Digital Commons Network^™

Inferring Gene Regulatory Networks From Expression Data Using Ensemble Methods, Janusz Slawek

Theses and Dissertations

High-throughput technologies for measuring gene expression made inferring of the genome-wide Gene Regulatory Networks an active field of research. Reverse-engineering of systems of transcriptional regulations became an important challenge in molecular and computational biology. Because such systems model dependencies between genes, they are important in understanding of cell behavior, and can potentially turn observed expression data into the new biological knowledge and practical applications. In this dissertation we introduce a set of algorithms, which infer networks of transcriptional regulations from variety of expression profiles with superior accuracy compared to the state-of-the-art techniques. The proposed methods make use of ensembles of …

Hospital: A Creature Of Duality, Gordon Mccormick

Theses and Dissertations

Hospitals can no longer be thought of as simply healing machines--they are healing organisms. It is Nature that permits every miracle of medicine, and it is Science that permits our understanding of medicine. By combining the two into a single idea, we aim to strike a balance between the duality of Nature and Technology, in order to design a space that relies more on the healing powers of Nature and less on the intrusiveness of Technology.

Benthic Macroinvertebrate Subsampling Effort And Taxonomic Resolution For Bioassessments Of Streams In The James River Watershed Of Virginia, Laurel Williams

Theses and Dissertations

Benthic macroinvertebrate diversity influences stream food web dynamics, nutrient cycling and material exchange between the benthos and the water column. Stream bioassessment has moved to the forefront of water quality monitoring in terms of benthic macroinvertebrate diversity in the recent past. The objectives of this study were to determine optimum subsample size and level of taxonomic resolution necessary to accurately and precisely describe macroinvertebrate diversity in streams flowing in the Piedmont province of the James River watershed in Virginia. Forty-nine sampling sites were selected from streams within the Piedmont Physiographic Province of the James River watershed. Ten sites were randomly …

Results Of 2013 Macroalgal Monitoring And Recommendations For Future Monitoring In Great Bay Estuary, New Hampshire, Elisabeth Cianciola, David M. Burdick

PREP Reports & Publications

The recently designated nitrogen impairment and reports of elevated macroalgal growth in Great Bay Estuary indicate ecological imbalance. However, reversing the Estuary’s ecological decline will require commitment of considerable resources and is complicated by the variety of sources that deliver nitrogen to the Estuary and the intermittent nature of historic macroalgal monitoring. To advance our understanding of the macroalgal and nitrogen dynamics of the Estuary, data were collected via three approaches: 1) assessing plant cover and biomass along transects; 2) assessing plant cover at randomly selected points; and 3) comparing the nitrogen isotope ratios of macroalgae collected from different habitats. …

Abstracts 2014: Highlights Of Student Research And Creative Endeavors, Columbus State University

Abstracts: Highlights of Student Research and Creative Endeavors

No abstract provided.

Indy Encodes A Regulator Of Intermediary Metabolism That Modulates Longevity In Drosophila Melanogaster, Ryan P. Rogers

Doctoral Dissertations

The Drosophila I’m Not Dead Yet (Indy) gene encodes a plasma membrane transporter of Krebs cycle intermediates, with robust expression in tissues associated with metabolism. Reduced INDY alters metabolism and extends longevity in a manner similar to caloric restriction (CR) with few biological tradeoffs; however, little is known about the tissue specific physiological effects of INDY reduction or how such changes contribute to fly health and longevity. The experiments described in this dissertation are focused on the effects of INDY reduction in the Drosophila midgut due to the importance of intestinal tissue homeostasis in healthy aging and longevity. The expression …

A Facile Route To Tailoring Peptide-Stabilized Gold Nanoparticles Using Glutathione As A Synthon, Rosina Ho Wu, Tan P. Nguyen, Grant W. Marquart, Thomas J. Miesen, Theresa Mau, Marilyn R. Mackiewicz

Chemistry Faculty Publications and Presentations

The preparation of gold nanoparticles (AuNPs) of high purity and stability remains a major challenge for biological applications. This paper reports a simple synthetic strategy to prepare water-soluble peptide-stabilized AuNPs. Reduced glutathione, a natural tripeptide, was used as a synthon for the growth of two peptide chains directly on the AuNP surface. Both nonpolar (tryptophan and methionine) and polar basic (histidine and dansylated arginine) amino acids were conjugated to the GSH-capped AuNPs. Ultracentrifugation concentrators with polyethersulfone (PES) membranes were used to purify precursor materials in each stage of the multi-step synthesis to minimize side reactions. Thin layer chromatography, transmission electron …

The Role Of Cytoprotective And Non-Protective Autophagy In Radiation Sensitivity In Breast Tumor Cells, Jade Le

Theses and Dissertations

In general, ionizing radiation promotes cytoprotective autophagy in a majority of breast tumor cells. Previous studies from our laboratory indicated that radiation (5x2 Gy) induces cytoprotective autophagy in MCF-7 cells. In the current work, inhibition of autophagy by silencing of Beclin-1 in MCF-7 cells resulted in an increase in sensitivity to radiation based both on cell number and clonogenic survival; however, there was no increase in apoptosis and the basis for this sensitization is currently under investigation. Unexpectedly, enhancement of autophagy by silencing of Bcl-2 also led to an increase in sensitivity to radiation, possibly through the conversion of cytoprotective …

Crossing Boundaries: Building A Model To Effectively Address Difference In Community Practice, Jason Sawyer

Theses and Dissertations

Community organizing has a rich tradition within the field of social work. Prevailing community practice models, approaches, and frameworks remain primarily based on practice wisdom, experience, and intuition. Difference, pervasive in various contemporary contexts of practice, largely mediates interactions at the community level. Although difference is addressed at various levels of the practice continuum and within the IFSW and NASW codes of ethics, few methodologically driven tools exist within the literature to guide practitioners. This grounded theory study initiates early development of a community practice model based on forging alliances across boundaries of difference. The Critical Difference Engagement model is …

Role Of Membrane Fusion Protein Ykt6 In Regulating Epithelial Cell-Cell And Cell-Matrix Adhesions., Supriya Joshi

Theses and Dissertations

Intercellular junctions and cell-matrix adhesions play important roles in the maintenance of epithelial integrity. Assembly and remodeling of the plasma membrane complexes are regulated by membrane trafficking and fusion. This thesis is aimed to elucidate the roles of an important membrane fusion protein, Ykt6, in the regulation of epithelial cell adhesion and migration. For the first time, we show that Ykt6 is essential for assembly of adherens junctions and tight junctions in human prostate epithelial cells. We also observed that Ykt6 negatively regulates both collective epithelial cell migration and cell invasion into Matrigel. The effects of YKT6 on epithelial junctions …

Conspecific Attraction In A Low-Density Population Of A Threatened Songbird, Daniel James Albrecht-Mallinger

Theses and Dissertations

Many organisms use both vegetation structure and social cues in selecting habitats. Many species of songbirds use the presence of breeding conspecifics as a social cue and sign of habitat quality, and can be induced to settle in unoccupied habitats by artificially broadcasting breeding song, a process referred to as “conspecific attraction”. In our study, we tested response to conspecific attraction a low-density population of the threatened Golden-winged Warbler (Vermivora chrysoptera) in Highland County, VA. Response to broadcast song was observed, with a modest increase in mean male abundance at survey points within 250 meters of treatments, and mean abundance …

Unification, Agency, Systemization, Intuition: My Art Making Process And Ideas, Zachary Duer

Theses and Dissertations

This essay is an attempt to describe my ideas about my work, my process, and my philosophy of art by examining five of the major pieces I created during the pursuit of a Master of Fine Arts degree at Virginia Commonwealth University. I will discuss the pieces in chronological order, first providing a description of the works’ salient characteristics, then delving into both my specific thoughts about the work as well as the background ideas that were pertinent to me during my process of creation.

Tethered Il-15 To Augment The Therapeutic Potential Of T Cells Expressing Chimeric Antigen Receptor: Maintaining Memory Potential, Persistence, And Antitumor Activity, Lenka Hurton

Dissertations and Theses (Open Access)

Tethered IL-15 to augment the therapeutic potential of T cells expressing chimeric antigen receptor: Maintaining memory potential, persistence, and antitumor activity

Adoptive immunotherapy can retarget T cells to CD19, a tumor-associated antigen (TAA) expressed on B-cell malignancies, by the expression of a chimeric antigen receptor (CAR). Infusion of CAR-modified T cells for the treatment B-cell malignancies has demonstrated promise in preclinical and clinical trials. These data highlight the ability of infused CD19-specific T cells to be synchronously activated by large burdens of CD19⁺ leukemia and lymphoma. This can lead to dramatic antitumor effects, but also exposes the recipient to …

Differential Regulation Of Iress In The Aurora A Mrna By Bfgf Through The Mtor Complex To Rc2 Modulates Aurora A Kinase Expression, Roy L. Voice Iii

Dissertations and Theses (Open Access)

Identifying the mechanisms that contribute to tumorigenesis is a major area of focus in our fight against cancer. Epithelial malignant tumors, such as breast, colon, ovarian and pancreatic cancers have been shown to overexpress proteins that control cell mitosis, growth, and proliferation. One of those proteins is the Aurora A kinase. Aurora A kinase is a member of a small family of kinases that contribute to mitotic events such as centrosome duplication, separation, and maturation. Aurora A overexpression leads to genomic instability, which can contribute to tumorigenesis, on the other hand, inhibiting Aurora A expression leads to apoptosis, making it …

Competition Between Grb2 And Plcγ1 For Binding To Fgfr2 Regulates Phospholipase And Pten Activity, Leading To Cell Invasion And Proliferation, Zahra Timsah

Dissertations and Theses (Open Access)

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Fluctuations in the relative concentrations of proteins in non-stimulated cells can lead to aberrant signaling. In a novel interaction, the SH3 domain of Plcγ1 competes with the SH3 domain of Grb2 for binding to FGFR2 in a concentration-dependent manner. Consequently, reduction of cellular concentrations of Grb2 lead to receptor-dependent recruitment of unphosphorylated Plcγ1. Bringing of the phospholipase to the membrane in this way …

Mechanisms Underlying Distinct Egfr Versus Fgfr-3 And -1 Dependency In Human Bladder Cancer Cells, Tiewei Cheng

Dissertations and Theses (Open Access)

The epidermal growth factor receptor (EGFR) and fibroblast growth factor receptor (FGFR) are activated by gene amplification, mutation and overexpression in bladder cancer, which drives tumor development and progression. Both EGFR and FGFR inhibitors are currently being tested in clinical trials. However, bladder cancer (BC) cells show remarkably heterogeneous sensitivities to both inhibitors, and the molecular determinants of this heterogeneity are presently unclear. Therefore, in this study, using selective EGFR and FGFR inhibitors in BC cells, we demonstrated that FGFR3 and FGFR1 play largely non-overlapping roles in mediating proliferation and invasion in the distinct “epithelial” and “mesenchymal” subsets of human …

Gain-Of-Function Mouse Models To Investigate Biological Roles Of Prmt6, Alessandra Di Lorenzo

Dissertations and Theses (Open Access)

Gain-of-function Mouse Models to Investigate Biological Roles of PRMT6

Alessandra Di Lorenzo, Ph.D. Candidate

Mentor: Dr. Mark T. Bedford

Protein Arginine Methyltransferase 6 (PRMT6) is the histone tail writer that methylates the H3R2 (arginine 2 of histone H3) residue, which counteracts the activating H3K4me3 mark. PRMT6 has been shown to behave both as transcriptional co-repressor (i.e. trhrombospondin-1, p21, p53), and co-activator (nuclear receptors). The co-repressor function of PRMT6 is likely the result of H3K4me3 antagonism, while the mechanism by which PRMT6 exerts its co-activator function has yet to be elucidated. PRMT6 is over-expressed in several types of tumors including small …

The Association Between The Il-1 Pathway, Isaac C. Wun

Dissertations and Theses (Open Access)

Cutaneous malignant melanoma (CMM) is a potentially lethal malignancy that warrants attention and further research, as it is known to that there is an increasing rate of incidence in theUnited States, and it is also known that exposure to UV light is its most crucial risk factor, and family history of melanoma is also an important risk factor. Melanoma is an aggressive and lethal cancer in humans. There are an estimated new 132,000 melanoma cases annually worldwide, and the trend has doubled in the past 20 years. However, attempts to treat melanoma have encountered considerable resistance and remained ineffective. The …

Development Of A Multi-Purpose Automated Synthesis Module For Production Of Novel Pet Radiopharmaceuticals, I Hong Shih

Dissertations and Theses (Open Access)

Among radiopharmaceuticals of positron emission tomography (PET), ¹⁸F-Fluorodeoxyglucose (¹⁸F-FDG) made from commercialized automated synthesis module is the most frequently used in tumor diagnoses. But the false positive findings, such as infectious tissues and post-operative surgical conditions, show strong uptake of ¹⁸F-FDG in PET scans which requires extra clinical procedures to confirm the results. Moreover, the false negative findings, such as low glycolytic activity tumors, reduce the accuracy of PET scans. Therefore, there will be new PET radiopharmaceuticals to redeem the defects of ¹⁸FDG-PET applications.

Current commercialized automated synthesis modules are suitable for clinical use, but …

Systematic Methodology For The Identification Of A Novel Autosomal Dominant Retinitis Pigmentosa Disease-Causing Gene, Jennifer D. Churchill

Dissertations and Theses (Open Access)

Retinitis pigmentosa (RP) is an inherited retinal disease that leads to degeneration of the retina through loss of rod and cone photoreceptor cells and subsequent loss of vision. RP affects approximately 1.5 million people world-wide. Mutations causing autosomal dominant retinitis pigmentosa (adRP) have been identified in 23 different genes. However, these mutations only account for approximately 70% of known adRP cases in Caucasians of Western-European origin and for an even smaller percentage of cases in other ethnicities. My research aims to increase the number of known genes associated with adRP by using an array of advanced genetic techniques to search …

The Novel Upstream Regulator Of Fbxw7, Ji-Hyun Shin

Dissertations and Theses (Open Access)

SCF^FBXW7 is a tumor suppressor E3 ligase protein that targets numerous oncoproteins such as Cyclin E, c-Myc, c-Jun and MCL1. The deregulation of these proteins often leads to the proliferation of cancer cells. Thus, intracellular stability and functional activity of FBXW7 is critical for regulating cancer. However, there is a gap of knowledge about the intracellular signaling pathway or if there is another ubiquitin ligase that regulates FBXW7 stability. Here, I identify a novel mechanism of FBXW7 stability regulation which involves constitutive photomorphogenic 1 (COP1), AKT and CSN6 (i.e. the COP9 signalosome 6).

COP1 is an E3 ubiquitin ligase …

Use Of Positron Emission To Mography For Proton Therapy Verification, Jongmin Cho

Dissertations and Theses (Open Access)

Positron emission tomography (PET), a tool commonly used for cancer staging and response monitoring, has recently been used for proton therapy verification. By imaging tissue activation following proton treatment, attempts have been made to verify proton dose and range. In this dissertation, two novel approaches were developed and tested for the purpose of help improve the proton dose and range estimation as well as verification.

Although there are still some challenges, attempts for proton dose verification using PET has been made by comparing Monte Carlo dose and PET simulations with treatment planned dose and measured PET. In this approach, …

Imbalance Between Neutrophil Elastase And Elafin Promotes Breast Cancer Growth And Progression, Joseph Anthony Caruso

Dissertations and Theses (Open Access)

Elafin, an endogenous serine protease inhibitor, is a critical component of the epithelial barrier against neutrophil elastase (NE) activity. The central hypothesis examined in this dissertation was that elafin has tumor suppressive properties in breast cancer. In support of this hypothesis, immunohistochemical (IHC) analysis revealed that elafin was downregulated in the majority of invasive breast tumors and a subset of pre-invasive ductal carcinoma in situ (DCIS) compared to elafin expression in the normal mammary epithelium. To understand the role of elafin in the mammary epithelium and the impetus for its downregulation during breast tumorigenesis, primary and immortalized human mammary epithelial …

Structure Based Prediction Of Drug-Protein Interactions At Allosteric Sites: To Wards Direct Inhibition Of The Ras Oncogene, Harrison Hocker

Dissertations and Theses (Open Access)

Ras is a monomeric G-protein that mediates multiple signaling pathways. When bound to GTP, Ras binds to and activates effectors and when bound to GDP it does not. Somatic mutations occur in ~15% of all human cancers and cause Ras to be predominantly bound to GTP. Recently, several studies revealed that Ras exists in an ensemble of at least two states when bound to GTP. In the state 1 conformation, Ras is unable to properly bind effectors but holds potential for binding ligands. Conversely, at allosteric sites, state 2 conformations readily bind effectors but not ligands.

To incorporate the flexibility …

Anti-Gd2 Etoposide-Loaded Immunoliposomes For The Treatment Of Gd2 Positive Tumors, Brandon S. Brown

Dissertations and Theses (Open Access)

Systemic chemotherapeutics remain the standard of care for most malignancies even though they frequently suffer from narrow therapeutic index, poor serum solubility, and off-target effects. Monoclonal antibodies that specifically bind antigens overexpressed on many tumors such as the ganglioside, GD2, can be conjugated to drug-loaded liposomes to create a targeted drug delivery system. In this study, we have encapsulated etoposide, a topoisomerase inhibitor effective against a wide range of cancers, in surface modified liposomes decorated with anti-GD2 antibodies. We characterized the properties of the liposomes using a variety of methods including dynamic light scattering, electron microscopy, and Fourier transformed infrared …

Image-Guided Proton Therapy For Online Dose-Evaluation And Adaptive Planning, Joey P. Cheung

Dissertations and Theses (Open Access)

The main advantage for using protons in radiotherapy is their finite range in patients, allowing for potential improved sparing of normal tissues. However, this comes at a cost of increased sensitivity to range uncertainties. Density changes along the beam path will affect the proton range and the resultant dose distribution, making it difficult to estimate the impact of visible anatomic changes to the patient dose distribution. In order to better understand the effect of anatomy change on proton dose, some form of treatment-time verification is required and methods to correct for observed changes would be beneficial. Therefore, this project aims …

Bioactivity And Cell-Mediated Targeting Of Multistage Nanoporous Silicon Particles, Jonathan O. Martinez

Dissertations and Theses (Open Access)

Progress in drug delivery approaches have not adequately translated into clinical advances in the diagnosis or treatment of inflammatory disorders (e.g., cancer). This disconnect is rooted in the inefficient delivery of imaging and therapeutic agents to the inflamed site upon systemic delivery. A multitude of biological barriers pose insurmountable obstacles limiting the ability of the agent to effectively reach and accumulate at the target site. Nanoparticles (NP) surfaced as potential vectors to encapsulate and deliver biological agents. However, even after surface decoration, NP have failed to evade biological barriers (i.e., MPS) and to accumulate at the tumor site at therapeutic …

Methodological Development Of A Multi-Parametric Quantitative Imaging Biomarker Framework For Assessing Treatment Response With Mri, Ryan J. Bosca

Dissertations and Theses (Open Access)

Quantitative imaging biomarkers (QIBs) are increasingly being incorporated into early phase clinical trials as a means of non-invasively assessing the spatially heterogeneous treatment response to anticancer therapies, particularly as indicators for early response. MR QIBs are derived from the analysis of in vivo imaging data, such as that acquired via dynamic contrast enhanced (DCE), dynamic susceptibility enhanced (DSC), and diffusion tensor imaging (DTI). To date, preclinical and clinical applications of such QIBs have provided strong evidence for potential efficacy, but efforts to create meaningful estimates of localized treatment response using multiple QIBs have been stifled by the need for rigorous …

Eye-Tracking Measures Of Attentional Bias In Cocaine Dependent Subjects, Nadeeka Dias

Dissertations and Theses (Open Access)

Cocaine-dependent (CD) subjects show evidence of attentional bias toward cocaine-related cues, and this measure of cue-reactivity is predictive of craving and relapse. In previous work, cue-reactivity and attentional bias have been assessed by models that present drug-relevant stimuli (e.g., cocaine-specific Stroop task) and measure physiological and behavioral reactivity (e.g., heart rate, reaction times). Studies have indicated competition between the higher-order cortical processes (frontal eye-fields, DLPFC) in voluntary eye control (i.e., anti-saccades) and more reflexive saccades driven by involuntary midbrain (superior colliculus) perceptual input (i.e., pro-saccades). In addition, neuroimaging studies in patients with cocaine dependence have shown activation in frontal regions …

Role Of Talin1 Phosphorylation In Beta1 Integrin Activation And Prostate Cancer Metastasis, Jung-Kang Jin

Dissertations and Theses (Open Access)

Talins are adaptor proteins that regulate focal adhesion signaling by conjugating integrins to the cytoskeleton. Talins directly bind and activate integrins but the mechanism by which this occurs is unknown. As integrin activation and overexpression of talins promote prostate cancer metastasis, understanding the mechanism by which talins activate integrins will better elucidate their roles in Prostate cancer metastasis. Phosphorylation of talins on serine 425 has been associated with β1 integrin functions. Work in this dissertation tested the hypothesis that increased talin1 S425 phosphorylation was required for β1 integrin activation and promotion of prostate cancer metastasis.

I first used shRNA to …