Biochemistry, Biophysics, and Structural Biology Commons^™

The Effects Of Extended Access To Methamphetamine Self-Administration On Dopaminergic Markers In The Striatum, Joe Luevano

Open Access Theses & Dissertations

Methamphetamine (METH) abuse is a persistent problem in the U.S. and abroad. Escalation of METH use among independent users occurs for a variety of physiological and psychological reasons. Methamphetamine dependence may be attributed to the rewarding effect of this drug via the dopaminergic systems of the central nervous system (CNS). The presence of METH in the CNS increases synaptic release of dopamine. This increase in dopaminergic neurotransmission is thought to be directly attributed to the rewarding effects of METH. Following METH use, compensatory changes have been found to occur in the dopaminergic system during various periods of abstinence. It is …

Examination Of The Neurochemical Mechanisms That Mediate Nicotine Withdrawal In Adolescent And Adult Rats, Luis Alberto Natividad

Open Access Theses & Dissertations

Introduction: The mechanisms that mediate nicotine withdrawal are presently unclear and age group differences in the neurochemical effects of withdrawal have been largely unexplored. Previous studies in our laboratory demonstrated that adult rats display a decrease in extracellular levels of dopamine in the nucleus accumbens (NAcc) during nicotine withdrawal and this decrease is reduced in adolescent rats (Natividad et al., 2010). The goal of this dissertation was to examine whether these age group differences in dopamine during withdrawal are mediated via excitatory and inhibitory mechanisms that modulate dopamine in the cell body region of the ventral tegmental area (VTA). Methods: …

Arachidonic Acid Signaling In Invasive And Non-Invasive Breast Cancer Cells, Debarshi Roy

Open Access Theses & Dissertations

Breast cancer is the second largest cause of cancer-related deaths in women all over the world. Epidemiological studies suggest that the consumption of high-fat diets can promote the incidence of breast cancers in both developed and developing countries. In particular, the lipid-rich diet contains arachidonic acid (AA, a C20:4 polyunsaturated fatty acid), which has been shown to be associated with tumor formation in breast tissues. Nevertheless, the actual mechanism by which AA induces the metastatic transformation and malignancy is not well understood. The goal of my dissertation, therefore, is to identify the molecules and unravel the pathways that participate in …

Map Kinases Couple Hindbrain-Derived Catecholamine Signals To Hypothalamic Adrenocortical Control Mechanisms During Glycemia-Related Challenges, Arshad Khan, Kimberly Kaminski, Graciela Sanchez-Watts, Todd Ponzio, J. Kuzmiski, Jaideep Bains, Alan Watts

Selected Works Temporary Series

No abstract provided.

Map Kinases Couple Hindbrain-Derived Catecholamine Signals To Hypothalamic Adrenocortical Control Mechanisms During Glycemia-Related Challenges, Khan, Kimberly Kaminski, Graciela Sanchez-Watts, Todd Ponzio, J. Kuzmiski, Jaideep Bains, Alan Watts

Departmental Papers (Biology)

No abstract provided.

Cloning, Expression, And Characterization Of The Aminoethylphosphonate Pathway In Trypanosoma Cruzi, Samuel I. Rodriguez^, Esteban M. Cordero, Igor C. Almeida*

COURI Symposium Abstracts, Summer 2011

No abstract provided.

Structural Study Of Mcry2: A Circadian Rhythm Regulator, Brenda L. Rodarte^, Gustavo A. Avila, Adrian S. Enriquez, Nicolas D. Silva, Tiffany H. Blankenship, Erquan Eric Zhang*, Chuan Xiao*

COURI Symposium Abstracts, Spring 2011

A circadian clock is a 24 hour biological rhythm that regulates physiological, psychological and behavioral processes in living organisms. Understanding the regulation mechanism of such circadian rhythms can have great impact in certain diseases such as sleeping disorders and cancers. There are many genes regulating circadian rhythms in different species. Cryptochromes (CRY) are photosensory receptors mediating light regulation of growth and development in certain species. Mouse cryptochrome protein mCRY2 has been found to encode a blue light photoreceptor and is important for mice circadian rhythm. The main goal of the project is to determine the atomic structure of mCRY2, via …

Biochemical Characterization And X-Ray Crystallography Of A Lysozyme Encoded By Pseudomonas Aeruginosa Bacteriophage Sn, Nadia Herrera^, Maxim V. Filchikov, Zacariah L. Hildenbrand, Sudheer K. Molugu, Vadim V. Mesyanzhinov, Konstantin A. Miroshnikov, Ricardo A. Bernal*

COURI Symposium Abstracts, Spring 2011

Bacteriophage SN is a virulent phage that selectively infects the bacterium Pseudomonas aeruginosa. It was isolated from Lake Chernoe in Russia and it is related to the PB1-like species of the Myoviridae family. The DNA genome is composed of 66,391 base pairs, has 89 predicted open reading frames, and encodes more than 20 structural proteins. One of the open reading frames of this newly discovered bacteriophage has high sequence identity to other lysozyme and chitinase genes. It is therefore assumed that this protein encoded by bacteriophage SN is utilized for digestion of the host cell wall prior to injection of …

Initialization Of Structural Proteomic Studies Of The Giant Marine Virus Crov, Duer Bolotaulo^, Nancy Rondeau, Gustavo A. Avila, Matthias G. Fischer, Curtis A. Suttle, Chuan Xiao*

COURI Symposium Abstracts, Spring 2011

The existence of cellular genes in viruses such as the nucleocytoplasmic large DNA viruses (NCLDV) has led to not only the redefinition of the virus but also the mystery of the origin of these genes. Cafeteria roenbergensis virus (CroV) is a giant marine virus in the NCLDV clade. Information obtained from structural proteomics studies of CroV can be compared with known cellular counterparts, elucidating the evolutionary relationship between virus and cell in a three-dimensional structural aspect. CroV's major capsid protein gene (MCP) and five CroV genes, (CDS 84, 115, 143, 149,152) including a photolyase and an oxidoreductase, have been chosen …

Enzymatic Characterization Of An Endolysin Mediated By Chaperonin In Bacteriophage Phi El, Diana A. Tafoya^, Nadia Herrera, Sudheer Molugu, Zachariah Hildenbrand, Maxim V. Filchikov, Vadim V. Mesyanzhinov, Konstantin A. Miroshnikov, Ricardo A. Bernal*

COURI Symposium Abstracts, Spring 2011

Bacteriophage phi-EL is a virus that attacks the human pathogen Pseudomonas aeruginosa. One of the gene products from phi-EL is a putative endolysin. Endolysin is an enzyme produced during gene expression in the lytic cycle of the bacteriophage. Its function is to digest the peptidoglycan layer of the host cell wall, thereby releasing the newly formed virions. In order to confirm the identity of this putative endolysin, the gene product was transformed into competent E. coli cells, expressed to high levels and purified to high homogeneity using nickel affinity and size exclusion chromatography. The peptidoglycan-hydrolyzing activity of the protein …

Synthesis, Self-Assembly And Biological Properties Of Self-Folding Cu(Ii) Coordination Polymers, Alejandro Arzola-Rubio

Open Access Theses & Dissertations

The synthesis of materials via molecular self-assembly is a powerful bottom-up approach for fabricating matter in the nano- and micro-meter scales. This methodology involves the spontaneous and reversible organization of small molecules that interact with one another to create larger structures driven by non-covalent interactions such as hydrogen bonding, hydrophobic forces and metal-ligand coordination interactions. In this thesis, the design, synthesis and characterization of a new set of molecules that spontaneously self-organize in water to form three-dimensional nanoscale toroidal structures was investigated. These supramolecular structures were designed with an intrinsic affinity to bind and condense DNA strands with the intent …

Inhibition Of Calcium Oxalate Calculi By Ndga - A Spectroscopic Study, Preethi Dacha

Open Access Theses & Dissertations

Formation of calculi in urinary tract leads to kidney stones. This process is known as Urolithiasis. Some of the causes of urolithiasis are metabolic disorders, genetic factors, and anatomic abnormalities in the urinary system. Nowadays, urolithiasis is very common disease in population of all over the world. The present study strives to understand calcium oxalate calculi formation as well as its inhibition by using Nordihydroguaiaretic acid (NDGA), which is a chemical extract of the Larrea Tridentata bush, a plant that is traditionally employed in the El paso region as a natural treatment for kidney stones and bladder diseases. Thus, in …

Phospholipid Analysis In Trypanosoma Cruzi, Melissa Rashonda Harris

Open Access Theses & Dissertations

Chagas disease, caused by the flagellate protozoan Trypanosoma cruzi is one of the most endemic and deadly infectious diseases. T.cruzi is distributed throughout most of South and Central America, where it infects 12 to 19 million people, with an annual incidence of 561,000. Another 35 million are exposed to infection, 2 to 3 million people have clinical symptoms of chronic Chagas disease, and about 45,000 of these may die every year due to cardiac failure. In addition to the growing number of incidences in other countries the disease is an emerging infectious disease in the U.S due to the migration …

Free Radical Stress-Induced Parkinsonian Lewy-Like Aggregation Prevented Through Polyphenolic Phytochemical Analog Intervention: Implications For Subcellular Trafficking And Neurodegenerative Disorders, Rituraj Pal

Open Access Theses & Dissertations

Protein disulfide isomerase (PDI), the chief endoplasmic reticulum (ER)-resident oxidoreductase chaperone, is known to catalyze the maturation of disulfide-bond-containing proteins primarily through oxidation-reduction and isomerization functions. The rate-determining step in the oxidative regeneration path of disulfide-bond-containing proteins generally couples chemical thiol-disulfide-exchange reactions to a physical conformational folding reaction. I have determined the impact of PDI and its subdomains on the rate-determining step in ribonuclease A folding and on the physical structure-forming step of select ER-processed proteins including RNase A. This was facilitated through application of a novel chemical tool to exclusively populate native-disulfide-containing intermediates in unstructured forms. The described biochemical …

Molecular Mechanisms Of Poly [Adp-Ribose] Polymerase-1 In Hiv-1 Infection, Daniel Reyes

Open Access Theses & Dissertations

Poly (ADP-ribose) polymerase-1 (PARP-1) is a cellular enzyme involved in genome stability and transcriptional regulation. The role of this protein in HIV-1 infection is largely controversial. Some reports indicated a fundamental role of PARP-1 in HIV-1 DNA integration and results from other laboratories do not support these conclusions. An important characteristic in all these experiments is that the HIV-1 target cells that were used express, in addition to PARP-1, the functional homologue PARP-2. We evaluated the role of PARP-1 in the chicken B lymphoblastoid cell line DT40. These cells naturally lack PARP-2 and support the early steps of HIV infection. …

Structural And Functional Investigation Of Φ-El-Chaperonin Mediated Protein Folding, Sudheer Kumar Molugu

Open Access Theses & Dissertations

Chaperonins are ubiquitous, sequence related protein complexes that aid in the folding of nascent and misfolded polypeptides in an ATP driven pathway. Recently a GroEL-like, 860 kilo Dalton chaperonin protein complex was identified and isolated from the bacteriophage EL, a virus that infects the Gram-negative bacterium Pseudomonas aeruginosa. The bacteriophage EL contains 201 predicted open reading frames and is the only known phage that encodes for its own chaperonin known as Φ-EL-chaperonin.

To understand the importance of Φ-EL-chaperonin in phage EL life cycle, the recombinant Φ-EL-chaperonin protein was expressed in Escherichia coli (E. coli) purified to homogeneity and the structure …

Identification And Characterization Of Fkbp52-Specific Inhibitors For The Treatment Of Prostate Cancer, Johanny Tonos De Leon

Open Access Theses & Dissertations

Steroid hormone receptors require the ordered assembly of various chaperone and cochaperone proteins in order to reach a functional state. The final stage in the receptor maturation process requires the formation of a mutimeric complex consisting of Hsp90 dimer, p23, and one of several large immunophilins. Studies conducted previously demonstrated that the large immunophilin FKBP52 acts to potentiate glucocorticoid, androgen, and progesterone receptor signaling pathways. The aim of these studies was to identify and characterize FKBP52-specific inhibitors that would not only serve as tools for the pharmacological analysis of FKBP52-receptor interactions, but may also lead to novel drugs with significant …

Interactions Of The Cellular Sumoylation System With Influenza A Virus And Its Non-Structural Protein Ns1a (Ns1a), Sangita Pal

Open Access Theses & Dissertations

The most important current anti-influenza weapons, vaccination and antiviral drugs, can be rapidly rendered fully ineffective thanks to the virus's high mutational rate, which produces viruses exhibiting new antigenic properties and structural proteins insensitive to the drug's mechanism of action. One attractive alternative is to develop drugs that modulate the activity of cellular systems either required for viral growth or able to neutralize viral growth. Here we demonstrate that the cellular SUMOylation system, a post-translational modification involving the conjugation of the Small Ubiquitin-like MOdifier (SUMO) to specific protein targets using a Ubiquitin-like enzymatic cascade, interacts closely with influenza virus during …

A Specific Regulatory Role For Sgtα On The Maturation And Activation Of Steroid Hormone Receptors, Atanu Paul

Open Access Theses & Dissertations

Steroid hormone receptors (SHRs) are ligand-dependent transcription factors belonging to the nuclear receptor superfamily. These receptors regulate various physiological functions in higher ordered eukaryotes. In the absence of hormone these receptors form a complex with molecular chaperones such as Hsp90 and Hsp70 and other cochaperones in the cytoplasm. Association with the Hsp90-Hsp70 chaperone machinery leads to the maturation of the Ligand Binding Domain (LBD) of the receptors and enables the receptors to bind hormone with high affinity. Upon binding with a specific hormone the receptors are translocated into the nucleus where they initiate transcription of specific genes. Although the involvement …

Evaluating The Role Of Evolutionarily Conserved Regions Of Ledgf/P75 In Hiv-1 Infection, Jose Adrian Garcia

Open Access Theses & Dissertations

LEDGF/p75 is an important cellular co-factor for lentiviral integration. LEDGF/p75-deficient cells are markedly resistant to HIV-1 infection and re-expression of the wild type protein rescues infectivity. Although the molecular mechanism of LEDGF/p75 in HIV-1 integration is not yet known, this co-factor activity requires the interaction of LEDGF/p75 with both the host chromatin and viral integrase. In order to evaluate the involvement of other LEDGF/p75 regions in HIV-1 infection we constructed a panel of deletion mutants targeting clusters of charged residues that are evolutionarily conserved and predicted to be post-translationally modified. These mutants were evaluated for their ability to rescue HIV-1 …

Ganglioside-Cytokine Interaction In The Induction Of Primary Brain Cell Death, John Charles Gorbet

Open Access Theses & Dissertations

Gangliosides have been implicated in multiple pathologies affecting the central nervous system (CNS) and recent research has implicated them in playing an active role in the pathogenesis of multiple sclerosis. Empirical studies and theoretical considerations have suggested the possibility of interactions between gangliosides, like GD3, and pro-inflammatory cytokines present in the nervous system. This study sought to investigate the possibility that either individual gangliosides acting alone or complexed with other species interact with the known immune response factor TNF&alpha to initiate or facilitate cell death in the CNS. I examined the cellular viability and gene expression in primary brain cell …

Computer Aided Drug Design Methods & Quantitative Structure-Activity/Property Relationships, Suman Sirimulla

Open Access Theses & Dissertations

The first part of dissertation consists of development of a QSAR model for 229 mutagenic aromatic amines and a QSPR model of partial molar volumes of amino acids. A common procedure for QSAR analysis consist of data selection (generally sets of homologous series of compounds and their corresponding biological activities), tabulation of trial physicochemical or molecular structural descriptors, followed by a multilinear statistical analysis to derive a statistically valid QSAR correlation of the activity data making use of a subset of the trial descriptors. A final important step is cross-validation to assess the putative predictive (rather than just correlative) capabilities …

Effects Of The Loss Of Multidrug Resistance Associated Protein 1 On Steroid Homeostasis, Dendritic Cell Function And Compensatory Mechanisms, Jeffrey Charles Sivils

Open Access Theses & Dissertations

The ATP-binding cassette (ABC) superfamily of membrane transporters use energy derived from ATP to eliminate a variety of exogenous and endogenous compounds from cells including anti cancer and anti viral drugs, metals steroids, bilirubin, cAMP, cGMP, leukotrienes , prostaglandins. The multi drug resistance associated protein family (MRP/ABBC) has been acknowledged as a major player involved in multi drug resistance (MDR), in which cancers stop responding a wide array of structurally and functionally unrelated chemotherapy drugs. Cancer is the second leading cause of death in adults in the United States. Although there have been great strides made the treatment of cancers …

Phosphorylation Of The Glycine Transporter 1, Javier Vargas Medrano

Open Access Theses & Dissertations

The extracellular levels of the neurotransmitter glycine in the brain are tightly regulated by the high-affinity glycine transporter 1 (GlyT1) and the clearance of glycine depends on its rate of transport and the levels of cell surface GlyT1. Over the past years, it has been shown that PKC activation diminishes the activity and promoted phosphorylation of several neurotransmitter transporters including the dopamine, serotonin and norepinephrine transporters however, its role is unknown for the glycine transporter. To get insights into the role of PKC activation on GlyT1 regulation, we used three N-terminus GlyT1 isoforms stably expressed in porcine aortic endothelial (PAE) …

Isolation, Characterization And Molecular Cloning Of Dnase Iiib From Drosophila Melanogaster, Brenda Cristina Anchondo

Open Access Theses & Dissertations

Nucleases are enzymes that breakdown nucleic acids; they are classified by their biochemical properties into different groups (Evans et al., 2003). The ββα-Me finger family of nucleases are enzymes that combine structurally different groups but they are defined by a highly evolutionary conserved active site, a stretch of 22 amino acids composed by a β-hairpin (ββ) and α-helix (α) that anchor a catalytic metal ion (Sokolowska et al, 2009). Within this family is found the DNA/RNA non-specific nucleases. Nucleases that belong to the DNA/RNA non-specific group hydrolyze both ds and ss DNA, as well as RNA at equal or similar …

The Role Of Sumoylation Of Ledgf/P75 In Hiv-1 Infection, Murilo Tadeu Domingues Bueno

Open Access Theses & Dissertations

The lens epithelium-derived growth factor (LEDGF) proteins p75 and p52 are transcriptional co-activators that protect cells from stresses through modulation of stress and heat shock-related genes. Besides regulating such genes, LEDGF/p75 is also important in the process of HOX gene expression and leukemia transformation driven by the MLL histone methyl transferase complex. By exploiting a similar mechanism of interaction between LEDGF/p75 and MLL, the HIV-1 viral protein Integrase (IN) associates with LEDGF/p75 in order to execute efficient viral DNA integration. This present work has identified that LEDGF proteins are posttranslationally modified by SUMO-1 and -3. SUMOylation was found to target …

The Role Of Ledgf/P75 In Transcriptional Regulation, Jeffrey Ryan Kugelman

Open Access Theses & Dissertations

The Lens Epithelial Derived Growth Factor p75 (LEDGF/p75) is a chromatin bound protein whose cellular function is not yet clearly known. A role in transcriptional regulation had been previously proposed based on its interaction with the basal transcriptional machinery and on its effects on the expression of genes involved in the cellular response to environmental stresses. To further elucidate the function of LEDGF/p75, we conducted a global and unbiased evaluation of the role of this protein in gene expression. To that aim, we performed a microarray analysis of cellular gene expression in cells that are severely depleted of LEDGF/p75. To …

Structural Investigation Of Atp-Utilizing Enzymes: Structures Involved In H+ Homeostasis And The Proliferation Of Hormone-Dependent Cancers, Zacariah Louis Hildenbrand

Open Access Theses & Dissertations

ATP is a multifunctional nucleotide considered to be the "molecular unit of currency" of intracellular energy transfer. ATP is utilized ubiquitously for the transport of chemical energy within the cell in addition to acting as a substrate in the regulation of many metabolic and signaling transduction pathways such as kinase-mediated signaling cascades. Interestingly, the functional mechanisms of many enzymes require the binding of ATP to trigger key structural and conformational changes that ultimately result in enzyme-directed catalysis. Two of the most omnipresent ATPases within the cell include the V-ATPase rotary proton pump and the Hsp90 protein-folding chaperone. Structural and biochemical …

Nerve, Muscle, Blood, Toil, Tears, And Sweat: England’S Pioneering Biophysicist, Soldier, And Statesman, Arshad Khan

Selected Works Temporary Series

No abstract provided.

Nerve, Muscle, Blood, Toil, Tears, And Sweat: England’S Pioneering Biophysicist, Soldier, And Statesman, Khan

Departmental Papers (Biology)

No abstract provided.