Molecular Biology Commons^™

Characterization Of Snrk1 Signaling In Rice Growth, Reproduction, And Stress Responses Using Phenotypic And Omics Analysis, Maria Clara Faria-Bates

Graduate Theses and Dissertations

SnRK1 is an evolutionarily conserved protein kinase belonging to the SNF1/AMPK family that is composed of a catalytic subunit (α) and two regulatory subunits (β and βγ), and it has a major role in adjusting growth in response to the energy status. SnRK1 phosphorylates and alters the activities of enzymes involved in metabolism and regulates gene expression by altering the activity of chromatin-remodeling enzymes or transcription factors. Rice contains three functional paralogs of SnRK1α: OsSnRK1αA (Os05g0530500), OsSnRK1αB (Os8g0484600), and OsSnRK1αC (Os03g0289100). Although SnRK1 is known to play a central role in plant growth and stress responses, the functional specialization of …

Evaluating The Effectiveness Of An Air Purification System In Reducing Bacterial Chondronecrosis With Osteomyelitis Lameness In Broiler Chickens, Abdulaziz Ali Alqahtani

Graduate Theses and Dissertations

Bacterial chondronecrosis with osteomyelitis (BCO) is the primary cause of lameness in commercial broiler production and has a profound impact on animal welfare and cost-effectiveness. The purpose of this experiment was to examine the effect of an air purification system on mitigating BCO lameness in broiler chickens. One thousand eight hundred broiler chicks were reared in two side-by-side research barns. Eight air filtration units were installed in one building, and none in the other. Treatment groups in both houses included positive control birds on wire flooring to induce BCO, as well as negative control, feed additive, vaccination, and a combination …

Implications Of Acetylation And Phosphorylation On Metabolic Enzymes, Nour Fatema

Graduate Theses and Dissertations

All living things depend on glycolysis and the TCA cycle for energy production and metabolic control. Post-translational modifications (PTMs) such as acetylation and phosphorylation, which can change enzyme activity, substrate binding, and overall metabolic balance, tightly regulate these pathways. Diseases like cancer and metabolic problems are associated with disruptions in these alterations.

Serine phosphorylation and lysine acetylation are two of the many PTMs that are evolutionarily conserved processes that alter protein function. Previously thought to be a static histone alteration, acetylation is now understood to be a dynamic regulator of metabolic enzymes that modifies contacts, charge, and conformation. In response …

Bang!: Real-Time Measurements And Transcriptomics Of Metabolic Reprogramming In Activated Macrophages At Fever Temperature, Kenneth Howard Taylor

Graduate Theses and Dissertations

We investigated the real-time metabolic rates of activated macrophage cell lines derived from mouse, chicken and rainbow trout. Each species showed a different kinetic signature with metabolic rates accelerating under fever conditions specific to each organism. Upon activation mouse macrophages increased their rate of glycolysis early and then a later reprogramming phase occurred with a dramatic decrease in oxidative phosphorylation (OXPHOS) accompanied by a reciprocal second increase in glycolytic rates. Chicken macrophages showed an initial increase in both glycolytic and OXPHOS rates. The late drop OXPHOS rates also occurred in chicken however there was no reprogramming that occurred as glycolytic …

Leveraging Natural Variation In Yeast To Understand Susceptibility Differences In Parkinson’S Disease, Julio Andres Molina Pineda

Graduate Theses and Dissertations

Parkinson’s Disease (PD) is a neurodegenerative disorder that causes countless suffering around the world. Both forms, familial and sporadic, have been associated with the misfolding and cytotoxicity of α-synuclein, an otherwise non-pathogenic protein suspected to have various roles in the normal maintenance of the central nervous system. Model organisms have emerged as great vessels to uncover the cellular and molecular mechanisms that shape α-syn biology, and great strides have been made to understand it. Yet, it is still unclear why some individuals are affected by α-syn toxicity, while others not so much. Since it’s extremely complicated to study and probe …

Evolutionarily Conserved Functions Of The Gene Frazzled In Midline Axon Guidance In Drosophila Melanogaster And Tribolium Castaneum., Piyasi Ghosh

Graduate Theses and Dissertations

Axon guidance in bilaterians is often controlled by various signaling pathways in the nervous system, which determine the fate of the axons if they cross the midline or not. One such pathway involved is the ligand-receptor pair Netrin (Net) and Frazzled (Fra), which is also known as the attractive pathway that promotes midline crossing axons in insects and other bilaterians. Orthologs of the pathway ligand Netrins and their receptors Frazzled [Fra] in insects and Deleted in Colorectal cancer [DCC] in vertebrates are widely conserved in bilaterians. How well these regulatory roles of the protein are conserved is poorly understood. In …

Bacterial Chondronecrosis With Osteomyelitis In Broiler Chickens: Experimental Lameness And Additive Probiotic Treatments, Amanda Anthney

Graduate Theses and Dissertations

With the global population already surpassing 8.2 billion and expected to reach 9.7 billion by 2050, the poultry industry has seen a surge in demand due to its unmatched efficiency and affordability for consumers across the globe. Selective breeding and quality nutrition developments since the industry's commercialization have allowed producers to grow broilers up to 7 pounds by market age. While this extraordinarily efficient process has allowed quality poultry products to be available worldwide, the modern-day broiler has developed a multitude of musculoskeletal issues. Due to the lack of integral skeletal development to match the rapid production of muscle tissue, …

Encapsulation Of Probiotics By Cellulose Nanocrystal-Alginate Composite Beads For Ph Stimuli-Responsive Delivery, Akrip Jati

Graduate Theses and Dissertations

Microencapsulation has garnered significant interest, with oral probiotics delivery systems showing enormous potential to help restore the gut microbiome. This method holds vast potential to protect and release specific microbial strains to the desired target site (i.e., colon) within the gastrointestinal tract (GIT). However, current encapsulation methodologies, utilizing either synthetic or biological materials as carriers, encounter challenges such as suboptimal encapsulation efficiency, premature probiotic release, and inadequate control over release kinetics. In this work, hydrogel microsphere (HM) composites of different cellulose nanocrystal (CNC) forms (i.e., colloidal (c), and crosslinked (x)) and alginate (ALG) were used as advanced controlled release systems …

L-Arabinose Induced Overexpression For Crystallographic Analysis Of The Spoiie Protein From Clostridioides Difficile, Danielle M. Maynard

Graduate Theses and Dissertations

The SpoIIE protein plays a crucial role in the sporulation process of Clostridioides difficile, a pathogen responsible for severe gastrointestinal diseases. Understanding the structural and functional aspects of SpoIIE is pivotal for deciphering its role in sporulation and exploring its potential as a therapeutic target. This study investigates the impact of varying concentrations of L-arabinose on the overexpression of SpoIIE in C. difficile, aiming to optimize protein yield and purity for subsequent crystallization and structural determination via X-ray crystallography. Using a recombinant expression system in Escherichia coli, different concentrations of L-arabinose were employed to induce SpoIIE overexpression. Protein purification was …

Exploring The Effects Of N,N-Dimethylbiguanide And Ω-3 Pufas On Muscle Stem Cell Differentiation, Enayah Alhshim

Graduate Theses and Dissertations

The impacts of omega-3 (ω-3) fatty acid and metformin hydrochloride (Met-HCl) on muscle stem cells differentiation, mimicking the fetal muscle development under gestational diabetes mellitus (GDM), were investigated. ω-3 fatty acids have been known for their ability to regulate adipogenic transcription factors such as Sterol Regulatory Element-Binding Protien (SREBPs) and Peroxisome Proliferator-Activated Receptors (PPARs). This regulation resulted in gene expression modification for lipid metabolism and adipocyte differentiation, thus preventing excessive fat accumulation. Additionally, emerging evidence suggested that ω-3 fatty acids may also exert direct effects on myogenic processes that influence muscle stem cells proliferation, differentiation, and maturation. Meanwhile, Met-HCl, an …

The Expression Of Recombinant Cas9 Proteins In E. Coli Bl21(De3) Strains, Morgan Reese

Graduate Theses and Dissertations

Abstract Extensively used for genome editing, CRISPR-Cas9 is a relatively new tool that has made a major impact in the genomic engineering landscape. Due to this, the production of CRISPR proteins that are not commercially available can limit research applications. Here, we present methods for optimizing laboratory scale production of CRISPR proteins including Cas9. The method uses IPTG to induce gene expression of the specified Cas9 and nickel column purification to isolate proteins. CRISPR proteins are validated for purity by SDS-PAGE gel, western blot, and for activity by in vitro digestion. We thoroughly validate and compare the effectiveness of BL21(DE3) …

Amyloid Fibrils Of Human Fgf-1 Induced By Different Detergents, Zeina Ismael Ibrahem Alraawi

Graduate Theses and Dissertations

Nature achieves molecular self-assembly through the ordered growth of nanoscale building blocks with high efficiency to fabricate macromolecular architectures. One example of self- assembly is peptides folding onto protein is one of the most astounding biological self-assembly processes. When proteins aggregate to form amyloid fibers, the secondary structure of the protein converts from its native state to a cross-beta-sheet. Fibroblast growth factors (FGFs) possess an essential role in neuronal survival during development. In addition, they are involved in neural stem cell (NSC) proliferation. Fibroblast growth factors (FGFs) are well known to be synthesized in the central nervous system (CNS) and …

Characterization Of Human Fibroblast Growth Factor 2 Variant To Determine Effects On Structure, Stability, And Cell Proliferation, Ryan Layes

Graduate Theses and Dissertations

Fibroblast growth factors (FGFs) are a family of cell signaling proteins conserved across multiple species. Each individual FGF elicits different cellular functions including, but not limited to, proliferation, migration, differentiation, angiogenesis, and wound healing. One of the most studied members, fibroblast growth factor 2 (FGF2), has demonstrated substantial wound healing capacity in a wide range of tissues including skeletal, muscular, neural, respiratory, epithelial, and cardiovascular. This ability makes FGF2 a potential therapeutic for a wide range of conditions and injuries. However, due to a short half-life at room temperature, therapeutic use of FGF2 is limited. It has been demonstrated that …

Phenotypic And Transcriptomic Characterization Of Rice Snrk1 Mutants Developed By Crispr/Cas9 Mutagenesis, Maria Clara Faria Chaves

Graduate Theses and Dissertations

SnRK1 is a heterotrimeric protein kinase that is composed of a catalytic subunit (α) and two regulatory subunits (β and βγ), and it has a main role in regulating energy homeostasis in the plant by modulating anabolic and catabolic process. SnRK1 phosphorylates and alters the activities of enzymes involved in metabolism and regulates gene expression by altering the activity of chromatin-remodeling enzymes or the transcription factors. Rice contains three functional paralogs of SnRK1α: SnRK1αa (LOC_Os03g17980), SnRK1αb (LOC_Os08g37800), and SnRK1αc (LOC_Os05g45420). This study focused on the function of these SnRK1 paralogs by evaluating the phenotypic and transcriptomic characteristics and the disease …

Molecular Characterization Of Compartment Boundary Formation During Epithelial Remodeling In Drosophila Melanogaster, Samia Parveen

Graduate Theses and Dissertations

The ability of epithelial cells to self-organize is crucial for the development of proper tissue structures and organs in multi-cellular organisms. Epithelia consist of inter-connected cells that form flat sheets, and specific groups of cells within these sheets are partitioned into distinct compartments via compartment boundaries (CBs). These CBs are specialized interfaces between cells characterized by stable, high-tension actomyosin cables, which act as fences to prevent movements between adjacent compartments during tissue reorganization. In the early Drosophila embryo, CBs are established in response to the asymmetrical localization of two cell-surface proteins the Leucine-Rich Repeat (LRR) protein Tartan and the Teneurin …

Investigating And Characterizing Septin Cellular Regulators During Infection Related Development In M. Oryzae, Rinalda Proko

Graduate Theses and Dissertations

The fungus Magnaporthe oryzae causes a devastating disease of rice and wheat, called blast, which poses a major threat to food security across the planet. To enter plant tissue, M. oryzae produces a remarkable pressure-generating infection cell called an appressorium, which mechanically ruptures the tough cuticle of host leaves through the application of enormous physical force directed onto a narrow penetration structure emerging from its base. Importantly, appressorium form and functionality depends on the regulated assembly of a toroidal ring-like structure, composed of septins, which forms within its base. Septins are a family of membrane-associated GTP-binding proteins that polymerize into …

Unraveling The Biogenesis And Roles Of Iron-Sulfur Proteins During Nitrogen Fixation By Methanosarcina Acetivorans, Jasleen Saini

Graduate Theses and Dissertations

Iron-sulfur (Fe-S) clusters, the ancient cofactors found in proteins across all life forms, play vital roles in numerous cellular processes. Fe-S clusters exhibit structural diversity, ranging from simple to complex forms. Methanogens are anaerobic archaea that produce methane as a metabolic by-product through methanogenesis, a process dependent on numerous Fe-S proteins. Notably, methanogens are capable of fixing nitrogen (diazotrophy) facilitated by the enzyme complex called nitrogenase, which contains both simple and complex Fe-S clusters. While methanogens possess the largest number of Fe-S proteins, the factors involved in Fe-S cluster biogenesis remain largely unknown. Bacteria possess three distinct and well-characterized Fe-S …

The Roles Of Estrogen Receptor Alpha-Interacting Rnas And Exosomes In Breast Cancer, And E-Cadherin In Carcinomas, Brihget Catalina Sicairos-Meza

Graduate Theses and Dissertations

Carcinomas are malignancies of epithelial cells and account for >80% of cancer-related deaths. Approximately 75% of breast cancers express estrogen receptor alpha (ERα). ERα promotes breast cancer progression by enhancing cancer cell proliferation. Tamoxifen is commonly used to treat ERα-positive breast cancers but can result in endocrine therapy resistance. The mechanisms underlying endocrine therapy resistance remain elusive. The Du lab recently found that ERα is an RNA-binding protein. However, the significance of the ERα-RNA interaction is unknown. We fractionated ERα-positive MCF7 cells into cytoplasmic and nuclear fractions, followed by immunoprecipitation of ERα with associated RNAs and RNA-sequencing. We identified many …

Cell Division Dynamics Of Escherichia Coli In Extreme Environments, Steven P. Murray

Graduate Theses and Dissertations

Life is remarkable in how resilient it can be. Many organism, classified as ex- tremophiles, can not only survive in extreme environments, but they can thrive in them. In the search for extraterrestrial life, the best candidates to harbor life exist with some kind of extreme condition. Europa, for example, is a favorite for the possibility of accommodating life as we know it within our solar system. Thought there is believed to be a liquid ocean under its icy surface, this habitat would be under immense pressures and high salinity. To best know where to look for extraterrestrial life, it …

The Antimicrobial Resistance Plasmid Mobilome Of Salmonella Enterica And Related Enteric Species And Factors That Influence The Transfer Efficiency., Suad Algarni

Graduate Theses and Dissertations

The dynamic distribution of antimicrobial resistance genes in Salmonella enterica is considered a public health risk. S. enterica is one of the most important etiological agents of foodborne illness and has a critical impact on global human health. In S. enterica and related species, mobile genetic elements (MGEs) serve as primary vehicles for the dissemination of antibiotic resistance genes in the bacterial evolution. This dissemination can be impacted by different selective pressures that leads to diverse antibiotic response phenotypes. This project focusses on the dynamics of antimicrobial resistance genes, particularly exploring the transfer efficiency of multidrug resistance plasmids in S. …

Using Molecular Dynamics Simulations To Decipher Mechanistic Details Of Biomolecular Processes Of Biology And Biotechnology Oriented Applications, Adithya Polasa

Graduate Theses and Dissertations

Researchers in chemistry and biology often utilize computer simulations, in conjunction with experimental data, to model and predict the structures, energies, kinetics, processes, and functions of the systems that are their focus of study, ranging from single molecules to whole viruses. Here, we use molecular dynamics (MD) techniques to gain a deeper understanding of biomolecular processes in biology and biotechnology-oriented applications. Using a mixture of equilibrium and non-equilibrium MD simulations, this work describes the insertion process of YidC at the atomic level. In order to better comprehend the insertion process, several docking models of YidC-Pf3 in the lipid bilayer were …

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 …

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 …

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 …