resistance to this therapeutic technique. If Breast Cancer Liver Metastasis (BCLM) is left untreated most patients survive only 4 to 8 months with a very rare 5-year survival. Therefore, it is imperative to analyze markers and molecular pathways that TNBC cells use to progress, invade, and metastasize to the liver. The aim of this study was to examine the overexpression of angiopoietin-like 4 (ANGPTL4) in TNBC cells …

Evaluating Bioenergetics And Mitochondrial Dynamics In Patient Fibroblasts With Pathogenic Mitochondrial Dna Mutations Causing Leigh Syndrome, Ajibola Bakare

Graduate Theses and Dissertations

Leigh syndrome (LS) is a rare fatal mitochondrial disorder of infants caused by pathogenic mutations in the nuclear (nDNA) or mitochondrial DNA (mtDNA) leading to mitochondrial dysfunction. The extent to which pathogenic mtDNA variants regulate disease severity in LS is not well understood. The heterogeneous nature of this disorder, based in part by complex mitochondrial genetics, and the nuclear and mitochondrial cross-talk has made it particularly challenging to investigate and develop therapies for treating LS . While the prognosis is poor, several studies are underway to understand the pathophysiology of LS. This dissertation provides a comprehensive structural and functional analysis …