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Improving Structural Features Prediction In Protein Structure Modeling, Ashraf Yaseen

Computer Science Theses & Dissertations

Proteins play a vital role in the biological activities of all living species. In nature, a protein folds into a specific and energetically favorable three-dimensional structure which is critical to its biological function. Hence, there has been a great effort by researchers in both experimentally determining and computationally predicting the structures of proteins.

The current experimental methods of protein structure determination are complicated, time-consuming, and expensive. On the other hand, the sequencing of proteins is fast, simple, and relatively less expensive. Thus, the gap between the number of known sequences and the determined structures is growing, and is expected to …

Evaluation Of The Epa Swmm Model To Simulate Low Impact Development Features In An Urban Stormwater Environment, Holly Ann Carpenter

Civil & Environmental Engineering Theses & Dissertations

This research thesis explores the use of the Environmental Protection Agency's (EPA) Stormwater Water Management Model (SWMM) to model an urban watershed with a developed stormwater management system and test the SWMM model's ability to simulate Low Impact Development (LID) features by proposing typical LID features that can be retrofitted to the developed study area. The SWMM model is established with an existing survey of the study area's stormwater management system, and due to the lack of field data for the study area, the model developed in this research thesis is calibrated with the consideration of a published stormwater model …

Autism Assessment Scale For Children (Aasc): The Development Of A Dsm-V Aiigned Questionnaire To Screen School-Aged Children For High Functioning Autism, Christine Hebert

Teaching & Learning Theses & Dissertations

The purpose of this dissertation is to analyze the latent factor structure underlying the Ellis Functional Assessment (EFA) for children with high-functioning autism (HFA), to compare the latent factor structures for under-identified subgroups of children (older children, gifted children, female children), and to design a pre-screening assessment for HFA based on those results. The scope of the study is limited to children who have been identified as having HFA and whose parents completed the EFA while patients of a mid-Atlantic clinical practice specializing in autism spectrum disorders. The methodology uses preliminary factor analysis and confirmatory factor analysis to both analyze …

Experimental And Computational Analysis Of The Synucleins, Agatha Munyanyi

Theses and Dissertations in Biomedical Sciences

The synuclein proteins α, β and γ which are located in the brain, have been a subject of intense research. Of particular interest is α-synuclein, which is found in misfolded forms in Lewy bodies that are associated with Parkinson's disease. Despite the efforts of researchers across the world, the physiological structure and function of the synucleins remains elusive. In recent years, highly controversial reports by some investigators indicate that in its natural form, α-synuclein exists as a tetramer instead of as an intrinsically unstructured monomer. This dissertation presents results of the experimental and computational analysis of the synucleins. First, we …

Multiplatform, Multidisciplinary Investigations Of The Impacts Of Modified Circumpolar Deep Water In The Ross Sea, Antarctica, Walker O. Smith, Kimberly T. Goetz, Daniel E. Kaufman, Bastien Y. Queste, Vernon Asper, Daniel P. Costa, Michael S. Dinniman, Marjorie A. M. Friedrichs, Eileen E. Hofmann, Karen J. Heywood, John M. Klinck, Josh T. Kohut, Craig M. Lee

CCPO Publications

In 2010–2011, three projects combined to characterize the temporal and spatial distributions of Modified Circumpolar Deep Water (MCDW) in the Ross Sea using icebreaker-based sampling, gliders, instrumented seals, and hindcasts from a numerical circulation model. Te fieldwork clearly identified MCDW throughout the Ross Sea, and the data were used to determine its influence on potential heat and nutrient inputs and biotic distributions. Furthermore, the numerical simulations confirm its apparent trajectory and location. Substantial small-scale variability in oceanographic and biological distributions suggests that such variability may play an important role in biogeochemical cycles. Data from the three projects provide a view …

Computational Analysis Of Gene Expression And Connectivity Patterns In The Convoluted Structures Of Mouse Cerebellum, Tao Zeng

Computer Science Theses & Dissertations

One significant difference between evolved mammalian brains and other species is that mammalian brains exhibit increasingly convoluted structures in the cerebral cortex. Groove and ridge shaped structures named gyri and sulci expand surface area of cerebral cortex, making more functions possible. Prior studies using neuroimaging techniques such as dMRI and DTI have revealed that neural fibers are heavily connected to gyri comparing to those connected to sulci, such macro-scale experiments indicates that gyri are involved in large scale information processing while sulci process information locally. However, molecular and cellar level evidences, namely, gene expression pattern and its resulting neuronal connectivity …

Redox Active Motifs In Selenoproteins, Fei Li, Yuliya Pepelyayeva, Elias S. J. Arner, Craig A. Bayse, Sharon Rozovsky

Chemistry & Biochemistry Faculty Publications

Selenoproteins use the rare amino acid selenocysteine (Sec) to act as the first line of defense against oxidants, which are linked to aging, cancer, and neurodegenerative diseases. Many selenoproteins are oxidoreductases in which the reactive Sec is connected to a neighboring Cys and able to form a ring. These Sec-containing redox motifs govern much of the reactivity of selenoproteins. To study their fundamental properties, we have used Se-77 NMR spectroscopy in concert with theoretical calculations to determine the conformational preferences and mobility of representative motifs. This use of Se-77 as a probe enables the direct recording of the properties of …

Transnational Organized Crime And The Illegal Wildlife Trade Global Ties And Global Crime, Zachariah Edward Long

Graduate Program in International Studies Theses & Dissertations

World biodiversity is faced with many different threats in today's globalized world. One such threat is the emergence of transnational organized crime in the illegal wildlife trade. But why would transnational organized crime which is traditionally associated with such crimes like illegal drugs, weapons, and human trafficking be interested in the illegal wildlife trade? This thesis seeks to explore why transnational organized crime as a rational business actor would it be interested in participating in the illegal wildlife trade. To explore this relationship, this thesis will look at several different variables. First the economic conditions oflocals living with wildlife and …

Novel Mechanism Of Attenuation Of Lps-Induced Nf-Kappab Activation By The Heat Shock Protein 90 Inhibitor, 17-N-Allylamino-17-Demethoxygeldanamycin, In Human Lung Microvascular Endothelial Cells, Gagan S. Thangjam, Christiana Dimitropoulou, Atul D. Joshi, Nektarios Barabutis, Mary C. Shaw, Yevgeniy Kovalenkov, Christopher M. Wallace, David J. Fulton, Vijay Patel, John D. Catravas

Bioelectrics Publications

Heat shock protein (hsp) 90 inhibition attenuates NF-kappaB activation and blocks inflammation. However, the precise mechanism of NF-kappaB regulation by hsp90 in the endothelium is not clear. We investigated the mechanisms of hsp90 inhibition by 17-N-allylamino-17-demethoxygeldanamycin (17-AAG) on NF-kappaB activation by LPS in primary human lung microvascular endothelial cells. Transcriptional activation of NF-kappaB was measured by luciferase reporter assay, gene expression by real-time RT-PCR, DNA binding of transcription factors by chromatin immunoprecipitation assay, protein-protein interaction by coimmunoprecipitation/immunoblotting, histone deacetylase (HDAC)/histone acetyltransferase enzyme activity by fluorometry, and nucleosome eviction by partial microccocal DNase digestion. In human lung microvascular endothelial cells, 17-AAG-induced …

Section Abstracts: Natural History And Biodiversity

Virginia Journal of Science

Abstracts of the Section Abstracts: Natural History and Biodiversity Section for the 92nd Annual Meeting of the Virginia Academy of Science, May 13-15, 2014, Virginia Commonwealth University, Richmond, Virginia

Section Abstracts: Statistics

Virginia Journal of Science

Abstracts of the Statistics Section for the 92nd Annual Meeting of the Virginia Academy of Science, May 13-15, 2014, Virginia Commonwealth University, Richmond, Virginia

Graduate News, Office Of Graduate Studies, Old Dominion University

Graduate News

April 2014 issue of Graduate News from the Office of Graduate Studies (now, ODU Graduate School).

Section Abstracts: Education

Virginia Journal of Science

Abstracts of the Education Section for the 92nd Annual Meeting of the Virginia Academy of Science, May 13-15, 2014, Virginia Commonwealth University, Richmond, Virginia

92nd Annual Meeting Best Paper Awards

Virginia Journal of Science

List of award winning papers by section from the 92nd Annual Meeting of the Virginia Academy of Science, 2014

Junior Academy Awards: 73rd Virginia Junior Academy Of Science Meeting Awards

Virginia Journal of Science

Awards by section for the 73rd Virginia Junior Academy of Science Meeting, 2014

Special Awards And Scholarships: Virginia Junior Academy Of Science

Virginia Journal of Science

Special Awards and Scholarships for the Virginia Junior Academy of Science, 2014

Editor And Journal Information

Virginia Journal of Science

Editor and journal information from the print version of the Virginia Journal of Science, vol. 65, no. 1 & 2, Spring/Summer 2014

Section Abstracts: Environmental Science

Virginia Journal of Science

Abstracts of the Environmental Science Section for the 92nd Annual Meeting of the Virginia Academy of Science, May 13-15, 2014, Virginia Commonwealth University, Richmond, Virginia

Circulation, Vol. 19, No. 1, Center For Coastal Physical Oceanography, Old Dominion University, John M. Klinck, Eileen E. Hofmann

CCPO Circulation

Spring 2014 issue of Circulation, featuring the article "Theoretical Models of Marine Infectious Diseases and the Effects of Climate Variability" by John Klinck and Eileen Hofmann

Section Abstracts: Botany

Virginia Journal of Science

Abstracts of the Botany Section for the 92nd Annual Meeting of the Virginia Academy of Science, May 13-15, 2014, Virginia Commonwealth University, Richmond, Virginia

Section Abstracts: Psychology

Virginia Journal of Science

Abstracts of the Psychology Section for the 92nd Annual Meeting of the Virginia Academy of Science, May 13-15, 2014, Virginia Commonwealth University, Richmond, Virginia

Table Of Contents

Virginia Journal of Science

Table of Contents for the Virginia Journal of Science, vol. 65, no. 1 & 2, Spring/Summer 2014

Section Abstracts: Agriculture, Forestry, And Aquaculture

Virginia Journal of Science

Abstracts of the Agriculture, Forestry, and Aquaculture Section for the 92nd Annual Virginia Academy of Science Meeting, May 2014, at Virginia Commonwealth University in Richmond, Virginia

Section Abstracts: Astronomy, Mathematics, And Physics With Materials Science

Virginia Journal of Science

Abstracts of the Astronomy, Mathematics, and Physics with Materials Science Section for the 92nd Annual Meeting of the Virginia Academy of Science, May 13-15, 2014, Virginia Commonwealth University, Richmond, Virginia

Section Abstracts: Biology With Microbiology And Molecular Biology

Virginia Journal of Science

Abstracts of the Biology with Microbiology and Molecular Biology Section for the 92nd Annual Meeting of the Virginia Academy of Science, May 13-15, 2014, Virginia Commonwealth University, Richmond, Virginia

Section Abstracts: Biomedical And General Engineering

Virginia Journal of Science

Abstracts of the Biomedical and General Engineering Section for the 92nd Annual Meeting of the Virginia Academy of Science, May 13-15, 2014, Virginia Commonwealth University, Richmond, Virginia

Section Abstracts: Structural Biology, Biochemistry, And Biophysics

Virginia Journal of Science

Abstracts of the Structural Biology, Biochemistry, and Biophysics Section for the 92nd Annual Meeting of the Virginia Academy of Science, May 13-15, 2014, Virginia Commonwealth University, Richmond, Virginia

Growth And Nitrogen Uptake Kinetics In Cultured Procentrum Donghaiense, Zhangxi Hu, Shunshan Duan, Margaret R. Mulholland

OES Faculty Publications

We compared growth kinetics of Prorocentrum donghaiense cultures on different nitrogen (N) compounds including nitrate, ammonium urea, glutamic acid, dialanine, and cynate. P. donghaiense exhibited standard Monod-type growth kinetics over a range of nitrogen concentrations for all N. Compounds tested. Cultures grown on glu and urea had the highest maximum growth rates. However, cultures grown on cyanate had lower half saturation constants. Nitrogen uptake kinetics were measured in nitrate-deplete and replete batch cultures of P. donghaiense. In nitrate-deplete batch cultures, P. donghaiense exhibited Michaelis-Menten type uptake kinetics for nitrate, ammonium, urea and algal amino acids; uptake was saturated at …

92nd Annual Meeting Of The Virginia Academy Of Science: Proceedings

Virginia Journal of Science

Full proceedings of the 92nd Annual Meeting of the Virginia Academy of Science, May 13-15, 2014, Virginia Commonwealth University, Richmond, Virginia

Section Abstracts: Chemistry

Virginia Journal of Science

Abstracts of the Chemistry Section for the 92nd Annual Meeting of the Virginia Academy of Science, May 13-15, 2014, Virginia Commonwealth University, Richmond, Virginia