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Biochemical And Structural Studies Of Aav-2 Rep68-Aavs1 Complex Assembly, Clayton Bishop

Theses and Dissertations

Multiple DNA transactions are at the center of almost all processes regulating the AAV life cycle. A common feature shared by all transactions is the binding of the large AAV Rep proteins Rep78/Rep68 onto DNA sites harboring multiple GCTC repeats. AAV mediated site-specific integration is contingent upon the formation of a productive complex between Rep78/Rep68 and the AAVS1 site located at chromosome 19. In order to understand the mechanistic details of the initial assembly process we carried out equilibrium binding experiments of Rep68 and its individual domains with a 42-mer AAVS1 site. Results show that although Rep68 binds AAVS1 with …

Clusters Bridging Disciplines, Swayamprabha Behera

Theses and Dissertations

Clusters constitute an intermediate state of matter between molecules and solids whose properties are size dependent and can be tailored. In recent years, cluster science has become one of the most exciting areas of research since their study can not only bridge our understanding between atoms and their bulk but also between various disciplines. In addition, clusters can serve as a source of new materials with uncommon properties. This dissertation deals with an in-depth study of clusters as a bridge across physics, chemistry, and materials science and provides a fundamental understanding of the structure-property relationships by focusing on three different …

Modified Seed Growth Of Iron Oxide Nanoparticles In Benzyl Alcohol: Magnetic Nanoparticles For Radio Frequency Hyperthermia Treatment Of Cancer, Stanley E. Gilliland Iii

Theses and Dissertations

Iron oxide nanoparticles have received sustained interest for biomedical applications as synthetic approaches are continually developed for precise control of nanoparticle properties. This thesis presents an investigation of parameters in the benzyl alcohol synthesis of iron oxide nanoparticles. A modified seed growth method was designed for obtaining optimal nanoparticle properties for magnetic fluid hyperthermia. With a one or two addition process, iron oxide nanoparticles were produced with crystallite sizes ranging from 5-20 nm using only benzyl alcohol and iron precursor. The effects of reaction environment, temperature, concentration, and modified seed growth parameters were investigated to obtain precise control over properties …

Experimental Development Of Advanced Air Filtration Media Based On Electrospun Polymer Fibers, Negar Ghochaghi

Theses and Dissertations

Electrospinning is a process by which polymer fibers can be produced using an electrostatically driven fluid jet. Electrospun fibers can be produced at the micro- or nano-scale and are, therefore, very promising for air filtration applications. However, because electrospun fibers are electrically charged, it is difficult to control the morphology of filtration media. Fiber size, alignment and uniformity are very important factors that affect filter performance. The focus of this project is to understand the relationship between filter morphology and performance and to develop new methods to create filtration media with optimum morphology.

This study is divided into three focus …

Fabrication And Characterization Of High Surface Area Gold Electrodes, Madhura S. Damle

Theses and Dissertations

High surface area gold electrodes are very good substrates for biosensors, catalysis and drug delivery. Their performance is characterized by good sensitivity, low detection limit and high signal. As a result, extensive research is being carried out in this field using different approaches of fabrication to generate high surface area porous electrodes of different morphology, pore size and structure. The morphology of the electrodes can be changed based on whether the approach involves a template or not, types of metal deposition, method and time of dealloying etc. The deposition of metal can be carried out using various approaches such as …

Snd1 Mediated Downregulation Of Ptpn23 In Hcc, Nidhi Jariwala

Theses and Dissertations

SND1 MEDIATED DOWNREGULATION OF PTPN23 IN HEPATOCELLULAR CARCINOMA

By Nidhi Jariwala, MS

A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science at Virginia Commonwealth University, 2014.

ADVISOR: Dr. Devanand Sarkar

Associate Professor, Department of Human and Molecular Genetics Blick Scholar Associate Scientific Director, Cancer Therapeutics VCU Institute of Molecular Medicine Massey Cancer Center

ABSTRACT

Staphyloccocal nuclease domain containing protein 1 (SND1) is identified as an oncogene in multiple cancers, including hepatocellular carcinoma (HCC). SND1 regulates gene expression at transcriptional as well as post-transcriptional level and mediates molecular pathways that culminate into carcinogenesis. SND1 …

Tissue Engineering Scaffold Fabrication And Processing Techniques To Improve Cellular Infiltration, Casey Grey

Theses and Dissertations

Electrospinning is a technique used to generate scaffolds composed of nano- to micron-sized fibers for use in tissue engineering. This technology possesses several key weaknesses that prevent it from adoption into the clinical treatment regime. One major weakness is the lack of porosity exhibited in most electrospun scaffolds, preventing cellular infiltration and thus hosts tissue integration. Another weakness seen in the field is the inability to physically cut electrospun scaffolds in the frontal plane for subsequent microscopic analysis (current electrospun scaffold analysis is limited to sectioning in the cross-sectional plane). Given this it becomes extremely difficult to associate spatial scaffold …

Using Structural Analysis To Investigate The Function Of Suppressor Of Ikk-Epsilon (Sike), Sean W. Mckinley

Theses and Dissertations

The innate immune system provides the body’s first line of defense against pathogenic challenge through pathogen recognition and initiation of the immune response. Among the various cellular mechanisms of pathogen recognition in mammals, Toll-like receptor 3 (TLR3) recognizes viral dsRNA. Stimulation of TLR3 signaling pathway leads to transcription of pro-inflammatory cytokines and type-1 Interferons. Suppressor of IKKε (SIKE) interacts with two kinases in the signaling pathway, IKKε and TANK binding kinase 1 (TBK1), inhibiting the transcription of type I interferons. Recently, the Bell Laboratory discovered that SIKE blocks TBK1-mediated activation of type I interferons by acting as a high affinity, …

Group Via Calcium-Independent Phospholipase A2 Regulates Bcl-Xl Protein Levels In Mice Lung, Sang-Jin Nam

Theses and Dissertations

With previous indication of the Group VIA phospholipase A2 (iPLA2β) enzyme regulating ER-stress induced apoptosis in β-cells by regulating the anti-apoptotic protein Bcl-xL via alternative splicing, our lab postulated iPLA2β to be utilizing a similar mechanism to regulate apoptosis in mice lung. Our previous lab work has shown implications of lung function compromise in iPLA2β-/- mice, and we speculated the cause to be due altered lung architecture stemming from the attenuation of apoptosis. The western blot analysis in this study suggested that iPLA2β is involved in the regulation of Bcl-xL, but the mRNA ratios of the splice variants suggested that …

Queer Alchemies: Radical Futurity In The Shell Of The Now, Elizabeth R. Canfield

Theses and Dissertations

This work operates at the intersection of academics, art, and activism. Within queer studies there is a tension between assimilation and liberation, sometimes situated as between pragmatism and utopia. This work re-examines Frankfurt school Marxist views of utopia through a queer theoretical lens in order to employ the radical imagination and queer futurity to examine new ways of practicing liberation. Drawing from theorists like Judith Butler, Jose Esteban Munoz, and Gloria Anzaldua, this work uses art (film, writing, zine-making, and sound) as a way to envision and enact a better world situated in the present.

Investigating The Role Of The Synaptic Transcriptome In Ethanol-Responsive Behaviors, Megan A. O'Brien

Theses and Dissertations

Alcoholism is a complex neurological disorder characterized by loss of control in limiting intake, compulsion to seek and imbibe ethanol, and chronic craving and relapse. It is suggested that the characteristic behaviors associated with the escalation of drug use are caused by long-term molecular adaptations precipitated by the drug’s continual administration. These lasting activity-dependent changes that underlie addiction-associated behavior are thought, in part, to depend on new protein synthesis and remodeling at the synapses. It is well established that mRNA can be transported to neuronal distal processes, where it can undergo localized translation that is regulated in a spatially restricted …

Characterization Of The Biological Role Of A Putative Porphyromonas Gingivalis Rna-Binding Protein, Ramana Cvitkovic

Theses and Dissertations

Porphyromonas gingivalis, a gram-negative anaerobic bacterium, is a major etiological agent in the initiation and progression of severe forms of periodontal disease. Oral bacteria like P. gingivalis are subject to continually changing conditions as a consequence of host eating, oral hygiene patterns and subgingival temperatures. As such survival requires an adaptive response to environmental cues, but little is known about the mechanism by which P. gingivalis controls co- and post-transcriptional regulation of RNA levels and potentially protein expression. RNA-binding proteins (RBPs) are evolutionarily conserved across species and are involved in such regulatory mechanisms. However, P. gingivalis currently has no identified …

Evolution And Divergence Of The Structural And Physical Properties Of Dna Binding By Methyl-Cytosine Binding Domain Family Members 2 And 3, Jason Cramer

Theses and Dissertations

The studies presented in this dissertation, Evolution And Divergence Of The Structural And Physical Properties Of DNA Binding By Methyl-Cytosine Binding Domain Family Members 2 And 3, pertain primarily to two key epigenetic regulators involved with the biological interpretation of methylated DNA marks. We provide insights into the emergence and evolution of the MBD2 and MBD3 and how those molecular entities influence heritable changes in gene activity. We further provide details regarding the mystery surrounding MBD3 function and the MBD2-mediated capacity of primitive animals to carry out methylation-specific epigenetic mechanisms. In chapter two, we describe the DNA binding properties of …

Mitochondrial Gene Expression In Human Mononuclear Cells, Monika Ruchala

Theses and Dissertations

MITOCHONDRIAL GENE EXPRESSION IN HUMAN MONONUCLEAR CELLS By Monika D. Ruchała, M.S. A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science at Virginia Commonwealth University. Virginia Commonwealth University, 2014. Director: Dr. James P. Bennett Jr, M.D., Ph.D., Bemiss Professor Departments of Neurology, Psychiatry and Physiology and Biophysics Adult neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS), have been intensively studied in recent years in pursuit of mechanisms responsible for origin and progression. One emerging theme is mitochondrial energetic deficiency as a mechanism of neuronal death. Recent descriptions of protocols to generate induced pluripotent stems …

Evaluation Of The Allometric Exponents In Prediction Of Human Drug Clearance, Da Zhang

Theses and Dissertations

Background. Allometric scaling (AS) is widely used in predicting human clearance (CL) based on animal data. Substantial prediction errors have been commonly observed and various modifications to AS have not provided a broad reliable improvement. In this study, an extensive data set was assembled including animal and human systemic CL and physiochemical properties. The allometric exponents were calculated based on multiple species AS and single-species AS methods. The correlations between the allometic exponents and physiochemical properties were evaluated in an attempt to find covariates that may explain the inter-compound variability in the allometric exponents. Lastly, the statistical approaches in analyzing …

Computational Study Of Protein-Protein Interactions In Misfolded States, Oscar Bastidas

Theses and Dissertations

Protein-protein interactions (PPI’s) play important roles in biological systems. In particular, intra-protein interactions help create and maintain correctly folded protein states and mutations that result in misfolded states may be associated with significant changes in PPI behavior. Six unrelated protein systems with known structure files, each consisting of a wild-type and mutant strain, were studied using the computational algorithm OpenContact©. OpenContact© is a simple tool that can be used to rapidly identify or map interactions “hot-spots” in a protein and was, consequently, used in this study as a starting point to examine the potential or possible role of PPI’s on …

Prediction Of Human Systemic, Biologically Relevant Pharmacokinetic (Pk) Properties Using Quantitative Structure Pharmacokinetic Relationships (Qspkr) And Interspecies Pharmacokinetic Allometric Scaling (Pk-As) Approaches For Four Different Pharmacological Classes Of Compounds, Gopichand Gottipati

Theses and Dissertations

This research developed and validated QSPKR models for predicting in-vivo human, systemic biologically relevant PK properties (i.e., reflecting the disposition of the unbound drug) of four, preselected, pharmacological classes of drugs, namely, benzodiazepines (BZD), neuromuscular blocking agents (NMB), triptans (TRP) and class III antiarrhythmic agents (AAR), as well as PK allometric scaling (PK-AS) models for BZD and NMB, using pertinent human and animal systemic PK information (fu, CLtot, Vdss and fe) from published literature. Overall, lipophilicity (logD7.4) and molecular weight (MW) were found to be the most important and statistically significant molecular properties, affecting biologically relevant systemic PK properties, and …

The Role Of Toll-Like Receptor 9 In Periodontitis, Paul Kim

Theses and Dissertations

Periodontitis is a biofilm-initiated inflammatory disease, resulting in soft tissue damage and alveolar bone loss. A nucleic acid sensor, toll-like receptor 9 (TLR9), has been recently implicated in periodontal inflammation. This study utilized an in vivo periodontitis model using TLR9 knockout (TLR9-/-) mice to assess the role of TLR9 in periodontitis. Significant bone loss was observed in wild type, but not in TLR9-/- mice. Further experiments using ex vivo assays revealed significantly higher IL-6 production in splenocytes of wild type mice compared to knockout cells in response to Porphyromonas gingivalis (a keystone pathogen for periodontitis) challenge. In conclusion, TLR9 contributes …

Historical Tidal Forest Composition And Contemporary Woody Recruitment Following Dam Removal From A Mid-Atlantic Coastal Plain Tidal Freshwater Wetland, Richard E. Ward Jr.

Theses and Dissertations

Tidal freshwater forest restoration after dam removal has been unexplored to date. This study elucidated pre-dam forest composition, as well as post-dam edaphic and microtopographical attributes and woody species recruiting along a narrow ecotone of a 29.3-ha tidal freshwater wetland. The ≈65-year-old historical forest (15 species, 200 stems ha-1) and ≈7-year-old contemporary forest (40 species and 11,009 stems ha-) community dominants were dissimilar (Fraxinus spp. vs. Liquidambar styraciflua, respectively). Pre-dam environmental conditions were unknown. Post-dam edaphic water content, organic matter, redox potential and microtopography differed significantly across tidal sites but were less variable in non-tidal sites. Shifts in the contemporary …

The Role Of Nitric Oxide Scavenging In Hemoglobin-Based Oxygen Carrier Induced Hypertension: Systemic And Microvascular Effects, Alan Ottarson

Theses and Dissertations

The purpose of this study was to identify the effects of a hemoglobin-based oxygen carrier, HBOC-201, on the cardiovascular system. Systemic cardiovascular parameters of mean arterial pressure (MAP), pulse pressure, heart rate, and oxygen saturation, as well as vascular resistance, were examined. A murine model of the cardiovascular system and microvasculature was employed. Sprague-Dawley rats (male; 230-530g; N = 13) were anaesthetised and surgically prepared for intravital microscopy of the spinotrapezius muscle. Increasing doses of HBOC-201 (2 mg/kg, 22 mg/kg, 230 mg/kg, and 780 mg/kg) and an iso-oncotic volume control were administered to assess for a dose-response relationship. MAP displayed …

Reversed-Phase Ion-Pairing Ultra Performance Liquid Chromatography-Mass Spectrometry In Characterization Of Glycosaminoglycans, Alhumaidi Alabbas

Theses and Dissertations

Glycosaminoglycans (GAGs) are a family of linear bio-polysaccharides, which are heterogeneously modified with negatively charged sulfate and carboxylate groups. They are located on every cell surface, extracellular matrix or intracellular space in the body. GAGs are composed of alternating units of an amino sugars (glucosamine or galactosamine) and hexuronic acid/hexose (iduronic acid, glucoronic acid/ or galactose), which are linked by glycosidic bonds with different geometries. In recent years, GAGs have attracted considerable interest. GAGs play vital roles in fundamental biological processes, such as hemostasis, angiogenesis, cell signaling, growth and differentiation. Thus, GAGs contribute to a number of diseases such as …

Fabrication Of Nanoporous Gold And Biological Applications, Badharinadh Uppalapati

Theses and Dissertations

FABRICATION OF NANOPOROUS GOLD AND BIOLOGICAL APPLICATIONS By Badharinadh Uppalapati A Dissertation submitted in partial fulfillment of the requirements for the degree of Master of Science at Virginia Commonwealth University. Virginia Commonwealth University, 2014 Major Director: Maryanne M. Collinson, Professor, Department of Chemistry Fabrication of nanoporous gold electrodes by dealloying Au:Ag alloys has attracted much attention in sensing applications. In the first part of this work, the electrochemical response of the redox active molecule, potassium ferricyanide, in a solution of bovine serum albumin in buffer, serum or blood was studied using nanoporous gold and comparisons made to planar gold. Nanoporous …

Development Of Bivalent Ligands Targeting The Putative Ccr5-Mor Heterodimer, Thomas Raborg

Theses and Dissertations

Chemokine receptor CCR5 (CCR5) is a G-protein coupled receptor (GPCR) predominantly expressed on leukocytes, or white blood cells.1–3 During inflammation, the body releases chemokines that bind to receptors such as CCR5 and attract leukocytes to the area of inflammation, leading to an immunological response.1 CCR5 is also an important receptor in the human immunodeficiency virus's (HIV-1) invasion of host cells, as CCR5 acts as a co-receptor that facilitates HIV-1 viral entry.4,5 The continued destruction of leukocytes as a result of HIV-1 viral entry produces a disease state called acquired immunodeficiency syndrome (AIDS).5 Of note, this receptor is also expressed on …

Fabrication Of Micropatterns For The Spatial Control Of Cell Propagation And Differentiation, Mahmoud Moustafa

Theses and Dissertations

Challenges in the development of successful cell therapies involve engineering and control of cues to regulate the balance between differentiation and self-renewal. However, the complexity of architecture and function make this an intriguing problem in the context of forming functional connections. Here we present the design and fabrication of microstructured scaffolds that present a biomimetic framework along which neural cell lines can organize into oriented constructs. Specifically, we show microfabricated non-linear architectures that promote cellular fate related to propagation of human neuroblastoma cells and directed differentiation towards neurons. By mimicking biological networks that allow for spreading of the cells instead …

A Route To Discover Small Molecule Inhibitors Of Psaa, A Potential Target For Streptococcus Pneumoniae, Ahmad J. Obaidullah

Theses and Dissertations

Due to the development of multidrug resistance in Streptococcus pneumoniae, research has begun to define new drug targets for pneumonia therapy. Different research groups have identified a lipoprotein, PsaA that is important for pneumonia virulence. PsaA is a manganese transporter that is required for bacterial virulence and growth. We have employed computer modeling to virtually screen a small-molecule database for inhibition of PsaA function by targeting the metal binding pocket, performing receptor-based virtual screening and molecular docking and scoring to identify potential inhibitors of PsaA function. We have developed an assay for screening compounds, including the use of a PsaA …

Therapeutic Efficacy Of Combination Of Mtor Inhibitors And Ampk Activators In Non-Small Cell Lung Cancer., Grinal Corriea

Theses and Dissertations

Pemetrexed (PTX), an antifolate drug, has been approved by the US FDA for first line therapy of mesothelioma and non-small cell lung cancer. In addition to its primary site of action on thymidylate synthase (TS), PTX also inhibits the second folate-dependent enzyme of purine biosynthesis aminoimidazolecarboxamide ribonucleotide formyltransferase (AICART). The accumulation of the substrate for AICART, ZMP, in PTX-inhibited cancer cells leads to activation of AMP-activated protein kinase (AMPK) with subsequent inhibition of mammalian target of rapamycin (mTOR) and hypophosphorylation of its downstream targets responsible for protein synthesis and cell proliferation. Inhibitors of mTORC1 like Rapamycin and its analogs (rapalogs) …

Affinity Enrichment And Mass Spectrometric Quantitation Of Protein Carbonyls, Suresh Narayanasamy

Theses and Dissertations

The importance of the role of oxidative stress in aging and numerous age-related diseases has become undeniable due to enormous weight of supporting evidence from the field of free radical biology. One of the most prominent oxidative modifications of proteins is the introduction of carbonyl groups. As with oxidative stress, protein carbonylation has been correlated with various disease states and natural aging. While protein carbonyls are relatively stable, reproducible detection and modification site localization are still challenging. This thesis details attempts to improve the analytical methodology used for the identification and quantitation of carbonylated proteins. We have studied the impact …

An Automated Dental Caries Detection And Scoring System For Optic Images Of Tooth Occlusal Surface, Leila Ghaedi

Theses and Dissertations

Dental caries are one of the most prevalent chronic diseases. Worldwide 60 to 90 percent of school children and nearly 100 percent of adults experienced dental caries. The management of dental caries demands detection of carious lesions at early stages. The research of designing diagnostic tools in caries has been at peak for the last decade. This research aims to design an automated system to detect and score dental caries according to the International Caries Detection and Assessment System (ICDAS) guidelines using the optical images of the occlusal tooth surface. There have been numerous works that address the problem of …

Domestic Violence: Contemporary Interventions And The Rise Of Specialized Domestic Violence Units, Laura E. Anderson

Theses and Dissertations

This dissertation examines recidivism for domestic violence offenders under both traditional probation and specialized probation conditions. This research compares recidivism at a traditional probation locality (Riverside Criminal Justice Services) and a specialized domestic violence unit (Chesterfield Community Corrections Services) in order to determine the nature of recidivism at both localities. In addition, the research aims to identify individual risk factors which are statistically associated with recidivism. The research is based on secondary data and draws on offender criminal records generated by the Virginia State Police, as well the extraction of information from probation files at both localities. The multivariate models …

Novel 3d Head And Neck Cancer Model To Evaluate Chemotherapeutic Efficacy, Kelly Morgan

Theses and Dissertations

HNSCC accounts for 7 percent of all new cancer occurrences. Despite currently available treatments, there continues to be a high mortality and recurrence rate in HNSCC. Well over 50 percent of all cancer patients receive chemotherapy as a standard treatment. However, only 5 percent of these cases have been shown to help with treatment of the disease. Formerly, two options were available for drug testing: in vivo animal models, and in vitro two-dimensional models. While in vivo models remain the most representative, their use is burdened by high costs, time constraints, and ethical concerns. 2D models are simple to use …