Biochemistry, Biophysics, and Structural Biology Commons^™

Role Of Cyp2a5 In Drug Metabolism, Chemical Toxicity, And Maintenance Of Steroid Hormone Homeostasis : Insights From Studies On A Novel Cyp2a5-Null Mouse Model, Xin Zhou

Legacy Theses & Dissertations (2009 - 2024)

The central hypothesis is that CYP2A5 plays an important role in the metabolism of xenobiotic substrates, and in the toxicity induced by over-exposure to drugs, as well as in the metabolism of endogenous compounds and regulation of steroid hormone homeostasis. The specific aims are: 1) to generate and characterize a Cyp2a5-null mouse; 2) to determine the role of CYP2A5 in the systemic clearance of nicotine and cotinine; and 3) to explore the mechanisms underlying the resistance of the lateral nasal gland (LNG) of male Cyp2g1-null/Cyp2a5-low mouse and Cyp2a5-null mouse to acetaminophen (AP) toxicity.

An Rnai Screen Targeting The Protein Tyrosine Kinases Identifies Bruton's Tyrosine Kinase (Btk) As A Breast Cancer Cell Survival Factor, Cheryl Lynne Eifert

Legacy Theses & Dissertations (2009 - 2024)

The receptor protein tyrosine kinases (RPTKs) and the non- receptor protein tyrosine kinases (PTKs) are among the most commonly up-regulated genes found in all types of cancers. Although, a large body of data implicates a majority of tyrosine kinases (TKs) in cancer, few have been extensively evaluated for any potential therapeutic benefit in any of the many subtypes of breast cancer. We have used RNA interference (RNAi) to perform a large-scale loss-of-function analysis to facilitate the identification of individual factors necessary for the survival of an ErbB2 positive breast cancer cell line. We have found that 30% of the TKs …

Molecular Evolution Of Genes Underlying Phenotypic Differences Between Humans And Chimpanzees, Santhoshi Bandla

Legacy Theses & Dissertations (2009 - 2024)

Chimpanzees (Pan troglodytes) and bonobos (P. paniscus) are often used as models to study the genetic and morphological changes on the lineage leading to the modern humans (Homo sapiens). Results of this dissertation suggest that, in comparison to other hominoids, chimpanzees and bonobos are more derived in their relative testes sizes and promiscuous mating systems. Phylogenetic analysis of genes that might underlie increased testes size revealed that, in addition to being a sex-determining gene, SRY displays Pan-specific amino acid replacements that make it a compelling candidate as a testes-size determining gene. Strikingly, SRY and another candidate gene, DMRT3, display patterns …

Study Of Dynamic Processes In Protein Synthesis Using Heterogeneous Ribosome Specimens, Jie Fu

Legacy Theses & Dissertations (2009 - 2024)

Single-particle reconstruction from cryo-electron microscopy (cryo-EM) images is a widely used technique in studying the structure of macromolecular complexes. This technique allows the visualization of molecules in their native hydrated state. The heterogeneity of two-dimensional projection images, resulting from the co-existence of different states of a macromolecular complex, remains a major obstacle, as it impairs the validity of reconstruction and limits the progress toward higher resolution. On the other hand, co-existing structures, if successfully extracted from a single dataset, can provide valuable information about the equilibrium and dynamics of the biological system being studied.

Regulation Of Intracellular Calcium Concentration By Nanosecond Pulsed Electric Fields, Shaka S. Scarlett, Jody A. White, Peter F. Blackmore, Karl H. Schoenbach, Juergen Kolb

Bioelectrics Publications

Changes in [Ca²⁺]_i response of individual Jurkat cells to nanosecond pulsed electric fields (nsPEFs) of 60 ns and field strengths of 25, 50, and 100 kV/cm were investigated. The magnitude of the nsPEF-induced rise in [Ca²⁺]_i was dependent on the electric field strength. With 25 and 50 kV/cm, the [Ca²⁺]_i response was due to the release of Ca²⁺ from intracellular stores and occurred in less than 18 ms. With 100 kV/cm, the increase in [Ca²⁺]_i was due to both internal release and to influx across the plasma …

Retrocyclin, A Potent Hiv-1 Entry Inhibitor, Nitya Venkataraman

Electronic Theses and Dissertations

Human immununodeficiency virus (HIV) infection is the leading cause of death due to viral infections worldwide. In the absence of an effective vaccine or consistent male condom use, there is a clear need for female-controlled preventatives such as topical vaginal microbicides. Recent attention has been focused on developing natural antimicrobial peptides, as anti-retroviral microbicides. Increasing evidence suggests that cationic antimicrobial peptides such as defensins are effective HIV-1 inhibitors. Human alpha- and beta-defensins contribute substantially to innate immune defenses against microbial and viral infections. Certain nonhuman primates also produce theta-defensins – 18 residue cyclic peptides that are potent HIV-1 entry inhibitors. …

Mcp-1 And App Involvement Of Glial Differentiation And Migration Of Neuroprogenitor Cells, Emmanuel Vrotsos

Electronic Theses and Dissertations

Neuroprogenitor cells are an important resource because of their potential to replace damaged cells in the brain caused by trauma and disease. It is of great importance to better understand which factors influence the differentiation and migration of these cells. Previously it has been reported that neuroprogenitor cells undergoing apoptotic stress have increased levels of Amyloid precursor protein (APP) and increased APP expression results in glial differentiation. APP activity was also shown to be required for staurosporine induced glial differentiation of neuroprogenitor cells. Monocyte chemoattractant protein-1 (MCP-1) is a chemokine that is expressed during inflammatory. The binding of MCP-1 to …

Letter From The Dean, Lalit Verma

Discovery, The Student Journal of Dale Bumpers College of Agricultural, Food and Life Sciences

No abstract provided.

Hmgb1 Mediates Endogenous Tlr2 Activation And Brain Tumor Regression, James Curtin, Naiyou Liu, Marianela Candolfi, Weidong Xiong, Hikmat Assi, Kader Yagiz, Matthew Edwards, Kathrin Michelsen, Kurt Kroeger, Chunyan Liu, Akm Ghulam Muhammad, Mary Clark, Moshe Arditi, Begonya Comin-Anduix, Antoni Ribas, Pedro Lowenstein, Maria Castro

Articles

BACKGROUND: Glioblastoma multiforme (GBM) is the most aggressive primary brain tumor that carries a 5-y survival rate of 5%. Attempts at eliciting a clinically relevant anti-GBM immune response in brain tumor patients have met with limited success, which is due to brain immune privilege, tumor immune evasion, and a paucity of dendritic cells (DCs) within the central nervous system. Herein we uncovered a novel pathway for the activation of an effective anti-GBM immune response mediated by high-mobility-group box 1 (HMGB1), an alarmin protein released from dying tumor cells, which acts as an endogenous ligand for Toll-like receptor 2 (TLR2) signaling …

Transcriptional Regulation Of Cholesterol 24-Hydroxylase By Histone Deacetylase Inhibitors., Marjan Shafaati, Riona O'Driscoll, Ingemar Bjorkhem, Steve Meaney

Articles

The mechanistic basis for the tissue specific expression of cholesterol elimination pathways is poorly understood. To gain additional insight into this phenomenon we considered it of interest to investigate if epigenetic mechanisms are involved in the regulation of the brain-specific enzyme cholesterol 24-hydroxylase (CYP46A1), a key regulator of brain cholesterol elimination. We demonstrated a marked time-dependent derepression of the expression of CYP46A1, in response to treatment with the potent histone deacetylase (HDAC) inhibitor Trichostatin A. The pattern of expression of the genes in the genomic region surrounding CYP46A1 was found to be diametrically opposite in brain and liver. Intraperitoneal injection …

Pressure-Driven Transport Of Particles Through A Converging-Diverging Microchannel, Ye Ai, Sang W. Joo, Xiangchun Xuan, Shizhi Qian

Mechanical & Aerospace Engineering Faculty Publications

Pressure-driven transport of particles through a symmetric converging-diverging microchannel is studied by solving a coupled nonlinear system, which is composed of the Navier-Stokes and continuity equations using the arbitrary Lagrangian-Eulerian finite-element technique. The predicted particle translation is in good agreement with existing experimental observations. The effects of pressure gradient, particle size, channel geometry, and a particle's initial location on the particle transport are investigated. The pressure gradient has no effect on the ratio of the translational velocity of particles through a converging-diverging channel to that in the upstream straight channel. Particles are generally accelerated in the converging region and then …

Due-B, A New Human Dna Replication Protein, Is The Functional Homolog Of S. Cerevisiae Sld3, Jianhong Yao

Browse all Theses and Dissertations

DNA unwinding elements (DUEs) are commonly found at DNA replication origins. The DUE binding protein (DUE-B) is crucial for the initiation of DNA replication in eukaryotes. The unique 59 amino acid C-terminal part of DUE-B shares nearly 50% similarity with yeast the C-terminus of Sld3. DUE-B plays a key role in eukaryotic DNA replication because it is required for the loading of Cdc45, the MCM helicase activator, on chromatin. Here we show that DUE-B, just like yeast Sld3, binds to Cdc45 and TopBP1 through its C-terminus in Sf9 cells and in vitro. We also show that DUE-B, Cdc45 and TopBP1 …

Dose-Dependent Effects Of Oxygen On Metabolism In Rat Cortico-Hippocampal Brain Tissue Slices, Jennifer Lynne Hollyfield

Browse all Theses and Dissertations

Studies have shown that 95% oxygen increases neuronal excitability and ROS production. We wanted to investigate the dose-dependent effects of oxygen on brain slice metabolism. We exposed rat brain cortico-hippocampal tissue slices to 0.40, 0.95, and 4.50 ATA O2 for 60 minutes, made dual-phase tissue extracts, and used multi-nuclear NMR experiments to elucidate the slice metabolism. We found that low doses of oxygen may shift metabolism toward anaerobic glycolysis. Elevated lactate suggests this shift, along with elevated ratios of NAD+/NADH which may drive the reactions toward the production of lactate. The results also suggest that high doses of oxygen may …

Molecular Systematics And Phylogeography Of The Genus Richardsonius, Derek Dee Houston

UNLV Theses, Dissertations, Professional Papers, and Capstones

The complex geological and climatic events that significantly altered the landscape throughout the Cenozoic Era impacted the diversification of many North American taxa, including freshwater fishes. Here, I employ an array of phylogenetic analyses using a multiple gene tree approach to address several questions regarding the phylogenetic relationships of the North American cyprinid genus Richardsonius and two other closely related genera, Clinostomus and Iotichthys. I also use divergence time estimates generated using fossil calibrations to qualitatively assess the phylogeographic implications of evolution within and among these three genera. Mitochondrial and nuclear DNA sequences show a sister relationship between Iotichthys and …

Reelin Signaling Promotes Radial Glia Maturation And Neurogenesis, Serene Keilani

Electronic Theses and Dissertations

The end of neurogenesis in the human brain is marked by the transformation of the neural progenitors, the radial glial cells, into astrocytes. This event coincides with the reduction of Reelin expression, a glycoprotein that regulates neuronal migration in the cerebral cortex and cerebellum. A recent study showed that the dentate gyrus of the adult reeler mice, with homozygous mutation in the RELIN gene, have reduced neurogenesis relative to the wild type. Based on the above findings, our first hypothesis states that Reelin expression is important for the formation of radial glia and the generation of neurons from the neural …

Vesicle Targeting In Plasmodium Falciparum: The Identification And Molecular Characterization Of Plasmodium Falciparum Family Of Of Snare Proteins, Lawrence Sumanjah Ayong

Electronic Theses and Dissertations

Proteins of the SNARE (Soluble N-ethylmaleimide sensitive factor attachment protein receptor) super-family have been characterized as playing an essential role in vesicle targeting and fusion in all eukaryotes. The intracellular malaria parasite Plasmodium falciparum exhibits an unusual endomembrane system that is characterized by an unstacked Golgi apparatus, a developmentally induced apical complex, and various organellar structures of parasite origin in the infected host cells. How malaria parasites target nuclear-encoded proteins to these novel compartments is a central question in Plasmodium cell biology. Ultrastructural studies elsewhere have implicated the participation of specialized vesicular elements in transport of virulence proteins, including various …

Choosing The Right Path: Enhancement Of Biologically Relevant Sets Of Genes Or Proteins Using Pathway Structure, Reuben Thomas, Julia M. Gohlke, Geffrey F. Stopper, Frederick M. Parham, Christopher J. Portier

Biology Faculty Publications

A method is proposed that finds enriched pathways relevant to a studied condition using the measured molecular data and also the structural information of the pathway viewed as a network of nodes and edges. Tests are performed using simulated data and genomic data sets and the method is compared to two existing approaches. The analysis provided demonstrates the method proposed is very competitive with the current approaches and also provides biologically relevant results.

Analysis Of N-Linked Oligosaccharides Of Prostate-Specific Antigen And Prostatic Acid Phosphatase In Prostatic Fluids, Krista Yaudes White

Theses and Dissertations in Biomedical Sciences

Presently, prostate cancer is the most common cancer afflicting men in the United States, with serum PSA being the "gold standard" protein biomarker used in the clinic for detecting and diagnosing prostate cancer. Nonetheless, serum PSA levels can also be elevated in non-cancerous conditions as well, such as benign prostatic hyperplasia (BPH). Due to this overlap, many unnecessary biopsies and radical prostatectomies occur, leading to patient distress. Despite recent advances to clinical assays which consider other clinical parameters, there is still a great need for improved clinical detection methodologies for prostate cancer, including improved biomarkers. Therefore, this research project aims …

Structure And Dynamics Of Metalloproteins In Live Cells, Jeremy D. Cook, James E. Penner-Hahn, Timothy L. Stemmler

Biochemistry and Molecular Biology Faculty Publications

X-ray absorption spectroscopy (XAS) has emerged as one of the premier tools for investigating the structure and dynamic properties of metals in cells and in metal containing biomolecules. Utilizing the high flux and broad energy range of X-rays supplied by synchrotron light sources, one can selectively excite core electronic transitions in each metal. Spectroscopic signals from these electronic transitions can be used to dissect the chemical architecture of metals in cells, in cellular components and in biomolecules at varying degrees of structural resolution. With the development of ever-brighter X-ray sources, X-ray methods have grown into applications that can be utilized …

Comparison Of Electrically Mediated And Liposome-Complexed Plasmid Dna Delivery To The Skin, Loree C. Heller, Mark J. Jaroszeski, Domenico Coppola, Richard Heller

Bioelectrics Publications

BACKGROUND: Electroporation is an established technique for enhancing plasmid delivery to many tissues in vivo, including the skin. We have previously demonstrated efficient delivery of plasmid DNA to the skin utilizing a custom-built four-plate electrode. The experiments described here further evaluate cutaneous plasmid delivery using in vivo electroporation. Plasmid expression levels are compared to those after liposome mediated delivery.

METHODS: Enhanced electrically-mediated delivery, and less extensively, liposome complexed delivery, of a plasmid encoding the reporter luciferase was tested in rodent skin. Expression kinetics and tissue damage were explored as well as testing in a second rodent model.

RESULTS: Experiments …

Molecular Characterisation Of A Bovine-Like Rotavirus Detected From A Giraffe, Emily Mulherin, Jill Bryan, Marijke Beltman, Luke O'Grady, Eugene Pidgeon, Lucie Garon, Andrew Lloyd, John Bainbridge, Helen O'Shea, Paul Whyte, Séamus Fanning

Department of Biological Sciences Publications

Background

Rotavirus (RV), is a member of the Reoviridae family and an important etiological agent of acute viral gastroenteritis in the young. Rotaviruses have a wide host range infecting a broad range of animal species, however little is known about rotavirus infection in exotic animals. In this paper we report the first characterisation of a RV strain from a giraffe calf.

Results

This report describes the identification and detailed molecular characterisation of a rotavirus strain detected from a 14-day-old Giraffe (Giraffa camelopardalis), presenting with acute diarrhea. The RV strain detected from the giraffe was characterized molecularly as G10P[11]. …

Estimating Kinetic And Thermodynamic Parameters From Single Molecule Enzyme-Inhibitor Interactions, Laura Porter-Peden, Sarah G. Kamper, Mark Vander Wal, Ronald Blankespoor

University Faculty Publications and Creative Works

We report the application of recently developed microscopic models to estimate the apparent kinetic and thermodynamic parameters in a single molecule force spectroscopy study of the carbonic anhydrase enzyme and a complementary sulfonamide inhibitor. The most probable rupture force for the enzyme-inhibitor interaction shows a nonlinear dependency on the log-loading rate. Estimates for the kinetic and thermodynamic parameters were obtained by fitting the nonlinear dependency to linear cubic potential and cusp potential models and compared to the standard Bell-Evans model. The reliability of the estimated parameters was verified by modeling the experimental rupture force distributions by the theoretically predicted distributions …

Oriented Cell Growth On Self-Assembled Bacteriophage M13 Thin Films, Jianhua Rong, L. Andrew Lee, Kai Li, Brandon Harp, Charlene M. Mello, Zhongwei Niu, Qian Wang

Faculty Publications

Fibrillar M13 bacteriophages were used as basic building blocks to generate thin films with aligned nanogrooves, which, upon chemical grafting with RGD peptides, guide cell alignment and orient the cell outgrowth along defined directions.

Characterization Of Heat Shock Protein A12b As A Novel Angiogenesis Regulator., Rebecca J. Steagall

Electronic Theses and Dissertations

Previously, we cloned Heat shock protein A12B (HspA12B), the newest member of a recently defined subfamily of proteins distantly related to the Hsp70 family that are enriched in atherosclerotic lesions. We have found that HspA12B is predominantly expressed in vascular endothelium, and that it is involved in angiogenesis which we probed by in vitro angiogenesis assays (Matrigel), migration assays and Directed In Vivo Angiogenesis Assay (DIVAA). Hsp70s are molecular chaperones that are inducible by stress and have been found to be anti-apoptotic (Li et al. 2000; Nylandsted et al. 2000; Garrido et al. 2001). Because of its homology to Hsp70, …

Detection Of Biomarkers By Mrs Requires Error Analysis, Jeffrey C. Hoch, Mark W. Maciejewski, Michael R. Gryk

UCHC Articles - Research

Using MRS imaging and singular value decomposition (SVD), Manganas et al. (Science 318, 980,2007) reported a nuclear magnetic resonance diagnostic for neural progenitor cells. Characteristics of MRS experiments are known to be problematic for SVD-based methods. Absent detection using alternate methods of spectrum analysis or controls to quantify the false discovery rate, little significance can be attached to their result.

Dendrimer Supramolecular Assembly For Gene Delivery, Karthikeyan Pasupathy

All Theses

Dendrimers have found many applications in the fields of polymer science, biophysics, nanomedicine and the petroleum industry. Poly(amidoamine) (PAMAM) was studied as a model dendrimer and squalane as a model hydrocarbon. The interaction between PAMAM and squalane is pH dependent. Specifically, at low or neutral pH the squalane is found on the periphery of the PAMAM while at high pH the hydrocarbon is entrapped inside the PAMAM molecules.

Single-molecule fluorescence revealed that the interaction between PAMAM and squalane is reversible. At a pH value of 8, the time constants for the approaching, binding and dissociation of single PAMAM to squalane …

Computational Design Of Orthogonal Ribosomes, Lon Chubiz, Christopher Rao

Biology Department Faculty Works

Orthogonal ribosomes (o-ribosomes), also known as specialized ribosomes, are able to selectively translate mRNA not recognized by host ribosomes. As a result, they are powerful tools for investigating translational regulation and probing ribosome structure. To date, efforts directed towards engineering o-ribosomes have involved random mutagenesisbased approaches. As an alternative, we present here a computational method for rationally designing o-ribosomes in bacteria. Working under the assumption that base-pair interactions between the 16S rRNA and mRNA serve as the primary mode for ribosome binding and translational initiation, the algorithm enumerates all possible extended recognition sequences for 16S rRNA and then chooses those …

Aminoacyl-Trna Synthetase Complexes: Molecular Multitasking Revealed, Corinne D. Hausmann, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The accurate synthesis of proteins, dictated by the corresponding nucleotide sequence encoded in mRNA, is essential for cell growth and survival. Central to this process are the aminoacyl-tRNA synthetases (aaRSs), which provide amino acid substrates for the growing polypeptide chain in the form of aminoacyl-tRNAs. The aaRSs are essential for coupling the correct amino acid and tRNA molecules, but are also known to associate in higher order complexes with proteins involved in processes beyond translation. Multiprotein complexes containing aaRSs are found in all three domains of life playing roles in splicing, apoptosis, viral assembly, and regulation of transcription and translation. …

Promoter Library Designed For Fine-Tuned Gene Expression In Pichia Pastoris, Franz S. Hartner, Claudia Ruth, David Langenegger, Sabrina N. Johnson, Petr Hyka, Geoff P. Lin-Cereghino, Joan Lin-Cereghino, Karin Kovar, James Cregg, Anton Glieder

College of the Pacific Faculty Articles

Although frequently used as protein production host, there is only a limited set of promoters available to drive the expression of recombinant proteins in Pichia pastoris. Fine-tuning of gene expression is often needed to maximize product yield and quality. However, for efficient knowledge-based engineering, a better understanding of promoter function is indispensable. Consequently, we created a promoter library by deletion and duplication of putative transcription factor-binding sites within the AOX1 promoter (P_AOX1) sequence. This first library initially spanned an activity range between ∼6% and >160% of the wild-type promoter activity. After characterization of the promoter library employing …

Pge2 Receptor Subsets Mediate Hcg Regulation Of The Plasminogen Activator/Plasmin System In Primate Periovulatory Follicles, Nune Markosyan

Theses and Dissertations in Biomedical Sciences

Elevated follicular prostaglandin E2 (PGE2) levels are necessary for follicle rupture during ovulation. As the degradation of the follicle wall requires proteolysis, it was hypothesized that regulation of proteolysis by gonadotropins is PGE2 mediated.

There are four PGE2 receptors: EP1, EP2, EP3 and EP4. To determine which PGE2 receptors are present in monkey periovulatory follicles, granulosa cells and whole ovaries were collected 0, 12, 24, and 36 hours after administration of an ovulatory dose of human chorionic gonadotropin (hCG), or 36 hours after hCG from monkeys that received the prostaglandin (PG) synthesis inhibitor celecoxib. All EP receptor mRNAs were present …