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Loss Of Hdmx Leads To Alterations In Gene Expression And Inhibition Of Cell Growth In Tumor Cells With Wild-Type P53, Katherine Ann Heminger

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Mutations in the p53 tumor suppressor gene are among the most prevalent molecular abnormalities in human cancer. While half of all human tumors possess p53 mutations, inactivation of wild-type p53 can also occur through a variety of mechanisms that do not involve p53 gene mutation or deletion. This dissertation focuses on human tumor cell lines harboring wild-type p53 protein and elevated levels of HdmX and/or Hdm2, two critical negative regulators of p53 function. My hypothesis is that loss of HdmX in tumor cells with wild-type p53 and over-expressed HdmX, will activate p53 and induce p53 target genes leading to growth …

An Evolutionary Programming Algorithm For Automatic Chromatogram Alignment, Bonnie Jo Schwartz

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Scientists use liquid chromatography/mass spectrometry (LC/MS) instruments to measure metabolic responses to external stimuli. The data from these instruments can be distorted due to changes in the testing environment. Automating the removal of distortions is crucial in processing the data. The purpose of this thesis is to develop an algorithm that will automate the process.

The data produced by the LC/MS instrument were treated as images and image registration techniques were applied. A polynomial transformation function was assumed. An evolutionary programming algorithm was used to determine the coefficients of the polynomial. The data was manipulated to determine the best registration …

Processing Nano Graphene Plates (Ngps) And Ngp Nanocomposite, Yena Li

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In recent years numerous efforts worldwide are addressing all aspects of the rapid developing field of nanocomposites. However, the most important fillers-- carbon nanotube and carbon nanofiber - are expensive. In this study, our efforts are aimed at bridging the gap in cost and properties by providing a systematic study of alternative nano materials -- nano graphene plate (NGP) and related composites. We fabricated nano graphene plates through the detailed study of raw materials, chemical treatment methods and nano particle dispersion methods. A series of thermal expansion experiments were conducted to investigate the best condition to expand acid treated graphite …

Structural And Signaling Elements Important For The Efficient Degradation Of Bhmt Through Macroautophagy, Carol A. Mercer

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Healthy cells maintain a dynamic and responsive intracellular environment that is marked by the synthesis and degradation of proteins, complex macromolecules and organelles. Autophagy, literally "self-eating," is a mechanism that delivers cellular cargo to the lytic compartment for digestion. Defects in the regulation of autophagy have been implicated in pathologies such as cancer and neurodegenerative disease, making the study of its regulation compelling. However, few studies have looked at the regulation of mammalian autophagy as a function of a specific cargo protein. Previous studies had indicated that the metabolic enzyme betaine homocysteine methyltransferase (BHMT) is degraded through an autophagic mechanism. …

Comparative Characterization Of Superconducting Thin Films Fabricated By Different Techniques, Padma Prasuna S. Vemulakonda

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The goal of this thesis is to compare the chemical and compositional profiles, grain structure and critical current densities of superconducting Yttrium Barium Copper Oxide(Y1Ba2Cu3O7-x or YBCO) layers grown by different competing techniques on a variety of substrates and buffer layers. The idea is to check if there can be variation of cationic ratios, impurities, possible diffusion of substrate/buffer layer atoms into the YBCO for different processing methods and microstructures. Pulsed Laser Deposition (PLD), Metal Organic Deposition (MOD) and Metal Organic Chemical Vapor Deposition (MOCVD) films on Ion Beam Assisted Deposited (IBAD)-textured buffer layers and, Rolling Assisted Biaxial textured substrate …

Data Mining And Analysis On Multiple Time Series Object Data, Chunyu Jiang

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Huge amount of data is available in our society and the need for turning such data into useful information and knowledge is urgent. Data mining is an important field addressing that need and significant progress has been achieved in the last decade. In several important application areas, data arises in the format of Multiple Time Series Object (MTSO) data, where each data object is an array of time series over a large set of features and each has an associated class or state. Very little research has been conducted towards this kind of data. Examples include computational toxicology, where each …

An Analysis Of Neutral Drift's Effect On The Evolution Of A Ctrnn Locomotion Controller With Noisy Fitness Evaluation, Gregory Robert Kramer

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This dissertation focuses on the evolution of Continuous Time Recurrent Neural Networks (CTRNNs) as controllers for control systems. Existing research suggests that the process of neutral drift can greatly benefit evolution for problems whose fitness landscapes contain large-scale neutral networks. CTRNNs are known to be highly degenerate, providing a possible source of large-scale landscape neutrality, and existing research suggests that neutral drift benefits the evolution of simple CTRNNs. However, there has been no in-depth examination of the effects of neutral drift on complex CTRNN controllers, especially in the presence of noisy fitness evaluation. To address this problem, this dissertation presents …

Investigating The Role Of Subunit Iii In The Structure And Function Of Rhodobacter Sphaeroides Cytochrome C Oxidase, R. Ryan Geyer

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The role of subunit III (SIII) in cytochrome c oxidase structure and function was investigated using enzyme isolated from the bacterium Rhodobacter sphaeroides. Energy minimization calculations suggested that in the absence of SIII, subunit I (SI) adopted a more open conformation. This observation was tested through the use of limited proteolysis using, á-chymotrypsin. The results showed that in the absence of SIII the solution structures of wild-type and I/II oxidase were not significantly different, and that proteolysis occurred exclusively at the N and C-termini of SI. Upon inactivation of I/II oxidase by catalytic turnover, and subsequent digestion with the protease …

Functional Interplay Between Subthreshold Ion Channels In Preautonomic Neurons Of The Hypothalamic Paraventricular Nucleus In Health And Disease Conditions, Patrick M. Sonner

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Under normal conditions, blood pressure is tightly regulated through autonomic tonic and reflex mechanisms. However, when the set-point for blood pressure is chronically elevated, hypertension occurs. Hypertension if untreated can lead to further complications including heart failure, stroke and kidney failure. Elevated sympathetic outflow is known to contribute to the development and/or maintenance of hypertension, and while the hypothalamic paraventricular nucleus (PVN), a preautonomic center, has been implicated in the elevation of sympathetic activity during hypertension, the precise pathophysiological mechanisms underlying sympathoexcitation remain unclear. Subthreshold ion channels, including the A-type K ⁺(I _A) and the T-type Ca ^{2+ …}

Fabrication And Testing Of Scaffolds For Cell Growth From Ionic Liquid Solubilized Fibroin, Maneesh Kumar Gupta

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The advent of tissue engineering has spurred research into developing materials to act as scaffolds for tissue growth. These scaffolds require materials capable of mimicking the in vivo conditions so that tissues can be grown effectively in vitro. Silk is an attractive biomaterial for use in tissue engineering applications because of its slow degradation, excellent mechanical properties, and biocompatibility. The major objective of the research in this thesis is to demonstrate a simple method to cast films directly from silk fibroin dissolved in an ionic liquid. The films cast from the silk ionic liquid solution were found to support normal …

Comparative Microarray Data Mining, Shihong Mao

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As a revolutionary technology, microarrays have great potential to provide genome-wide patterns of gene expression, to make accurate medical diagnosis, and to explore genetic causes underlying diseases. It is commonly believed that suitable analysis of microarray datasets can lead to achieve the above goals. While much has been done in microarray data mining, few previous studies, if any, focused on multiple datasets at the comparative level. This dissertation aims to fill this gap by developing tools and methods for set-based comparative microarray data mining. Specifically, we mine highly differentiative gene groups (HDGGs) from given datasets/classes, evaluate the concordance of datasets …

C-Fos As A Proapoptotic Agent In Trail-Induced Apoptosis In Prostate Cancer Cells, Xiaoping Zhang, Liang Zhang, Hongmei Yang, Xu Huang, Hasan H. Otu, Towia A. Libermann, William C. Dewolf, Roya Khosravi-Far, Aria F. Olumi

Department of Electrical and Computer Engineering: Faculty Publications

Tumor necrosis factor–related apoptosis-inducing ligand (TRAIL)/Apo-2L promotes apoptosis in cancer cells while sparing normal cells. Although many cancers are sensitive to TRAIL-induced apoptosis, some evade the proapoptotic effects of TRAIL. Therefore, differentiating molecular mechanisms that distinguish between TRAIL-sensitive and TRAIL-resistant tumors are essential for effective cancer therapies. Here, we show that c-Fos functions as a proapoptotic agent by repressing the antiapoptotic molecule c-FLIP(L). c-Fos binds the c-FLIP(L) promoter, represses its transcriptional activity, and reduces c-FLIP(L) mRNA and protein levels. Therefore, c-Fos is a key regulator of c-FLIP(L), and activation of c-Fos determines whether a cancer cell will undergo cell death …

Serum Proteome Profiling Detects Myelodysplastic Syndromes And Identifies Cxc Chemokine Ligands 4 And 7 As Markers For Advanced Disease, Manuel Aivado, Dimitrios Spentzos, Ulrich Germing, Gil Alterovitz, Xiao-Ying Meng, Franck Grall, Aristoteles A. N. Giagounidis, Giannoula Klement, Ulrich Steidl, Hasan H. Otu, Akos Czibere, Wolf C. Prall, Christof Iking-Konert, Michelle Shayne, Marco F. Ramoni, Norbert Gattermann, Rainer Haas, Constantine S. Mitsiades, Eric T. Fung, Towia A. Libermann

Department of Electrical and Computer Engineering: Faculty Publications

Myelodysplastic syndromes (MDS) are among the most frequent hematologic malignancies. Patients have a short survival and often progress to acute myeloid leukemia. The diagnosis of MDS can be difficult; there is a paucity of molecular markers, and the pathophysiology is largely unknown. Therefore, we conducted a multicenter study investigating whether serum proteome profiling may serve as a noninvasive platform to discover novel molecular markers for MDS. We generated serum proteome profiles from 218 individuals by MS and identified a profile that distinguishes MDS from non-MDS cytopenias in a learning sample set. This profile was validated by testing its ability to …

Regional Mechanical Properties And Stress Analysis Of The Human Anterior Lens Capsule, Ryan M. Pedrigi, G. David, J. Dziezyc, J. D. Humphrey

Department of Mechanical and Materials Engineering: Faculty Publications

The lens capsule of the eye functions, in part, as a deformable support through which the ciliary body applies tractions that can alter lens curvature and corresponding refractive power during the process of accommodation. Although it has long been recognized that characterization of the mechanical properties of the lens capsule is fundamental to understanding this physiologic process as well as clinical interventions, prior data have been limited by one-dimensional testing of excised specimens despite the existence of multiaxial loading in vivo. In this paper, we employ a novel experimental approach to study in situ the regional, multiaxial mechanical behavior of …

A Scientific Foundation Of Collaborative Engineering, S. C.-Y. Lu, W. Elmaraghy, G. Schuh, R. Wilhelm

Department of Mechanical and Materials Engineering: Faculty Publications

Collaborative engineering is the practical application of collaboration sciences to the engineering domain. In today’s highly connected technology-driven economy, the production industry must rely on the best practices of collaborative engineering to stay competitive when designing, manufacturing, and operating complex machines, processes, and systems on a global scale. Despite its importance, collaborative engineering is currently more of a practiced art than a scientific discipline. A better understanding of how engineers should collaborate with all stakeholders to accomplish complex tasks that fulfill our increasing social responsibilities is a grand challenge. However, because we currently lack well-defined sciences of human collaboration, we …

Biological Opinion On The Operation Of The Missouri River Main Stem System, Operation And Maintenance Of The Missouri River Bank Stabilization And Navigation Project, And Operation Of The Kansas River Reservoir System

United States Army Corps of Engineers, Omaha District

The U.S. Army Corps of Engineers (Corps) has prepared this annual report for interested parties in accordance with reporting requirements of the Biological Opinion (BiOp) on the Operation of the Missouri River Main Stem System (System), Operation and Maintenance of the Missouri River Bank Stabilization and Navigation Project and Operation of the Kansas River Reservoir System, prepared by the U.S. Fish and Wildlife Service (USFWS) dated November 30, 2000, and the Amendment thereto, dated December 16, 2003. This annual report also documents the Corps activities implemented under the Missouri River Bank Stabilization and Navigation Fish and Wildlife Mitigation Project, Iowa, …

A “Sprinkler” Vegetative Treatment System, Jason Gross, Chris G. Henry

Department of Agricultural and Biological Systems Engineering: Presentations and White Papers

Vegetative Treatment Systems have historically been a practice for the treatment and utilization of open lot livestock wastes. Use of these systems has been rejuvenated in recent years. A “sprinkler” vegetative treatment area (VTA) has been designed and developed as a proof of concept for addressing challenges experienced with small and medium Animal Feeding Operations. The focus of this paper is to report on the design, economics, challenges and the lessons learned on the development of this system. Cost data shows the cost of a “sprinkler” VTS to range between $31 to $63/head, compared to $51 to $170/head for a …

Sharing Distance Education Courses Among Universities, Leon Schmacher, Thomas Brumm, John Slocombe, Jack L. Schinstock

Department of Agricultural and Biological Systems Engineering: Presentations and White Papers

Four universities collaborated to develop mechanized systems management (agricultural systems management, agricultural systems technology, etc.) courses to be shared via distance education. Funded by a USDA Higher Education Challenge Grant, these undergraduate and graduate courses were initially offered to students at Iowa State University, Kansas State University, the University of Missouri, and the University of Nebraska-Lincoln. This effort is affiliated with the Great Plains Interactive Distance Education Alliance (Great Plains IDEA).

The objectives of this cooperative effort were to: (1) develop a collaborative, multi-state educational effort to add depth and breadth to each university’s instructional program in mechanized systems management; …

Discrimination Of Bacteria And Bacteriophages By Raman Spectroscopy And Surface-Enhanced Raman Spectroscopy, Lindsay J. Goeller, Mark R. Riley

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Detection of pathogenic organisms in the environment presents several challenges due to the high cost and long times typically required for identification and quantification. Polymerase chain reaction (PCR) based methods are often hindered by the presence of polymerase inhibiting compounds and so direct methods of quantification that do not require enrichment or amplification are being sought. This work presents an analysis of pathogen detection using Raman spectroscopy to identify and quantify microorganisms without drying. Confocal Raman measurements of the bacterium Escherichia coli and of two bacteriophages, MS2 and PRD1, were analyzed for characteristic peaks and to estimate detection limits using …

Introducing Journal Of Biological Engineering, Mark R. Riley

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Welcome to Journal of Biological Engineering (JBE), the flagship publication of the Institute of Biological Engineering. Biological Engineering is a new and unique discipline that encompasses a wide range of engineering theory and practice connected to and derived from biology. This emerging science-based engineering discipline and related applications are experiencing rapid growth. Prior to publication of JBE there is no refereed publication that encompasses the breadth and depth of biological engineering as a science- based discipline, rather than a collection of applications. Our goal in publishing JBE is to provide a forum for topics that address the foundational …

Biocompatibility Of Te–As–Se Glass Fibers For Cell-Based Bio-Optic Infrared Sensors, Allison A. Wilhelm, Pierre Lucas, Diana L. Derosa, Mark R. Riley

Department of Agricultural and Biological Systems Engineering: Faculty Publications

The chemical stability and toxicity of Te–As–Se (TAS) infrared fibers are investigated. These fibers are used for biosensing applications that involve direct contact with live cultivated human cells. It is shown that TAS fibers exhibit a small oxidation layer after extended exposure to air. This layer is highly soluble in water and easily removed. However, the TAS glass itself is stable in water over several days. While oxidized fibers release arsenate ions, which result in toxic effects to the cells, fresh or washed fibers show no toxic effects. A good correlation is shown between surface etching and the disappearance of …

Subsurface Characterization Using Textural Features Extracted From Gpr Data, R. S. Freeland, Lameck O. Odhiambo

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Subsurface conditions can be non-intrusively mapped by observing and grouping patterns of similarity within ground-penetrating radar (GPR) profiles. We have observed that the intricate and often visually indiscernible textural variability found within a complex GPR image possesses important parameters that help delineate regions of similar subsurface characteristics. In this study, we therefore examined the feasibility of using textural features extracted from GPR data to automate subsurface characterization. The textural features were matched to a “fingerprint” database of previous subsurface classifications of GPR textural features and the corresponding physical probings of subsurface conditions. Four textural features (energy, contrast, entropy, and homogeneity) …

Analysis Of An Ion‐Selective Electrode Based Methodology For Integrated On‐The‐Go Mapping Of Soil Ph, Potassium, And Nitrate Contents, B. Sethuramasamyraja, V. I. Adamchuk, D. B. Marx, A. Dobermann, G. E. Meyer, D. D. Jones

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Knowledge of the spatial variation of soil attributes is critical for precision agriculture. On‐the‐go soil sensors have been able to provide relatively high mapping density while assessing this variation. A new ion‐selective electrode (ISE) based approach was developed and tested for simultaneous mapping of soil pH, residual nitrate (NO3 -), and soluble potassium (K+) contents. In this article, results of laboratory experiments investigating the effects of key measurement factors on ISE performance are presented. In addition to four different soils, these factors included: soil/water ratio (SWR), quality of water used for electrode rinsing (QWR) and for …

Protection With Recombinant Clostridium Botulinum C1 And D Binding Domain Subunit (Hc) Vaccines Against C And D Neurotoxins, Robert P. Webb, Theresa J. Smith, Patrick M. Wright, Vicki A. Montgomery, Michael M. Meagher, Leonard A. Smith

Michael Meagher Publications

Recombinant botulinum Hc (rBoNT Hc) vaccines for serotypes C1 and D were produced in the yeast Pichia pastoris and used to determine protection against four distinct BoNT C and D toxin subtypes. Mice were vaccinated with rBoNT/C1 Hc, rBoNT/D Hc, or with a combination of both vaccines and challenged with BoNT C1, D, C/D, or D/C toxin. Mice receiving monovalent vaccinations were partially or completely protected against homologous toxin and not protected against heterologous toxin. Bivalent vaccine candidates completely survived challenges from all toxins except D/C toxin. These results indicate the recombinant C1 and D Hc vaccines are not only …

Spatiotemporal Variations In Growing Season Exchanges Of Co2, H2o, And Sensible Heat In Agricultural Fields Of The Southern Great Plains, Marc L. Fischer, Dave P. Billesbach, Joseph A. Berry, William J. Riley, Margaret S. Torn

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Climate, vegetation cover, and management create finescale heterogeneity in unirrigated agricultural regions, with important but not well quantified consequences for spatial and temporal variations in surface CO2, water, and heat fluxes. Eddy covariance fluxes were measured in seven agricultural fields—comprising winter wheat, pasture, and sorghum—in the U.S. Southern Great Plains (SGP) during the 2001–03 growing seasons. Land cover was the dominant source of variation in surface fluxes, with 50%–100% differences between fields planted in winter–spring versus fields planted in summer. Interannual variation was driven mainly by precipitation, which varied more than twofold between years. Peak aboveground biomass and growing season …

Energy And Environmental Contributions Of Corn-Ethanol, Adam Liska, Kenneth Cassman, Haishun Yang

Adam Liska Papers

Rapid development of regulatory mechanisms to mitigate greenhouse gas (GHG) emissions requires that the biofuel industry employ standard methods to evaluate biofuel systems comprising both crop production systems and biorefineries. Biofuel systems associated with a variety of organic feedstocks have a range of performance capabilities, and recent life-cycle assessment studies of these different systems have used inconsistent methods, leading to confusion about biofuel energy efficiency and GHG mitigation. Hence, there is a critical need for well documented life-cycle metrics for consistent biofuel evaluation that are established and supported by a national or international governing body. Standardization of net energy and …

Effect Of Water On The Electrochemical Oxidation Of Gas-Phase So2 In A Pem Electrolyzer For H2 Production, John Staser, Ramaraja P. Ramasamy, Premkumar Sivasubramanian, John W. Weidner

Faculty Publications

Water plays a critical role in producing hydrogen from the electrochemical oxidation of SO2 in a proton exchange membrane (PEM) electrolyzer. Not only is water needed to keep the membrane hydrated, but it is also a reactant. One way to supply water is to dissolve SO2 in sulfuric acid and feed that liquid to the anode, but this process results in significant diffusion resistance for the SO2. Alternatively, we have developed a process where SO2 is fed as a gas to the anode compartment and reacts with water crossing the membrane to produce sulfuric acid. There was concern that the …

Modeling Redox-Based Magnetohydrodynamics In Three-Dimensional Microfluidic Channels, Hussameddine S. Kabbani, Aihua Wang, Xiaobing Luo, Shizhi Qian

Mechanical Engineering Faculty Research

RedOx-based magnetohydrodynamic MHD[1] flows in three-dimensional microfluidic channels are investigated theoretically with a coupled mathematical model consisting of the Nernst-Planck equations for the concentrations of ionic species, the local electroneutrality condition for the electric potential, and the Navier-Stokes equations for the flow field. A potential difference is externally applied across two planar electrodes positioned along the opposing walls of a microchannel that is filled with a dilute RedOx electrolyte solution, and a Faradaic current transmitted through the solution results. The entire device is positioned under a magnetic field which can be provided by either a permanent magnet or an electromagnet. …

Improved Parameterization To Invert Rayleigh-Wave Data For Shallow Profiles Containing Stiff Inclusions, Carlos Calderon-Macias, Barbara Luke

Civil and Environmental Engineering and Construction Faculty Research

Inversion of shear-wave velocity profiles from phase-velocity measurements of Rayleigh-wave energy for sites containing stiff layers can be erroneous if such layers are not characterized in the starting or reference model. Incorporation of a priori knowledge then is key for converging upon a realistic or meaningful solution. Resolving soil profiles in desert regions where stiff layers cemented with calcium carbonate are intermixed with softer, uncemented media is an application for which locating shallow stiff inclusions has important implications. Identification of the stiff layers is critical for foundation design and cost estimating of excavations. A parameterization that seems adequate for this …

Women In Science And Engineering: Politics Of Gender, Ibironke Lawal

VCU Libraries Faculty and Staff Publications

Women are fewer than men in science and engineering, therefore, the assumption is that women generally prefer arts and humanities. But to some analysts, the reason for the low percentage of women in these careers may be due to innate mental and psychological differences between them and men. Others contend that women have the capacity to excel in any profession and that their fewness in science and engineering can be attributed to other factors. They urge educational institutions and employers to develop programs and specific policies that would allow women to strike a better balance between the demands of work …