Biochemistry, Biophysics, and Structural Biology Commons^™

Growth Hormone Alters Components Related To Differentiation, Metabolism And Milk Synthesis And Secretion In Mac-T Cells, Tasha Lynn Johnson

Master's Theses

The mammary alveolar cell-T (MAC-T) cell line is able to uniformly differentiate and secrete casein proteins in response to dexamethasone, insulin and prolactin and is extensively used to study bovine mammary epithelial cell function. Growth hormone (GH) has been shown to increase milk protein synthesis both in vivo and in mammary cell models, and induce cytoskeletal rearrangement in 3T3 fibroblast cell line and a Chinese hamster ovary (CHO) cell line. Few studies have focused on identifying the mechanisms involved in differentiated MAC-T cells’ response to GH. We tested the hypothesis that MAC-T cells would respond directly to GH and that …

Ricin B Chain-Insulin Fusion Protein Immunomodulation Of Type 1 Diabetes, James Edward Carter Iii

Loma Linda University Electronic Theses, Dissertations & Projects

Type 1 diabetes mellitus (T1D) is a debilitating chronic inflammatory disease of the insulin-producing pancreatic islet β-cells that results from a combination of genetic and environmental factors. Attempts to suppress Th1-mediated autoimmune diseases such as T1D by mucosal delivery of autoantigens for immunotolerization have yielded only partial success. Attainment of satisfactory levels of sustained immunological tolerance remains to be accomplished. To restore self-tolerance requires delivery of sufficient amounts of autoantigen to stimulate regulatory T helper cells that function to survey the gut and induce tolerance to consumed antigens such as food. Oral delivery of autoantigens has previously been shown to …

Poisonous Rangeland Plants In San Luis Obispo County, Sara Litten, Amanda Ou

Animal Science

Poisonous Rangeland Plants in San Luis Obispo County is a comprehensive educational guide to rangeland plants that are toxic to domestic livestock. This guide begins with an exploration of how the biological systems are affected by the poisonous plant toxins. The biochemistry behind these toxins is included in the discussion. Next, reference material for fourteen plants that inhabit San Luis Obispo County is provided. This information includes specific toxins found in poisonous plants, affected animals, symptoms of poisoning, stages of growth, lethal dose, and distribution of the plant in California. This section of the guide is filled with helpful photos …

Mimosa: A System For Minimotif Annotation, Jay Vyas, Ronald J. Nowling, Thomas Meusburger, David P. Sargeant, Krishna Kadaveru, Michael R. Gryk, Vamsi Kundeti, Sanguthevar Rajasekaran, Martin Schiller

Life Sciences Faculty Research

BACKGROUND:

Minimotifs are short peptide sequences within one protein, which are recognized by other proteins or molecules. While there are now several minimotif databases, they are incomplete. There are reports of many minimotifs in the primary literature, which have yet to be annotated, while entirely novel minimotifs continue to be published on a weekly basis. Our recently proposed function and sequence syntax for minimotifs enables us to build a general tool that will facilitate structured annotation and management of minimotif data from the biomedical literature.

RESULTS:

We have built the MimoSA application for minimotif annotation. The application supports management of …

Intrinsic Contact Geometry Of Protein Dynamics, Yosi Shibberu, Allen Holder, David Cooper

Mathematical Sciences Technical Reports (MSTR)

We introduce a new measure for comparing protein structures that is especially applicable to analysis of molecular dynamics simulation results. The new measure generalizes the widely used root-mean-squared-deviation (RMSD) measure from three dimensional to n-dimensional Euclidean space, where n equals the number of atoms in the protein molecule. The new measure shows that despite significant fluctuations in the three dimensional geometry of the estrogen receptor protein, the protein's intrinsic contact geometry is remarkably stable over nanosecond time scales. The new measure also identifies significant structural changes missed by RMSD for a residue that plays a key biological role in …

Determination Of The Myogenic Potential Of Human Embryonic Stem Cell-Derived Mesenchymal Stem Cells, Rory Coleman

Honors Scholar Theses

Human embryonic stem cells (hESCs) have the potential to

differentiate to all adult somatic cells. This property makes hESCs a very promising area of research for the treatment of disorders in which specific cell populations need to be restored. Despite this potential, research that focuses on producing mesodermally derived cell populations from hESCs is decidedly limited, notwithstanding the prevalence of disorders involving mesodermal tissues for which treatment options are limited. Skeletal muscle myoblasts are derivatives of mesodermal cells and are characterized by the expression of the MyoD gene. These cells are difficult to obtain from hESCs in a reproducible and …

Characterization Of The Putative Xyloglucan Glycosyltransferase Gt14 In Arabidopsis Thaliana, Najam R. Syed

Honors Scholar Theses

Plant cell walls largely consist of matrix polysaccharides that are linked to cellulose microfibrils. Xyloglucan, the primary hemicellulose of the cell wall matrix, consists of a repeating glucose tetramer structure with xylose residues attached to the first three units ('XXXG'). In Arabidopsis thaliana, the core XXXG structure is further modified by enzymatic addition of galactose and fucose residues to the xylose side chains to produce XLXG, XXLG, XLLG and XLFG structures. GT14 is a putative glycosyltransferase in the GT47 gene family. Initial predictions of GT14's hydrophobic regions, based on its translated amino acid sequence, are almost identical to its Arabidopsis …

Alkylphenol Contamination In Homarus Americanus, Jennifer Renee Urban

Honors Scholar Theses

Alkylphenols are pollutants that are present in marine sediments and fishes. In earlier work it has been discovered that alkylphenols are present in the Homarus americanus, or the American lobster. Research suggests that alkylphenols could behave as endocrine disruptors as they have been found to affect juvenile hormone activity. It has been hypothesized that lobsters may be able to rid themselves of alkylphenol contamination through secreting these compounds into the environment or sequestering them in their tissues. In this study, I address the question of how lobsters may rid themselves of alkylphenols by analyzing hemolymph, muscle, gill, and shell samples …

Dopaminergic Innervation Of The Subventricular Zone In The Murine Brain, Linda Beth Drozdowicz

Honors Scholar Theses

The subventricular zone (SVZ) is one of two areas in the brain that, in a healthy mouse, continually generate neurons throughout adulthood. While it was previously thought that only the A9 neurons of the substantia nigra sent dopaminergic afferents to the SVZ, recent studies suggest that the A10 neurons of the ventral tegmental area may innervate this area. This project has aimed to discover which, if either, model is correct.

Examination of the Aphakia (AK) mouse was used to determine the role of distinct midbrain regions in SVZ regulation. Additionally, intraperitoneal injections of the chemical MPTP were used to deduce …

A Computational Biology Approach To The Analysis Of Complex Physiology: Coagulation, Fibrinolysis, And Wound Healing, Nathan Menke

Theses and Dissertations

The birth of complexity research derives from the logical progression of advancement in the scientific field afforded by reductionist theory. We present in silico models of two complex physiological processes, wound healing and coagulation/fibrinolysis based on two common tools in the study of complex physiology: ordinary differential equations (ODE) and Agent Based Modeling (ABM). The strengths of these two approaches are well-suited in the analysis of clinical paradigms such as wound healing and coagulation. The complex interactions that characterize acute wound healing have stymied the development of effective therapeutic modalities. The use of computational models holds the promise to improve …

A Novel Role Of Sirt1 In Sildenafil Induced Cardioprotection In Mice, Mona Shalwala

Theses and Dissertations

Phosphodiesterase-5 inhibitor, sildenafil (SIL) protects against myocardial ischemia/reperfusion (I-R) injury. We hypothesized that SIL-induced protection may be mediated through activation of SIRT1, an enzyme which deacetylates proteins involved in cellular stress response. Adult male ICR mice were treated with SIL (0.7mg/kg ip), Resveratrol (RSV) (5mg/kg ip) (positive control), or saline (0.2 ml ip). The hearts were harvested 24 h later and homogenized for SIRT1 activity analysis. Both SIL and RSV increased cardiac SIRT1 activity (P<0.001) as compared to Saline. Adult mouse ventricular cardiomyocytes pre-treated with either SIL or RSV (1µM) in vitro also upregulated SIRT1 activity (P<0.05). SIL also reduced infarct size following 30 min. ischemia and 24 h reperfusion in vivo. Sirtinol (5mg/kg in 10% DMSO, ip), a SIRT1 inhibitor abolished the infarct-limiting effect of SIL and RSV (P<0.001). In conclusion, activation of SIRT1 by SIL plays an essential role in cardioprotection against I-R injury.

Overexpression And Partial Purification Of Recombinant Human Serine Hydroxymethyltransferase: A Potential Anticancer Target, Suprit Singh Deol

Chemistry and Biochemistry

Serine Hydroxymethyltransferase (SHMT) is a member of the thymidylate synthase cycle that provides pyrimidine nucleotides to actively dividing cells, including cancer cells. The other two enzymes involved in this cycle have been targets for clinical anticancer drugs, suggesting that inhibitors of SHMT may also be used as clinical anticancer drugs. In order to test potential inhibitors against SHMT, human SHMT has been overexpressed in E. coli and partially purified by selective ammonium sulfate fractionation followed by anion-exchange fast protein liquid chromatography. A coupled assay using L-allo-threonine and alcohol dehydrogenase was used to identify active fractions, which were analyzed …

Terminal Deoxynucleotidyl Transferase: The Story Of A Misguided Dna Polymerase, Edward A. Motea, Anthony J. Berdis

Chemistry Faculty Publications

Nearly every DNA polymerase characterized to date exclusively catalyzes the incorporation of mononucleotides into a growing primer using a DNA or RNA template as a guide to direct each incorporation event. There is, however, one unique DNA polymerase designated terminal deoxynucleotidyl transferase that performs DNA synthesis using only single-stranded DNA as the nucleic acid substrate. In this chapter, we review the biological role of this enigmatic DNA polymerase and the biochemical mechanism for its ability to perform DNA synthesis in the absence of a templating strand. We compare and contrast the molecular events for template-independent DNA synthesis catalyzed by terminal …

Non-Natural Nucleotides As Probes For The Mechanism And Fidelity Of Dna Polymerases, Irene Lee, Anthony J. Berdis

Chemistry Faculty Publications

DNA is a remarkable macromolecule that functions primarily as the carrier of the genetic information of organisms ranging from viruses to bacteria to eukaryotes. The ability of DNA polymerases to efficiently and accurately replicate genetic material represents one of the most fundamental yet complex biological processes found in nature. The central dogma of DNA polymerization is that the efficiency and fidelity of this biological process is dependent upon proper hydrogen-bonding interactions between an incoming nucleotide and its templating partner. However, the foundation of this dogma has been recently challenged by the demonstration that DNA polymerases can effectively and, in some …

Conformational Motion Associated With Catalysis In Indole-3-Glycerol Phosphate Synthase From S. Solfataricus, Tomasz Kurcon

Theses, Dissertations and Culminating Projects

Indole-3-glycerol phosphate synthase from Sulfolobus solfataricus (SsIGPS) belongs to a broad family of (βα)₈-barrel enzymes. It catalyzes the fifth step in tryptophan biosynthesis, converting l-(o-carboxylphenylamino)-l-deoxyribulose-5-phosphate (CdRP) to indole-3-glycerol phosphate (IGP). Site selective mutagenesis was used to introduce a single cysteine in two loops near the active site, generating two recombinant proteins, each containing a single cysteine handle. The two construct were labeled, each with two different thiol-reactive probes generating four labeled constructs that were used for this study. Steady-state kinetic parameters of the labeled mutants and the wild type SsIGPS were well characterized using fluorescence spectroscopy. Subsequent experiments …

A Novel Filarial Parasite (B. Malayi) Stress-Activated Protein Kinase As A Potential Drug Target, Akruti Patel

Theses, Dissertations and Culminating Projects

Lymphatic filariasis (or elephantiasis) is a major neglected disease with an estimated 120 million individuals infected and approximately 1.5 billion at risk in endemic regions. It is a highly disfiguring and debilitating disease and one of the major causes of global morbidity. Treatment options for this disease are few and new drug targets and therapies need to be identified. We have identified a protein kinase ortholog of human p38 mitogen-activated protein kinase (p38) expressed in the filarial parasite, Brugia malayi (B. malayi), one of three causative agent of lymphatic filariasis. We hypothesize that this protein kinase, BmMPKl, is important for …

Investigation Of Near-Infrared Fluorescence And Photobleaching Of Human Volar Side Fingertips In Vivo: Antioxidants And Melanin, Colin Wright

Renée Crown University Honors Thesis Projects - All

Noninvasive in vivo blood glucose determination in the skin of volar side of human fingertips by near-infrared (NIR) Raman spectroscopy relies on fluorescence to quantify blood volume. Fluorescence does not only come from blood, which is composed of plasma and red blood cells; in fact, most fluorescence produced by human fingertips originates in the static tissues, e.g. skin, interstitial fluid, etc.. It will soon be possible to quantify the precise contributions of red blood cells, plasma, and static tissue to the overall fluorescence emission. Observations reveal a systematic decay in fluorescence, which, if not caused by blood movement, challenges our …

The Role Of Cuticular Hydrocarbons In The Pre-Mating Isolation Of Two Pissodes Species, Stephanie L. Teale

Renée Crown University Honors Thesis Projects - All

Pissodes strobi and P. nemorensis are weevils (Coleoptera, Curculionidae) that infest pines (Pinus spp.) and spruces (Picea spp.). Previous studies indicate that they are able to hybridize. In the spring, breeding site specificity maintains reproductive isolation, but in the late summer, both species occupy lateral branches of host trees. Aggregation pheromones for P. nemorensis have been identified but the mechanism for late summer isolation is unknown. Cuticular hydrocarbons have been shown to play a role in the chemical recognition of species, sex, kin, and caste in many groups of insects. The large number of possible compounds and the …

Mtor In Cell Signaling And Size Enlargement As A Target For The Chemico-Physical Therapy Of Cancer, Gabriela Krawiec

Renée Crown University Honors Thesis Projects - All

mTOR is a kinase protein meaning it phosphorylates target proteins affecting their cell signaling properties¹. The drug Rapamycin, analogs of Rapamycin, and cell signaling proteins that interact with mTOR control the activities mediated by mTOR¹. mTOR is located in the cytoplasm at a convergent point of many signaling pathways that regulate a multiplicity of cellular processes including metabolism that precede cell enlargement (cell “growth”), cell proliferation (cell division), and angiogenesis^1,2. Cells with mTOR inappropriately activated can proceed with cell enlargement and cell proliferation in the absence of normal cell signaling². Rapamycin and …

The Effect Of Exogenous Estrogens On Primordial Follicle Assembly In Vivo, Jenna Rose Karavan

Renée Crown University Honors Thesis Projects - All

During embryogenesis in the mouse, primordial germ cells develop, move to the genital ridge of the embryo, and form germline cysts as the ovary develops. The cells in these cysts are linked by intercellular bridges. The cysts then undergo a breakdown process which ultimately results in primordial follicles, each of which consists of a single oocyte surrounded by somatic cells called granulosa cells. During this cyst breakdown process, approximately one-third of the original oocytes become enclosed in primordial follicles, the amount of which is representative of the number of eggs a female will have available to her during her reproductive …

Dna Polymerases: Perfect Enzymes For An Imperfect World, Anthony J. Berdis

Chemistry Faculty Publications

This Special Thematic Issue explores the molecular properties of DNA polymerases as extraordinary biological catalysts. In this short introductory chapter, I briefly highlight some of the most important concepts from the articles contained within this Special Issue. The contents of this Special Issue are arranged into distinct sub-categories corresponding to mechanistic studies of faithful DNA polymerization, studies of "specialized" DNA polymerases that function on damaged DNA, and DNA polymerases that are of therapeutic importance against various diseases. Emphasis is placed on understanding the dynamic cellular roles and biochemical functions of DNA polymerases, and how their structure and mechanism impact their …

Host Signaling Response To Adhesion Of Bifidobacterium Infantis, Reed N. Gann

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Investigations of the molecular binding partners of the probiotic bacterium Bifidobacterium longum subspecies infantis (B. infantis) and the pathogen Salmonella enterica subspecies enterica serovar Typhimurium LT2 (Salmonella ser. Typhimurium) found that these two very different bacteria bind gangliosides. However, these organisms lead to completely different host health outcomes when present in the gut. B. infantis is the founding microbial population in the intestinal tract of breast-fed infants. S. typhimurium is the most important food-borne pathogen that results in humans. This study used an in vitro gut epithelial cell model to examine the host cellular response to adhesion …

Role Of Secondary Interactions (Π, Agostic) As Well As Solvent Influence On Alkali Metal Complexes, Elizabeth D. Nagle

Renée Crown University Honors Thesis Projects - All

We here attempt to synthesize heterobimetallic alkali metal complexes with bulky phenolate ligands via solid state direct metallation. The solid state route may offer a facile method of producing these heterobimetallic species. Synthesis of heterobimetallic alkali metal compounds remains a challenge, as the homometallic complexes are generally favored over formation of the heterobimetallic species. Previous work has shown that the alkali metals have a strong solvent dependency; the recrystallization of heterobimetallic products from toluene yields the heterobimetallic, while recrystallization from THF yields the homometallic. However, the ability for phenolate ligands to stabilize metal centers through secondary interactions, such as M∙∙∙π …

Understanding The Genetic And Molecular Mechanisms Of The Shl3 Phenotype In Arabidopsis Thaliana, Sukeerti Kesar

Renée Crown University Honors Thesis Projects - All

The study of plant genetics and the molecular mechanisms regulating plant-pathogen interactions is an intensely studied area of research in molecular genetics. Gaining an understanding of the defense mechanisms of plants has proven highly useful in the construction of transgenic plants for increased crop yield. The focus of my research was on the defense mechanisms of Arabidopsis thaliana, a plant in the mustard family. Several features of Arabidopsis make it an excellent model plant for molecular genetic studies. A few of these include a short life cycle (approximately 8 weeks), a completely sequenced genome, high fecundity, and the availability …

The Role Of A2b Adenosine Receptor Signaling In Adenosine Dependent Lung Disease, Yang Zhou

Dissertations and Theses (Open Access)

Chronic lung diseases and acute lung injuries are two distinctive pulmonary disorders that result in significant morbidity and mortality. Adenosine is a signaling nucleoside generated in response to injury and can serve both protective and destructive functions in tissues and cells through interaction with four G-protein coupled adenosine receptors: A1R, A2AR, A2BR, and A3R. However, the relationship between these factors is poorly understood. Recent findings suggest the A2BR has been implicated in the regulation of both chronic lung disease and acute lung injury. The work presented in this dissertation utilized the adenosine deaminase-deficient mouse model and the bleomycin-induced pulmonary injury …

Carboxylases Involved In Microbial Acetone And Acetophenone Metabolism, Ameya Mashruwala

All Graduate Plan B and other Reports, Spring 1920 to Spring 2023

A number of bacteria are capable of growth with acetone and acetophenone as their sole sources of carbon and/or energy. The pathways and enzymes involved in the transformation of these molecules into useable carbon and energy are unique. Among these are two novel enzymes, acetone carboxylase and acetophenone carboxylase, which represent a fundamentally novel classes of carboxylases.

The initial step in acetone metabolism, in X. autotrophicus st Py2, R. capsulatus st B10 and R. rhodochrous, is the thermodynamically unfavorable reaction to yield acetoacetate. This step is catalyzed by the enzyme acetone carboxylase and is coupled with the unprecedented, concomitant hydrolysis …

Glycopeptidome Of A Heavily N-Glycosylated Cell Surface Glycoprotein Of Dictyostelium Implicated In Cell Adhesion, Christa L. Feasley, Jennifer M. Johnson, Christopher M. West, Catherine P. Chia

School of Biological Sciences: Faculty Publications

Genetic analysis has implicated the cell surface glycoprotein gp130 in cell interactions of the social amoeba Dictyostelium, and information about the utilization of the 18 N-glycosylation sequons present in gp130 is needed to identify critical molecular determinants of its activity. Various glycomics strategies, including mass spectrometry of native and derivatized glycans, monosaccharide analysis, exoglycosidase digestion, and antibody binding, were applied to characterize a nonanchored version secreted from Dictyostelium. s-gp130 is modified by a predominant Man8GlcNAc4 species containing bisecting and intersecting GlcNAc residues and additional high-mannose N-glycans substituted with sulfate, methyl-phosphate, and/or core R3-fucose. Site mapping confirmed the occupancy …

The Development Of A Comprehensive Mechanism For Intracellular Calcium Oscillations: A Theoretical Approach And An Experimental Validation, Amanda A. Borges, Deanna Salter, Sandor Kadar, Steven B. Symington

Pell Scholars and Senior Theses

Calcium is an important second messenger for cellular communication. Theoretical models help scientists understand its signalling mechanism. A comprehensive model was developed in order to minimize any limitations in the models currently presented in the literature. Experimental results support the model and therefore the theoretical model provides a plausible explanation of the dynamics of the calcium-signaling mechanism. In the future, additional verification will be performed using various experimental configurations on PC12 cells. Further, the model will be used to predict the response of cells to environmental factors such as pesticides and heavy metals.

Bacillus Cereus And Bacillus Anthracis Germination Kinetics: A Michaelis-Menten Approach, Helen Luu

UNLV Theses, Dissertations, Professional Papers, and Capstones

Bacillus species are rod-shaped, gram-positive bacteria that are capable of producing endospores. In this dormant stage, the endospores can persist in hostile physical and chemical environments. Once conditions become favorable, the spores germinate into actively dividing cells, vegetative cells. Germination is a crucial step for the pathogenicity of the Bacilli in affecting a host organism.

Our study applies mathematical approaches to spore germination to determine whether the binding of one germinant will affect the binding of another germinant. We pursued this approach with two different species, B. cereus and B. anthracis, both pathogenic organisms. B. cereus is a widely known …

Xenoestrogen-Specific Mechanisms Of Developmental Reprogramming Correlate With Gene Expression And Tumor Development, Kristen L. Greathouse

Dissertations and Theses (Open Access)

Environmental exposures during sensitive windows of development can reprogram normal physiological responses and alter disease susceptibility later in life in a process known as developmental reprogramming. We have shown that neonatal exposure to the xenoestrogen diethylstilbestrol (DES) can developmentally reprogram the reproductive tract in genetically susceptible Eker rats giving rise to complete penetrance of uterine leiomyoma. Based on this, we hypothesized that xenoestrogens, including genistein (GEN) and bisphenol A (BPA), reprogram estrogen-responsive gene expression in the myometrium and promote the development of uterine leiomyoma. We proposed the mechanism that is responsible for the developmental reprogramming of gene expression was through …