Biochemistry, Biophysics, and Structural Biology Commons^™

Mechanisms Of Connexin-46 And -50 Intercellular Channel Function And Stability By Molecular Dynamics Simulations, Bassam George Haddad

Dissertations and Theses

Gap junctions make up a class of intercellular channels that characteristically connect the cytoplasm of directly apposed cells through large assemblies, or plaques, constituted by a multitude of intercellular channels. Gap junction mediated intercellular communication is critical for a variety of physiological functions, from coordinating electrical impulses in the heart and brain to maintaining homeostasis in most tissues. There are 21 isoforms of connexins, the constituent subunit of the gap junction, expressed in a tissue dependent manner. Gap junctions formed from different isoforms exhibit distinct biophysical properties, such as gating kinetics and sensitivity, as well as unique permeability and selectivity …

Automated Parsing Of Flexible Molecular Systems Using Principal Component Analysis And K-Means Clustering Techniques, Matthew J. Nwerem

Computational and Data Sciences (MS) Theses

Computational investigation of molecular structures and reactions of biological and pharmaceutical interests remains a grand scientific challenge due to the size and conformational flexibility of these systems. The work requires parsing and analyzing thousands of conformations in each molecular state for meaningful chemical information and subjecting the ensemble to costly quantum chemical calculations. The current status quo typically involves a manual process where the investigator must look at each conformation, separating each into structural families. This process is time-intensive and tedious, making this process infeasible in some cases, and limiting the ability of theoreticians to study these systems. However, the …

The Role Of The Msaabcr Operon In Cell Wall Integrity And Programmed Cell Death During Biofilm Development, Bibek G C

Dissertations

Staphylococcus aureus is an important human pathogen in both community and health care settings. Biggest challenges with S. aureus as a pathogen is its ability to acquire antibiotic resistance and produce robust biofilms. In this work, we investigated the nature of the cell wall defect in the msaABCR operon mutant in the Mu50 (VISA) and USA300 LAC methicillin-resistant Staphylococcus aureus (MRSA) strains. Results showed that msaABCR-mutant cells had decreased cell wall thickness and cell wall crosslinking in both strains. These defects are most likely due to increased murein hydrolase activity and/or nonspecific processing of murein hydrolases mediated by increased …

Investigations In The Cellular And Molecular Biology Of Human Airway Mucociliary Tissue, Vincent Manna

Graduate School of Biomedical Sciences Theses and Dissertations

Our laboratory has integrated the use of a human-derived, in vitro model of airway mucociliary tissue. We isolate human nasal epithelial cells (HNECs) from the nasal mucociliary tissue of donors with a small brush and expand the airway progenitor cells in culture. The HNECs are then seeded onto semi-permeable transwell inserts. The inserts are in contact with the media in the lower chamber but don’t contain media in the upper chamber therefore the cells are exposed to the air while drawing nutrients from the media below, this is called the Air-Liquid Interface (ALI). HNECs cultured at the ALI initiate a …

Effects Of Trans-Acting Factors On The Translational Machinery In Yeast, Brandon M. Trainor

Graduate School of Biomedical Sciences Theses and Dissertations

Synthesis of proteins, or translation, is a complex biological process requiring the coordinated effort of numerous protein and RNA factors. Central to translation is the ribosome, a complex macromolecular complex consisting of both ribosomal RNA (rRNA) and ribosomal protein (r-protein). Ribosomes are essential and are one of the oldest and most abundant biomolecules across all forms of life. In addition to the ribosome, translation requires messenger RNA (mRNA), transfer-RNA conjugated to an amino acid (aa-tRNA), translation factors, and energy in the form of ATP and GTP. Translation universally occurs in four major stages, initiation, elongation, termination, and recycling, with initiation …

College Of Natural Sciences Newsletter, August 2021, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 2, Issue 8.

Page 1 Dean's Message
Page 2 Awards and Recognition
Page 3 Student Summer Research
Page 4 Media Coverage of CNS
Page 5 Wintrode Student Success Center
Page 6-7 Welcome to our new Faculty & Staff!
Page 8 One Day for State: Thursday, Sept. 2nd
Page 7 Open PRAIRIE Data; Fall Faculty Retreat 2021

Modification Of Cell Wall Polysaccharide Guides Cell Division In Streptococcus Mutans., Svetlana Zamakhaeva, Catherine T Chaton, Jeffrey S. Rush, Sowmya Ajay Castro, Cameron W Kenner, Alexander E Yarawsky, Andrew B Herr, Nina M Van Sorge, Helge C Dorfmueller, Gregory I Frolenkov, Konstantin V Korotkov, Natalia Korotkova

Molecular and Cellular Biochemistry Faculty Publications

In ovoid-shaped, Gram-positive bacteria, MapZ guides FtsZ-ring positioning at cell equators. The cell wall of the ovococcus Streptococcus mutans contains peptidoglycan decorated with serotype c carbohydrates (SCCs). In the present study, we identify the major cell separation autolysin AtlA as an SCC-binding protein. AtlA binding to SCC is attenuated by the glycerol phosphate (GroP) modification. Using fluorescently labeled AtlA constructs, we mapped SCC distribution on the streptococcal surface, revealing enrichment of GroP-deficient immature SCCs at the cell poles and equators. The immature SCCs co-localize with MapZ at the equatorial rings throughout the cell cycle. In GroP-deficient mutants, AtlA is mislocalized, …

Modulation Of Glucose Homeostasis By Nucleotide P2y2 Receptor And Biological Sex, Hailee Anne Marino

Graduate Theses/Dissertations

Recent insights into the pathological role of Nucleotide P2Y₂ receptor suggest P2Y₂R involvement in high fat diet-induced obesity and potentiates insulin resistance. However, these recent insights do not demonstrate how P2Y₂R modulates glucose homeostasis under physiological conditions. Further, it remains unknown how sex biological factors influence P2Y₂R receptor signaling in the regulation of glucose homeostasis. The research objective for the present study is to elucidate the novel roles of P2Y₂ in fasting blood glucose and glucose tolerance (basal insulin sensitivity) under resting conditions in males and females. We expected that under physiological …

Nucleotide P2y₂ Receptor-Dependent Leukocyte-Endothelial Interaction, Spencer E. Thomas

Graduate Theses/Dissertations

Extracellular nucleotides (ATP, UTP) released from cells act on nucleotide receptors to promote vascular inflammation. Increased leukocyte-endothelial interaction is a hallmark of vascular inflammation. The nucleotide P2Y₂ receptor (P2Y₂R), activated by extracellular ATP≈UTP, plays a role in cardiovascular homeostasis and immune regulation. Moreover, accumulating evidence from studies in vitro and in vivo models have implicated the P2Y₂R in the inflammatory response significantly contributing to the progression and pathogenesis of asthma, atherosclerosis, sepsis, and ischemia. I hypothesized that P2Y₂R activation by UTP, an agonist of the receptor, increased leukocyte rolling and adhesion in the microvasculature from baseline. To test the hypothesis, …

Neuronal Migration In Developmental Hyperserotonmia: Assessment Of Vesicular Glutamate In The Raphe Nuclei, Trey M. Shupp

Graduate Theses/Dissertations

The neurotransmitter serotonin is involved in the early development of the central nervous system and the organization of neurons throughout the cerebral cortex and cerebellum. It is proposed that serotonin indirectly interacts with cells in the marginal zone of the cerebral cortex known as Cajal-Retizus (CR) cells. These cells secrete the extracellular matrix protein reelin, which is known for its role in neuronal organization and migration during early neural development. It has been observed that low levels of serotonin are associated with similarly low levels of reelin during development and have been reported to result in disorganization of neurons in …

Cyclic Sulfones From Double Conjugate Addition Of Rongalite, Hao Zong

Theses, Dissertations and Culminating Projects

We report a cyclic sulfone synthesis method from the addition of sodium hydroxymethanesulfinate to doubly electrophilic dienone substrates. The novel synthesis of the cyclic sulfone thus avoided the using the toxic and odorous sulfides, and also oxidizing reagents. We prepared both the symmetrical and unsymmetrical substrates, and then used the substrate for the synthesis of cyclic sulfone.

Molecular Simulation Of Rna Conformational Dynamics : An Example Of Micro-Rna Targeting Messenger Rna : Mir-34a-Msirt1, Parisa Ebrahimi

Legacy Theses & Dissertations (2009 - 2024)

MicroRNA (miRNA), as a distinct class of biological regulators and a ”guide” member of non-coding RNA-protein complexes (RNPs), regulates more than 60% of protein-coding genes expression through base-pairing with targeted messenger RNA (mRNA) in the RNA-Induced Silencing Complex (RISC). Most of miRNAs identified in human, are conserved in other animals, which have preferentially conserved interaction sites particularly in 3’ untranslated regions (3’UTRs) of many human messenger mRNAs.The capability of a single miRNA to target more than hundreds of mRNAs, suggests that miRNAs influence essentially all developmental process and diseases, which also makes them interesting candidates as therapeutics agents. The primary …

Molecular Simulation Of Rna Conformational Dynamics : An Example Of Micro-Rna Targeting Messenger Rna : Mir-34a-Msirt1, Parisa Ebrahimi

Legacy Theses & Dissertations (2009 - 2024)

MicroRNA (miRNA), as a distinct class of biological regulators and a ”guide” member of non-coding RNA-protein complexes (RNPs), regulates more than 60% of protein-coding genes expression through base-pairing with targeted messenger RNA (mRNA) in the RNA-Induced Silencing Complex (RISC). Most of miRNAs identified in human, are conserved in other animals, which have preferentially conserved interaction sites particularly in 3’ untranslated regions (3’UTRs) of many human messenger mRNAs.The capability of a single miRNA to target more than hundreds of mRNAs, suggests that miRNAs influence essentially all developmental process and diseases, which also makes them interesting candidates as therapeutics agents. The primary …

Molecular And Cellular Characterizations Of Glucosylceramide Transferase (Synthase) In Giardia Lamblia, Vanessa Enriquez

Open Access Theses & Dissertations

Giardiasis, caused by an intestinal protozoan, Giardia lamblia, is a major public health problem worldwide. Giardia infection is spread through the fecal-oral route via contaminated water and food. It is estimated that over 280 million people are infected with Giardia across the globe. Giardia is a non-invasive parasite and consists of a two-stage life cycle: trophozoites and cysts. Ingested cysts undergo excystation in the proximal small intestine, releasing two trophozoites (excyzoites). Upon reaching the distal small intestine and colonizing there, trophozoites transform into cysts by encystation. It has been reported earlier that the process of encystation induced the synThesis of …

Investigations Of Elastin Recoil On Molecular And Macroscopic Levels., Nour Mohammad Jamhawi

Electronic Theses and Dissertations

Elastin is one of the most hydrophobic proteins, and it is extremely flexible when hydrated. The driving force for recoil is the decrease in entropy of the protein and/or the hydrating solvent. This dissertation is a study of both mechanisms. Following an introduction (Chapter 1), Chapters 2 and 3 investigate the recoil mechanism on the molecular level in the hydrating solvent and in the protein, respectively. Chapter 4 examines macroscopic properties of recoil by thermomechanics. Conclusions are discussed in Chapter 5. Using double quantum NMR, the deuterated water ordering at the elastin surface was studied quantitatively as a function of …

Development Of High Value Oil Traits Using The Model Oilseed Crop Camelina Sativa, Evan Updike

Department of Biochemistry: Dissertations, Theses, and Student Research

Plant oils are an important source of food, fuel, and feed in our society today. The oil found in the seeds of plants is composed almost entirely of triacylglycerol (TAG) molecules, which consist of three fatty acids esterified to a glycerol backbone. As crude oil supplies decline, vegetable oils are gaining traction as a renewable substitute to petroleum-based materials in fuels, lubricants, and specialty oleochemicals. However, as it currently stands vegetable oils do not possess the properties necessary to fill the void of a petroleum free world.

To address this problem, plant biotechnologists have done extensive work on genetic engineering …

Characterization Of Sphingolipid Biosynthesis And Modification In Plants, Dongdong Zhang

Department of Biochemistry: Dissertations, Theses, and Student Research

Sphingolipids are ubiquitous membrane lipids in eukaryotic cells. Ceramides, the backbone of sphingolipids, are synthesized by ceramide synthases (CerSs), which form amide bonds between long-chain bases (LCBs) and the acyl groups of acyl-CoAs. Class I CerS works predominantly towards C16-CoA, whereas Class II CerS works towards C24-CoA. Plant sphingolipids generally have 16-carbon and 24-carbon as the major acyl groups. However, the sphingolipids of Oryza sativa and Zea mays have 20-carbon and 24-carbon as the predominant acyl groups. This dissertation aims to understand the substrate preference of CerSs in monocots such as rice. Phylogenetic analysis shows the Class I CerSs from …

Stimuli Responsive Dye-Containing Peg-Pla Block Copolymer Micelles And Computationally Assisted Design Of A Stapled Peptide Bundle, Tyler L. Odom

Graduate Theses/Dissertations

In this thesis, I report the preparation and characterization of dye-containing PEG-b-PLA block copolymer micelles and the computational design of a novel coiled-coil peptide bundle. The PEG-b-PLA micelles encapsulate hydrophobic molecules into their core and have strong potential as nanocontainers or delivery vesicles. In theory, these internalized molecules can be released upon exposure to mechanical forces that disrupt the micellar structures. This force-responsive nature is one of the inherent properties of micellar systems. However, there is a stark lack of research that utilize this property in applications. Along those lines, I have studied the behavior of …

The 4d Living Genome, Julianna Arlene Sherman Goelzer

Boise State University Theses and Dissertations

Over the last few decades great advances have been made in our understanding of gene expression and the human genome. In 2003 the human genome was sequenced for the first time, allowing us to discover its true importance in human health. While sequencing the human genome was a great advance, it ultimately created more questions than it answered. It is known that the genomic sequence is extremely important in genome regulation, however recent studies have shown that the 4D (spatiotemporal) organization and dynamics of the living genome plays an equally critical role in regulation of gene expression. A key factor …

Bone Morphogenetic Protein Signaling Requirement In Centripetal Migration In Drosophila Melanogaster Oogenesis, Sheila Mosallaei

UNLV Theses, Dissertations, Professional Papers, and Capstones

Cells interact with each other via signals to coordinate migration for proper tissue development and maintenance, immunity and tissue repair. Signals regulate migration via changes to cytoskeletal components or transcriptional regulation. Here, I used Drosophila melanogaster to investigate whether and how a transcriptional signal, Bone Morphogenetic Protein signaling, drives a cell migration, centripetal migration. The migrating cells, centripetal follicle cells, consist of two subsets of cells, “leading” and “following” centripetal follicle cells, that although adjacent to each other, migrate differently. The differences in modes of migration correlate to differential gene expression in the centripetal follicle cells. The leading centripetal follicle …