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Virginia Commonwealth University Graduate And Professional Programs Bulletin [2010], Virginia Commonwealth University

VCU Bulletins

Graduate and professional programs bulletin for Virginia Commonwealth University for the academic year 2010-2011. It includes information on academic regulations, degree requirements, course offerings, faculty, academic calendar, and tuition and expenses for graduate programs.

Virginia Commonwealth University Undergraduate Bulletin Courses [2010], Virginia Commonwealth University

VCU Bulletins

Listing of undergraduate courses for 2010-2011.

Putative Cis-Regulatory Elements Associated With Heat Shock Genes Activated During Excystation Of Cryptosporidium Parvum, Benjamin Cohn, Patricio A. Manque, Ana M. Lara, Myrna G. Serrano, Nihar U. Sheth, Gregory A. Buck

Microbiology and Immunology Publications

Abstract

Background

Cryptosporidiosis is a ubiquitous infectious disease, caused by the protozoan parasitesCryptosporidium hominis and C. parvum, leading to acute, persistent and chronic diarrhea worldwide. Although the complications of this disease can be serious, even fatal, in immunocompromised patients of any age, they have also been found to lead to long term effects, including growth inhibition and impaired cognitive development, in infected immunocompetent children. The Cryptosporidium life cycle alternates between a dormant stage, the oocyst, and a highly replicative phase that includes both asexual vegetative stages as well as sexual stages, implying fine genetic regulatory mechanisms. The …

Development And Vulnerability Factors In Adolescent Alcohol Use, Karen G. Chartier, Michie N. Hesselbrock, Victor M. Hesselbrock

Social Work Publications

This article provides an overview of the characteristics of adolescent alcohol use, normative and subgroup variations in drinking behavior, and important factors associated with an increased risk for developing alcohol problems in later adolescence and young adulthood. A parental/family history of alcoholism, temperament traits, conduct problems, cognitive functioning, alcohol expectancies, and peer and other social relations are identified as influencing an adolescent’s susceptibility for initiating a variety of alcohol use behaviors. The Deviance Prone Model, proposed by Sher (1991), is presented as an important tool for testing possible relationships among the various risk factors and their sequencing that leads to …

Traumatic Brain Injury And The Effects Of Diazepam, Diltiazem, And Mk-801 On Gaba-A Receptor Subunit Expression In Rat Hippocampus, Cynthia J. Gibson, Rebecca C. Meyer, Robert J. Hamm

Psychology Publications

Background

Excitatory amino acid release and subsequent biochemical cascades following traumatic brain injury (TBI) have been well documented, especially glutamate-related excitotoxicity. The effects of TBI on the essential functions of inhibitory GABA-A receptors, however, are poorly understood.

Methods

We used Western blot procedures to test whether in vivo TBI in rat altered the protein expression of hippocampal GABA-A receptor subunits α1, α2, α3, α5, β3, and γ2 at 3 h, 6 h, 24 h, and 7 days post-injuy. We then used pre-injury injections of MK-801 to block calcium influx through the NMDA receptor, diltiazem to block L-type voltage-gated calcium influx, …

A Survey Of Current Software For Network Analysis In Molecular Biology, Sterling Thomas, Danail Bonchev

Study of Biological Complexity Publications

Software for network motifs and modules is briefly reviewed, along with programs for network comparison. The three major software packages for network analysis, CYTOSCAPE, INGENUITY and PATHWAY STUDIO, and their associated databases, are compared in detail. A comparative test evaluated how these software packages perform the search for key terms and the creation of network from those terms and from experimental expression data.

A High-Throughput Cloning System For Reverse Genetics In Trypanosoma Cruzi, Michel Batista, Fabricio K. Marchini, Paola A.F. Celedon, Stenio P. Fragoso, Christian M. Probst, Henrique Preti, Luiz S. Ozaki, Gregory A. Buck, Samuel Goldenberg, Marco A. Krieger

Study of Biological Complexity Publications

Background

The three trypanosomatids pathogenic to men, Trypanosoma cruzi, Trypanosoma brucei andLeishmania major, are etiological agents of Chagas disease, African sleeping sickness and cutaneous leishmaniasis, respectively. The complete sequencing of these trypanosomatid genomes represented a breakthrough in the understanding of these organisms. Genome sequencing is a step towards solving the parasite biology puzzle, as there are a high percentage of genes encoding proteins without functional annotation. Also, technical limitations in protein expression in heterologous systems reinforce the evident need for the development of a high-throughput reverse genetics platform. Ideally, such platform would lead to efficient cloning and …

Localized Surface Plasmon Resonance Enhanced Magneto-Optical Activity In Core-Shell Fe-Ag Nanoparticles, L. Wang, K. Yang, C. Clavero, A. J. Nelson, K. J. Carroll, E. E. Carpenter, R. A. Lukaszew

Chemistry Publications

Metallic nanoparticles (NPs) are suitable platforms for miniaturized biosensing based on their optical and magneto-opticalproperties. It is possible to enhance the sensitivity of specific kinds of NPs by exploiting their optical and magneto-opticalproperties under suitable external magnetic field modulation. Here, the magneto-opticalproperties of Fe–Ag core-shell ferromagnet-noble metal NPs have been investigated as a function of the incident light frequency. For Fe–Ag NPs with a concentration ratio around 25:75, an optical absorption band centered at 3 eV due to localized surface plasmon resonance (LSPR) excitation is observed. A strong enhancement of the Faraday rotation is also observed, greatly exceeding the value …

Spectrally Tunable Magnetic Nanoparticles Designed For Distribution/Recollection Applications, Nicholas B. Mcdowall, James R. Wilkins, Kyler J. Carroll, Jarrod D. Edwards, Jean D. Nelson, Everett E. Carpenter, Garry P. Glaspell

Chemistry Publications

The comprehensive goal of this research is the synthesis and characterization of nanomaterials that are spectrally tunable in terms of their electromagnetic signal, are robust, magnetic (allowing their piloted movement), and have the potential to be functionalized for the detection of CBRNE threats. Various chemical methods were utilized for synthesis of magnetic (iron) and luminescent rare earth (RE) components, and their mixtures. Effects of integrating an iron core into RE luminescent lattices (excited by UV, emit in the VIS) were investigated. The determination of the optimum balances between magnetic and luminescent components such that the magnetism was maximized while maintaining …

Genome-Scale Metabolic Analysis Of Clostridium Thermocellum For Bioethanol Production, Seth B. Roberts, Christopher M. Gowen, J. Paul Brooks, Stephen S. Fong

Chemical and Life Science Engineering Publications

Background

Microorganisms possess diverse metabolic capabilities that can potentially be leveraged for efficient production of biofuels. Clostridium thermocellum (ATCC 27405) is a thermophilic anaerobe that is both cellulolytic and ethanologenic, meaning that it can directly use the plant sugar, cellulose, and biochemically convert it to ethanol. A major challenge in using microorganisms for chemical production is the need to modify the organism to increase production efficiency. The process of properly engineering an organism is typically arduous.

Results

Here we present a genome-scale model of C. thermocellum metabolism, iSR432, for the purpose of establishing a computational tool to study the …

A Signal Processing Method To Explore Similarity In Protein Flexibility, Simina Vasilache, Nazanin Mirshahi, Soo-Yeon Ji, James Mottonen, Donald J. Jacobs, Kayvan Najarian

Computer Science Publications

Understanding mechanisms of protein flexibility is of great importance to structural biology. The ability to detect similarities between proteins and their patterns is vital in discovering new information about unknown protein functions. A Distance Constraint Model (DCM) provides a means to generate a variety of flexibility measures based on a given protein structure. Although information about mechanical properties of flexibility is critical for understanding protein function for a given protein, the question of whether certain characteristics are shared across homologous proteins is difficult to assess. For a proper assessment, a quantified measure of similarity is necessary. This paper begins to …

Parametric Frailty Models For Clustered Data With Arbitrary Censoring: Application To Effect Of Male Circumcision On Hpv Clearance, Xiangrong Kong, Kellie Archer, Lawrence H. Moulton, Ronald H. Gray, Mei-Cheng Wang

Biostatistics Publications

Background

In epidemiological studies, subjects are often followed for a period during which study outcomes are measured at selected time points, such as by diagnostic testing performed on biological samples collected at each visit. Although test results may indicate the presence or absence of a disease or condition, they cannot provide information on when exactly it occurred. Such study designs generate arbitrarily censored time-to-event data, which can include left, interval and right censoring. Adding to this complexity, the data may be clustered such that observations within the same cluster are not independent, such as time to recovery of an infectious …

Making Informed Choices About Microarray Data Analysis, Mark A. Reimers

Biostatistics Publications

This article describes the typical stages in the analysis of microarray data for non-specialist researchers in systems biology and medicine. Particular attention is paid to significant data analysis issues that are commonly encountered among practitioners, some of which need wider airing. The issues addressed include experimental design, quality assessment, normalization, and summarization of multiple-probe data. This article is based on the ISMB 2008 tutorial on microarray data analysis. An expanded version of the material in this article and the slides from the tutorial can be found at http://www.people.vcu.edu/~mreimers/OGMDA/index.html.

An Analytical Tool For Elucidating Ion-Channel Molecular Mechanisms From Macroscopic Current Traces, Miguel Fribourg, Belen Galocha-Iraguen, Fernando Las Heras-Andres, Diomedes E. Logothetis, Vladimir Brezina

Physiology and Biophysics Publications and Presentations

Building models to describe the dynamics of macroscopic currents through ion channels has been the object of numerous studies in the literature with the aim of understanding ion-channel function. Following a perturbation, typically a step in voltage or ligand concentration, the response is formed by a combination of different processes such as activation or inactivation that pull the measured quantity (macroscopic current) in the same or opposite directions with different strengths and different time constants. Although this dynamic response can be readily recorded in time, the relationship between the underlying processes cannot be easily teased apart without structural analysis or …

A Molecular Dynamics Investigation Of Lipid Bilayer Perturbation By Pip2, Dmitry Lupyan, Mihaly Mezei, Diomedes E. Logothetis, Roman Osman

Physiology and Biophysics Publications and Presentations

Abstract

Phosphoinositides like phosphatidylinositol 4,5-bisphosphate (PIP₂) are negatively charged lipids that play a pivotal role in membrane trafficking, signal transduction, and protein anchoring. We have designed a force field for the PIP₂ headgroup using quantum mechanical methods and characterized its properties inside a lipid bilayer using molecular dynamics simulations. Macroscopic properties such as area/headgroup, density profiles, and lipid order parameters calculated from these simulations agree well with the experimental values. However, microscopically, the PIP₂ introduces a local perturbation of the lipid bilayer. The average PIP₂ headgroup orientation of 45° relative to the bilayer …

Long-Term Fish Oil Supplementation Induces Cardiac Electrical Remodeling By Changing Channel Protein Expression In The Rabbit Model, Xulin Xu, Min Jiang, Yuhong Wang, Timothy Smith, Clive M. Baumgarten, Mark A. Wood, Gea-Ny Tseng

Physiology and Biophysics Publications and Presentations

Clinical trials and epidemiological studies have suggested that dietary fish oil (FO) supplementation can provide an anti-arrhythmic benefit in some patient populations. The underlying mechanisms are not entirely clear. We wanted to understand how FO supplementation (for 4 weeks) affected the action potential configuration/duration of ventricular myocytes, and the ionic mechanism(s)/molecular basis for these effects. The experiments were conducted on adult rabbits, a widely used animal model for cardiac electrophysiology and pathophysiology. We used gas chromatography - mass spectroscopy to confirm that FO feeding produced a marked increase in the content of n-3 polyunsaturated fatty acids in the phospholipids of …

Understanding The Transition Between High School And College Mathematics And Science, S. A. Culpepper, C. Basile, C. A. Ferguson, J. A. Lanning, M. A. Perkins

Journal of Mathematics and Science: Collaborative Explorations

Mathematics and science education is gaining increasing recognition as key for the well-being of individuals and society. Accordingly, the transition from high school to college is particularly important to ensure that students are prepared for college mathematics and science. The goal of this study was to understand how high school mathematics and science course-taking related to performance in college. Specifically, the study employed a nonparametric regression method to examine the relationship between high school mathematics and science courses, and academic performance in college mathematics and science courses. The results provide some evidence pertaining to the positive benefits from high school …

The Unprecedented Event: Acknowledging Badiou’S Challenge To Art And Its Education, Jan Jagodzinski

Journal of Social Theory in Art Education

In terms of this year’s journal theme, ”unprecedented,” there is no other contemporary philosopher who has a more radical notion than Alain Badiou when it comes to theorizing the new; that is, the emergence of an unprecedented Event ex nihilio—not novel or innovative, but free of the authority of any prior example—to make a truth claim. For art educators, especially for the Social Caucus, Badiou offers a challenge to what has largely captured the theoretical writing in this journal — namely aesthetics and representation. As well intentioned as these theorizations have been concerning identity politics and critical theory stemming from …

Restageactivist Art/Disruptive Technologies, Karen Keifer-Boyd

Journal of Social Theory in Art Education

In this article, I explore, with you, artists’ socio-political disruptions with communication technologies to inspire political action and social change, and how such art can be environmentally and socially useful. How does art function politically? What is activist art? What non-violent forms of dissent or disruptions to harmful practices are possible today with digital technologies, and how do artists manifest political perspectives in their practice?

Historical Consciousness And Ethnicity: How Signifying The Past Influences The Fluctuations In Ethnic Boundary Maintenance, Paul Zanazanian

Ethnic Studies Review

Theorists tend to limit 'history's' role in the dynamics of ethnicity to that generally played by collective memory. By bringing the notion of historical consciousness to the fore, new possibilities may, however, emerge for discerning how history, as one cultural mode of remembering among many others, impacts both ethnicity delineations and fluctuations in boundary maintenance. In encapsulating the many forms of commemoration as well as the different dimensions of historical thinking, the contribution of historical consciousness accordingly lies on how group members historicize temporal change for moral orientation in time. By likewise signifying past events for negotiating their ethnicity and …

Chicano/Mexican "Culture" As A Rational Instrument In The Human Sciences, Alexandro José Gradilla

Ethnic Studies Review

The use of "culture" as an analytical category by social scientists presents an opportunity to examine how professional discursive formations are used to make empirical assertions. The social fact of culture is neither uniform nor unitary. Traditionally, culture has been thought of as a product of disciplinary research, not necessarily a variable for empirical study. When culture is used as a tool or instrument of scientific methodology, it loses its fluid nature as a disciplinary discourse. In this essay, I examine the specific discussion of the epidemiologic health paradox that states that the Chicano/Mexican immigrant "culture" serves as a protective …

The Effects Of Pet Ownership On Physical Well-Being In Older Adults, Tami Pohnert

Theses and Dissertations

A large percentage of Americans own pets which may impact their health. This study examines pet ownership’s effect on well being in older adults looking at race/ethnicity. A sample of 6,565 older adults (>60) was selected from the Third National Health and Nutrition Survey. Pet owners comprised 28.3% of the sample. The theories of symbolic interaction and social integration were used to examine pet ownership’s effect on physical components of well-being. The descriptive results showed statistically significant differences in age, education, income, and marital status between pet owners and non-pet owners. Pet owners were younger, more educate, higher income …

The Role Of The Ca2+-Dependent Protein Kinase, Camk-Ii, In Heart And Kidney Development In The Zebrafish, Danio Rerio, Sarah Rothschild

Theses and Dissertations

Ca2+/calmodulin-dependent protein kinase type II (CaMK-II) is a multifunctional serine/threonine kinase that is ubiquitously expressed throughout the lifespan of metazoans. Mammals encode four genes (α, β, γ, δ) that generate over forty splice-variants. CaMK-II is important in a myriad of functions, including ion channel regulation, cell-cycle progression, and long term potentiation. In adults, alterations in activation of CaMK-II induce cardiac arrhythmias and heart failure. Developmental roles for CaMK-II are not as well understood since mouse knockouts are embryonic lethal. Therefore the identification of other vertebrate CaMK-II genes will add to our understanding of development. Zebrafish encode seven catalytically active CaMK-II …

Biochemical Characterization Of Suppressor Of Ikk-Ε And Nak-Associated Protein 1, Jonathan Forbes

Theses and Dissertations

Innate immunity provides the first line of defense against invading pathogen by recognizing and mounting a response to the pathogenic challenge. Among the cellular mechanisms of the innate immune response, Toll-like receptor 3 (TLR3) recognizes viral dsRNA and signals subsequent production of type-I interferon. The TLR3:interferon signaling cascades contains a kinase complex composed of two kinases and a scaffold protein, NAK-associated protein 1 (NAP1). The role of NAP1 in modulating kinase activation or regulation is unknown. A key inhibitory protein identified in the TLR3:interferon pathway, silencer of inhibitor of κBα kinase ε (SIKE), blocks the activity of this kinase complex …

Role Of Oxidative Reactive Species And Antioxidants In Metabolism And Transport Of Therapeutic Drugs, Svetlana Verenich

Theses and Dissertations

Oxidative stress (OS) is a frequent complication of various disease conditions such as Alzheimer’s and Parkinson’s disease, atherosclerosis, preeclampsia, rheumatoid arthritis, diabetes including gestational diabetes, etc. OS is defined as an imbalance between the production of reactive species and the ability of an organism to detoxify the reactive intermediates and repair the damage. As a result of OS, the excess of reactive species such as oxygen superoxide (O2-), hydroxyl radical (OH), peroxynitrite (ONOO−), 4-hydroxynonenal (4HNE), etc., have a tendency to react with nearby proteins/nucleic acids/lipids changing their functionality or inactivating them completely. The organism has many ways to protect itself …

P53 Mediated Cell Motility In H1299 Lung Cancer Cells, Mi-Yon Choi

Theses and Dissertations

Studies have shown that gain-of- function mutant p53, AKT, and NFκB promote invasion and metastasis in tumor cells. Signals transduced by AKT and p53 are integrated via negative feedback between the two pathways. Tumor derived p53 was also indicated to induce NFκB gene expression. Due to the close relationship between p53/AKT and p53/NFκB, we hypothesized that AKT and NFκB can enhance motility in cells expressing mutant p53. Effects on cell motility were determined by scratch assays. CXCL5- chemokine is also known to induce cell motility. We hypothesized that enhanced cell motility by AKT and NFκB is mediated, in part, by …

Autotaxin: A Regulator Of Oligodendrocyte Differentiation, Larra Yuelling

Theses and Dissertations

In order for oligodendrocyte progenitor cells (OPCs) to differentiate into fully mature, myelinating oligodendrocytes, they must be specified at the correct times and undergo coordinated changes in both gene expression and morphology. As oligodendrocytes differentiate, they transition from a bipolar morphology into a morphology characterized by a complex network of multiple processes, which will eventually generate membranous structures necessary for myelination of axonal segments. As changes are observed in cellular morphology, oligodendrocytes also undergo changes in their gene expression profile and express genes necessary for both early and later stages of development such as olig1 and myelin basic protein (mbp), …

Amendment (2010)

Amendment, 2004-

Amendment is a VCU student-produced progressive literature and art journal that provides a platform for students to promote equality, tolerance, and social progression through artistic expression.

Virginia Dental Journal (Vol. 87, No. 1, 2010)

Virginia Dental Journal

No abstract provided.

Prediction Of Human Systemic, Biologically Relevant Pharmacokinetic (Pk) Properties Based On Quantitative Structure Pharmacokinetic Relationships (Qspkr) And Interspecies Pharmacokinetic Allometric Scaling (Pk-As), Prajakta Badri

Theses and Dissertations

This research developed validated QSPKR and PK-AS models for predicting human systemic PK properties of three, preselected, pharmacological classes of drugs, namely opioids, β-adrenergic receptor ligands (β-ARL) and β-lactam antibiotics (β-LAs) using pertinent human and animal systemic PK properties (fu,, CLtot, Vdss, fe) and their biologically relevant unbound counterparts from the published literature, followed by an assessment of the effect of different molecular descriptors on these PK properties and on the PK-AS slopes for CLtot and Vdss from two species (rat and dog). Lipophilicity (log (D)7.4) and molecular weight (MW) were found to be the most statistically significant and biologically …