Biochemistry, Biophysics, and Structural Biology Commons^™

Reconstitution Of Munc18-Dependent Mast Cell Degranulation, Matthew Grant Arnold

Master's Theses

Mast cells are specialized secretory leukocytes that play diverse roles in the body, mediated by release of histamine and other pharmacologically active substances. Although offering essential protection in innate and adaptive immunity, mast cells are also essential to the progression of inflammatory diseases, including allergy and asthma, (Theoharides et al., 2012). Exocytosis of pro-inflammatory mast cell mediators in response to otherwise innocuous antigens relies on evolutionarily-conserved membrane fusion machinery. These proteins, called SNAREs are regulated by the Sec1/Munc18 (SM) protein family (Axle Lorentz, Baumann, Vitte, & Blank, 2012). Mast cells express three mammalian Munc18 isoforms (a, b, and c), which …

Investigating The Roles Of Δnp63 As A Suppressor Of Migration, Invasion, And Metastasis, Ramon E. Flores Gonzalez

Dissertations and Theses (Open Access)

Cancer is one of the leading causes of death and disease in the world. Considerable resources are spent to study and understand cancer, with the hope of developing new treatments and eventually cures that will help millions of people. Efforts to understand cancer are hindered by its inherent complexity and instability. Nonetheless, understanding the basics of tumor development and progression are the key to focused on studying the role of ΔNp63 in cancer, a p53 family member known to be involved in epithelial development, microRNA biogenesis, and stem cell maintenance. Using the strength of in vivo mouse models, we found …

Define The Epigenetic Profiles And Subtype-Specific Genes Of Breast Cancer, Wenqian Li

Dissertations and Theses (Open Access)

Molecular profiling has identified 5 distinct subtypes of breast cancer, luminal A, luminal B, HER2-enriched, basal-like, and claudin-low breast cancer. These 5 subtypes correlate with hormone response, patient prognosis, and response to therapy. Although steady state gene expression patterns have been explored using expression microarrays, very little is known about the initial, disease-driving transcriptional changes in these cancers or epigenetic changes associated with the differential gene expression signatures. Defining these changes may provide new insights into the mechanisms by which these subtypes arise, as well as new avenues for breast cancer prevention, diagnosis, and treatment. Using Chromatin Immunoprecipitation sequencing and …

Defining The Functions Of Usp22 And Usp44 In Regulation Of H2bub1 Levels, Xianjiang Lan

Dissertations and Theses (Open Access)

Aberrant levels of histone ubiquitination are involved in various human diseases including neurodegenerative disorders and cancers. Particularly, Histone H2B monoubiquitination (H2Bub1) is highly associated with gene regulation in both normal cells and diseases. Many deubiquitinases (mainly USPs) are defined to regulate global H2Bub1 levels. However, how these USPs are regulated and how they contribute to diseases are not well understood.

USP22, part of the deubiquitination module (DUBm) in the SAGA complex, is a well-defined regulator of H2Bub1 levels. ATXN7, another crucial subunit of the SAGA DUBm, is involved in a neurodegenerative disease, spinocerebellar ataxia type 7 (SCA7), due to a …

Characterization Of Histone Mutants Associated With Mitotic Defects In Saccharomyces Cerevisiae, Md Riajul Hossain

Graduate Theses and Dissertations

Nucleosomes, the basic unit and the building blocks of chromatin have an essential role in the tight packaging of DNA into higher order chromatin. Work from our lab and others have provided information on the contributions of different histone proteins and specific domains within the nucleosome made to create the centromeric chromatin structure required for normal chromosome segregation during mitosis. The DNA entry/exit site is a particular region of the nucleosome where histone H2A, H3 and H4 form critical interactions that appear to be essential for the association of Sgo1, a tension sensing protein that monitors kinetochore-microtubule attachment. In our …

Exploring The Relationship Between Behaviour And Neurochemistry In The Polyphenic Spider, Anelosimus Studiosus (Araneae: Theridiidae), Jennifer B. Price

Electronic Theses and Dissertations

The importance of social behaviour is evident in human society, but there are both costs and benefits associated with cooperation and sociality throughout the animal kingdom. At what point do the benefits outweigh the costs, and when do selective pressures favour sociality and colonization over solitude and independence? To investigate these questions, we have focused on an anomalous species of spider, Anelosimus studiosus, also known now as the northern social spider. Throughout its broad range, A. studiosus is solitary and aggressive, but recently, colonies of cooperative and social individuals have been observed at northern latitudes. This leads to two …

Tackling Adverse Environment—Molecular Mechanism Of Plant Stress Response And Biotechnology Tool Development, Ning Yuan

All Dissertations

Abiotic and biotic stresses such as drought, salt, nutrition starvation, and pathogen infection are major factors threatening our agricultural production. With the rapidly increasing population and limited arable land area, genetic engineering of crops for new products with more stable and higher yield than conventional cultivars under adverse environment provides a powerful new tool for use in developing novel GMOs (Genetically Modified Organisms) to feed the large population in the immediate future. To develop novel GMOs with enhanced performance under adverse conditions, we need first to understand molecular mechanisms underlying plant stress response. To better understand how signaling transduction pathway …

The San1 Ubiquitin Ligase Functions Preferentially With Ubiquitin-Conjugating Enzyme Ubc1 During Protein Quality Control, Rebeca Lea Ibarra

UNLV Theses, Dissertations, Professional Papers, and Capstones

Protein quality control (PQC) is a critical process wherein misfolded or damaged proteins are cleared from the cell to maintain protein homeostasis. In eukaryotic cells, the removal of misfolded proteins is primarily accomplished by the ubiquitin-proteasome system (UPS). In the UPS, ubiquitin-conjugating enzymes and ubiquitin ligases append poly-ubiquitin chains onto misfolded protein substrates signaling for their degradation. The kinetics of protein ubiquitylation are paramount since a balance must be achieved between the rapid removal of misfolded proteins versus providing sufficient time for protein chaperones to attempt refolding. To uncover the molecular basis for how PQC substrate ubiquitylation rates are controlled, …

Heparin-Peptide Interactions, Jacqueline Anastasia Morris

Graduate Theses and Dissertations

Heparin is a polydispersed sulfated molecule that is part of the family called glycosaminoglycans found in the extracellular matrix and cell surfaces. This molecule is extremely important for the activation of proteins and protein-receptor interactions that are responsible for downstream cell signaling pathways. Heparin has been isolated from porcine intestine and used as an anticoagulant for the prevention of embolisms, heart thrombosis, and clotting during heart surgeries. This so-called miracle drug was in use until 2008, when isolated batches were found to be contaminated with other glycosaminoglycans similar to heparin. From 2008, there has been a dire need for a …

Applications Of The Gst- Affinity Tag In The Purification And Characterization Of Proteins, Wibke Beatrice Kachel

Graduate Theses and Dissertations

With the latest innovations in biological sciences, large quantities of biologically active polypeptides as well as high throughput screening methods to quickly evaluate if these biomolecules potentially have therapeutic, diagnostic, or industrial purposes are required. The synthesis and purification of peptides and small proteins continue to be demanding as the production of high yields through chemical synthesis can involve large costs. On the other hand, there are only few examples of acquiring those biomolecules through cloning and expression in bacterial systems in form of recombinant fusion proteins. Glutathione S-Transferase (GST) is not only a very commonly used affinity tag to …

Innate Immunity In Chickens: In Vivo Responses To Different Pathogen Associated Molecular Patterns, Kristen Alicia Byrne

Graduate Theses and Dissertations

Pattern recognition receptors (PRRs) on host cells recognize motifs known as pathogen associated molecular patterns (PAMPs) that are common to groups of microbes. Examples include LPS on Gram-negative bacteria, the structural motif PGN common to all bacteria, MDP the smallest immunostimulatory unit of PGN, and poly I:C the dsRNA analog. PAMP recognition by and stimulation of the innate immune system is crucial to an individual’s ability to quickly limit microbial growth and stimulate the adaptive immune system. Characterization of the in vivo immune responses initiated by PAMPs has not been directly addressed. Using growing feathers (GF) as a novel intradermal …

Two-Electron Quenching Of Dinuclear Ruthenium(Ii) Polypyridyl Complexes, Yinling Zhang

Graduate Theses and Dissertations

A bridging ligand 5,5’-Bi- 1,10-phenanthroline, diphen, was prepared using dichlorobis(triphenylphosphine)Ni(II), Ni(PPh3)2Cl2 as catalyst with a yield of 40%. Yellow cubic crystals were able to obtain from the good purity product for single crystal analysis. The torsion angle between the planes of the subunit phenanthrolines is about 66 degrees.

A dinuclear ruthenium (II) polypyridyl complex, (phen)2Ru(diphen)Ru(phen)24+, was synthesized by using polymeric ruthenium carbonyl compound as the entry point, diphen as the bridging ligand and 1,10-phenanthroline, phen, as the terminal legand. Brown needlelike crystals were precipitated from acetonitrile that were not suitable for single crystal diffraction.

The photochemistry of the dimer was …

Investigation Of The Interaction Of Dimeric Ruthenium Complexes With Cytochrome B5, Christopher Dain Rupar

Graduate Theses and Dissertations

Photoreactive complexes to study the kinetics of electron transfer of proteins have been in use for a long time. It has always been speculated that complexes bind near the heme or the electron transfer reaction would not occur. But it is unkown exactly how the complex interacts with the protein. The structural, thermodynamic, and kinetic properties of rat liver microsomal cytochrome b5 were investigated when bound to ruthenium dimer complexes. Heteronuclear Single Quantum Coherence studies support a dynamic binding model of a dimer Ru complex bound near the protein’s heme involving residues H39, E44, G42, V61, G62, and H63. The …

Mechanism Of Rapid Electron Transfer Reactions Involving Cytochrome Bc1, Cytochrome C And Cytochrome Oxidase, Jeremy Erik Durchman

Graduate Theses and Dissertations

Electron transfer between mitochondrial proteins complexes represents the primary means by which living things acquire the requisite energy for survival. The coupling of electron transfer to proton translocation creates an electrochemical gradient that drives the synthesis of highly energetic compounds such as ATP. The purpose of these studies is to measure rates of electron transfer and elucidate the important governing factors in the redox events involving cytochrome bc1, cytochrome c and cytochrome oxidase. Using rapid initiation of redox events triggered by laser flash excitation of ruthenium compounds, and strategically monitoring unique spectral properties of these proteins in the visible region …

Use Of Clustering Techniques For Protein Domain Analysis, Eric Rodene

School of Computing: Dissertations, Theses, and Student Research

Next-generation sequencing has allowed many new protein sequences to be identified. However, this expansion of sequence data limits the ability to determine the structure and function of most of these newly-identified proteins. Inferring the function and relationships between proteins is possible with traditional alignment-based phylogeny. However, this requires at least one shared subsequence. Without such a subsequence, no meaningful alignments between the protein sequences are possible. The entire protein set (or proteome) of an organism contains many unrelated proteins. At this level, the necessary similarity does not occur. Therefore, an alternative method of understanding relationships within diverse sets of proteins …

Competent Overall Water-Splitting Electrocatalysts Derived From Zif-67 Grown On Carbon Cloth, Xin Liu, Jinmei Dong, Bo You, Yujie Sun

Chemistry and Biochemistry Faculty Publications

The design of nonprecious, bifunctional, and highly competent electrocatalysts for both H₂ and O₂evolution reactions (HER and OER) has attracted increasing interest recently. Herein, we report a cobalt-based electrocatalyst derived from ZIF-67 grown on carbon cloth (Co–P/NC/CC) for overall water splitting electrocatalysis. The as-prepared Co–P/NC/CC catalyst exhibited remarkable catalytic performance in 1 M KOH with Tafel slopes of 52 and 61 mV dec⁻¹ for HER and OER, respectively. When serving as catalysts for both the cathode and anode, our Co–P/NC/CC demonstrated high efficiency and strong robustness. A thorough comparison with other control samples and detailed characterization …

Fulleretic Well-Defined Scaffolds: Donor–Fullerene Alignment Through Metal Coordination And Its Effect On Photophysics, Derek E. Williams, Ekaterina A. Dolgopolova, Danielle C. Godfrey, Evgeniya D. Ermolaeva, Perry J. Pellechia Dr., Andrew B. Greytak Prof. Dr., Mark Smith Dr., Stanislav M. Avdoshenko, Dr., Alexey A. Popov Dr., Natalia B. Shustova Prof. Dr.

Faculty Publications

Herein, we report the first example of a crystalline metal–donor–fullerene framework, in which control of the donor–fullerene mutual orientation was achieved through chemical bond formation, in particular, by metal coordination. The 13C cross-polarization magic-angle spinning NMR spectroscopy, X-ray diffraction, and time-resolved fluorescence spectroscopy were performed for comprehensive structural analysis and energy-transfer (ET) studies of the fulleretic donor–acceptor scaffold. Furthermore, in combination with photoluminescence measurements, the theoretical calculations of the spectral overlap function, Förster radius, excitation energies, and band structure were employed to elucidate the photophysical and ET processes in the prepared fulleretic material. We envision that the well-defined fulleretic donor–acceptor …

Nmrfx Processor: A Cross-Platform Nmr Data Processing Program, Michael Norris, Bayard Fetler, Jan Marchant, Bruce A. Johnson

Advanced Science Research Center

NMRFx Processor is a new program for the processing of NMR data. Written in the Java programming language, NMRFx Processor is a cross-platform application and runs on Linux, Mac OS X and Windows operating systems. The application can be run in both a graphical user interface (GUI) mode and from the command line. Processing scripts are written in the Python programming language and executed so that the low-level Java commands are automatically run in parallel on computers with multiple cores or CPUs. Processing scripts can be generated automatically from the parameters of NMR experiments or interactively constructed in the GUI. …

Long-Range Acoustic Interactions In Insect Swarms: An Adaptive Gravity Model, Dan Gorbonos, Reuven Ianconescu, James G. Puckett, Rui Ni, Nicholas T. Ouellette, Nir S. Gov

Physics and Astronomy Faculty Publications

The collective motion of groups of animals emerges from the net effect of the interactions between individual members of the group. In many cases, such as birds, fish, or ungulates, these interactions are mediated by sensory stimuli that predominantly arise from nearby neighbors. But not all stimuli in animal groups are short range. Here, we consider mating swarms of midges, which are thought to interact primarily via long-range acoustic stimuli. We exploit the similarity in form between the decay of acoustic and gravitational sources to build a model for swarm behavior. By accounting for the adaptive nature of the midges' …

The Confounding Effects Of Particle Size And Substrate Bulk Density On Phanerochaete Chrysosporium Pretreatment On Panicum Virgatum, Amanda N. Hickman, Sue E. Nokes, William S. Sympson, Mathew J. Ruwaya, Michael D. Montross, Barbara L. Knutson

Biosystems and Agricultural Engineering Faculty Publications

Phanerochaete chrysosporium treatment is less effective as a biological pretreatment on feedstock with larger particle sizes. We hypothesized that the improved effectiveness of the pretreatment when smaller particle sizes are used may be due to the inherently higher bulk density with smaller particle sizes. The effects of substrate bulk density and particle size on the efficacy of P. chrysosporium pretreatment of switchgrass (Panicum virgatum) was tested experimentally. Phanerochaete chrysosporium was grown on senesced switchgrass (2 different particle sizes) with various bulk densities. In all treatments, the fungal-pretreated samples released more glucose during enzymatic saccharification than the control sample. …