Digital Commons Network^™

Method For Identification Of Virulence Determinants, Raul G. Barletta, Beth Harris

School of Veterinary and Biomedical Sciences: Faculty Publications

Disclosed are methods for the determination of virulence determinants in bacteria and in particular bacteria of the genus Mycobacterium. Also disclosed are compositions and methods for stimulating an immune response in an animal using bacteria and virulence determinants identified by the methods of the present invention.

Testing Of Rtk-Level Satellite-Based Tractor Auto-Guidance Using A Visual Sensor System, Dwight Easterly, Viacheslav I. Adamchuk, Roger M. Hoy, Michael F. Kocher

Department of Agricultural and Biological Systems Engineering: Faculty Publications

The use of satellite-based positioning has advanced considerably in the world of agriculture, providing a range of technical solutions that include the automated steering of tractors and self-propelled machinery. With the development of auto-guidance systems comes the need to evaluate their performance. Given that current precision and accuracy claims are relatively small in magnitude, it is imperative there be a testing system capable of detecting errors with ten times greater accuracy-- possibly as little as a few millimeters. A visual sensor was adopted to achieve this level of measurement resolution. The sensor was used to determine the cross-track error estimates …

Numerically Predicting Seepage Gradient Forces And Erosion: Sensitivity To Soil Hydraulic Properties, Garey A. Fox, Derek M. Heeren, Glenn V. Wilson, E. J. Langendoen, Amanda K. Fox, Maria L. Chu-Agor

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Research has suggested that streambank seepage can be an important mechanism of bank instability; however, limited information is available on the level of soil characterization necessary to accurately predict seepage gradient forces and erosion. The objective of this research was to quantify the expected range of predicted seepage gradients for various degrees of site characterization. Uncertainty analysis on seepage gradient predictions was performed relative to variability in soil hydraulic properties. A two-dimensional unsaturated/saturated groundwater flow model was used to simulate a homogeneous soil layer for sand and loamy sand soils packed at various bulk densities, ρ_b. A pedotransfer …

Regulation Of Sealing Ring Formation By L-Plastin And Cortactin In Osteoclasts, Tao Ma, Kavitha Sadashivalah, Nandakumar Madayiputhiya, Meenakshi A. Chellaia

Department of Biochemistry: Faculty Publications

The aim of this study is to identify the exact mechanism(s) by which cytoskeletal structures are modulated during bone resorption. In this study, we have shown the possible role of different actin-binding and signaling proteins in the regulation of sealing ring formation. Our analyses have demonstrated a significant increase in cortactin and a corresponding decrease in L-plastin protein levels in osteoclasts subjected to bone resorption for 18 h in the presence of RANKL, M-CSF, and native bone particles. Time-dependent changes in the localization of L-plastin (in actin aggregates) and cortactin (in the sealing ring) suggest that these proteins may be …

Phosphatidylinositol 5-Phosphate Links Dehydration Stress To The Activity Of Arabidopsis Trithorax-Like Factor Atx1, Ivan Ndamukong, David R. Jones, Hanna Lapko, Nullin Divecha, Zoya V. Avramova

School of Biological Sciences: Faculty Publications

Background: Changes in gene expression enable organisms to respond to environmental stress. Levels of cellular lipid second messengers, such as the phosphoinositide PtdIns5P, change in response to a variety of stresses and can modulate the localization, conformation and activity of a number of intracellular proteins. The plant trithorax factor (ATX1) trimethylates the lysine 4 residue of histone H3 (H3K4me3) at gene coding sequences, which positively correlates with gene transcription. Microarray analysis has identified a target gene (WRKY70) that is regulated by both ATX1 and by the exogenous addition of PtdIns5P in Arabidopsis. Interestingly, ATX1 …

Evolution Of The Kdo2-Lipid A Biosynthesis In Bacteria, Stephen O. Opiyo, Rosevelt L. Pardy, Hideaki Moriyama, Etsuko N. Moriyama

School of Biological Sciences: Faculty Publications

Background: Lipid A is the highly immunoreactive endotoxic center of lipopolysaccharide (LPS). It anchors the LPS into the outer membrane of most Gram-negative bacteria. Lipid A can be recognized by animal cells, triggers defense-related responses, and causes Gram-negative sepsis. The biosynthesis of Kdo₂-lipid A, the LPS substructure, involves with nine enzymatic steps.

Results: In order to elucidate the evolutionary pathway of Kdo₂-lipid A biosynthesis, we examined the distribution of genes encoding the nine enzymes across bacteria. We found that not all Gram-negative bacteria have all nine enzymes. Some Gram-negative bacteria have no genes encoding …

Isolation And Characterization Of Bacteria Resistant To Metallic Copper Surfaces, Christophe Espírito Santo, Paula Vasconcelos Morais, Gregor Grass

School of Biological Sciences: Faculty Publications

Metallic copper alloys have recently attracted attention as a new antimicrobial weapon for areas where surface hygiene is paramount. Currently it is not understood on a molecular level how metallic copper kills microbes, but previous studies have demonstrated that a wide variety of bacteria, including Escherichia coli, Staphylococcus aureus, and Clostridium difficile, are inactivated within minutes or a few hours of exposure. In this study, we show that bacteria isolated from copper alloy coins comprise strains that are especially resistant against the toxic properties exerted by dry metallic copper surfaces. The most resistant of 294 isolates were …

Mate Choice And Learning, Eileen Hebets, Laura Sullivan-Beckers

Eileen Hebets Publications

While an individual’s genetic framework is a major contributor in determining its eventual mate choice, the role of the environment in further influencing mating decisions has long been recognized. Animals gather information from the environment throughout life, and in some cases, may apply this information to increase their odds of obtaining a high-quality mate. In short, these individuals learn. Moreover, such learning can have a social component. “Social learning” is a general term that describes any learning based on observing, interacting with, and/or imitating others in a social context. Social learning can transmit information vertically, generation to generation (e.g., parent …

Nm23-H1 Can Induce Cell Cycle Arrest And Apoptosis In B Cells, Tathagata Choudhuri, Masanao Murakami, Rajeev Kaul, Sushil K. Sahu, Suchitra Mohanty, Subhash C. Verma, Pankaj Kumar, Erle S. Robertson

School of Biological Sciences: Faculty Publications

Nm23-H1 is a well-known tumor metastasis suppressor, which functions as a nucleoside-diphosphate kinase converting nucleoside diphosphates to nucleoside triphosphates with an expense of ATP. It regulates a variety of cellular activities, including proliferation, development, migration and differentiation known to be modulated by a series of complex signaling pathway. Few studies have addressed the mechanistic action of Nm23-H1 in the context of these cellular processes. To determine the downstream pathways modulated by Nm23-H1, we expressed Nm23-H1 in a Burkitt lymphoma derived B-cell line BJAB and performed pathway specific microarray analysis. The genes with significant changes in expression patterns were clustered in …

Mitochondrial-Nuclear Epistasis Affects Fitness Within Species But Does Not Contribute To Fixed Incompatibilities Between Species Of Drosophila, Kristi L. Montooth, Colin D. Meiklejohn, Dawn N. Abt, David M. Rand

School of Biological Sciences: Faculty Publications

Efficient mitochondrial function requires physical interactions between the proteins encoded by the mitochondrial and nuclear genomes. Co-evolution between these genomes may result in the accumulation of incompatibilities between divergent lineages. We test whether mitochondrialnuclear incompatibilities have accumulated within the Drosophila melanogaster species subgroup by combining divergent mitochondrial and nuclear lineages and quantifying the effects on relative fitness. Precise placement of nine mtDNAs from D. melanogaster, D. simulans and D. mauritiana into two D. melanogaster nuclear genetic backgrounds reveals significant mitochondrial-nuclear epistasis affecting fitness in females. Combining the mitochondrial genomes with three different D. melanogaster X chromosomes reveals significant epistasis …

Synaptic Clustering Of Psd-95 Is Regulated By C-Abl Through Tyrosine Phosphorylation, Karen Perez De Arce, Lorena Varela-Nallar, Olivia Farias, Alejandra Cifuentes, Paulina Bull, Brian A. Couch, Anthony J. Koleske, Nibaldo C. Inestrosa, Alejandra R. Alvarez

School of Biological Sciences: Faculty Publications

The c-Abl tyrosine kinase is present in mouse brain synapses, but its precise synaptic function is unknown. We found that c-Abl levels in the rat hippocampus increase postnatally, with expression peaking at the first postnatal week. In 14 d in vitro hippocampal neuron cultures, c-Abl localizes primarily to the postsynaptic compartment, in which it colocalizes with the postsynaptic scaffold protein postsynaptic density protein-95 (PSD-95) in apposition to presynaptic markers. c-Abl associates with PSD-95, and chemical or genetic inhibition of c-Abl kinase activity reduces PSD-95 tyrosine phosphorylation, leading to reduced PSD-95 clustering and reduced synapses in treated neurons. c-Abl can phosphorylate …

Purification Of Parvalbumin From Carp: A Protocol That Avoids Heat Treatment, Stef J. Koppelman, Roland A. Romijn, Harmen H. J. De Jongh, Julie A. Nordlee, Sander Piersma, Martin Hessing, Steve L. Taylor

Department of Food Science and Technology: Faculty Publications

Parvalbumin from carp, a major allergen,was purified to homogeneity using ion exchange chromatography and size exclusion chromatography (estimated purity > 95% to 98% based on SDS-PAGE and native PAGE) with a yield of 318 mg, and a number of basic biochemical characteristics were determined. The identity was confirmed by peptide-mass fingerprinting, and IgE-binding was demonstrated. The UV/Vis absorbance spectra were explained using the previously published amino acid sequences. Far UV-CD spectroscopy was used to confirm the folding character of parvalbumin. We conclude that parvalbumin from carp can be purified on a comparatively large (hundreds of milligrams) scale using a purification protocol …

Are Brand Name Medicine Prices Really Lower In Ciudad Juárez?, Thomas M. Fullerton Jr., Osvaldo Miranda

Border Region Modeling Project

Relatively high brand name pharmaceutical prices have led many United States residents to cross the border into Mexico as “medical tourists.” To examine the savings potentially available to consumers willing to cross into Mexico, data are collected and analyzed for brand name prescription medicines sold in El Paso, Texas and Ciudad Juárez, Mexico. Retail pharmacy prices are generally lower on the south side of the border and substantial savings result for some medicines. For some products, however, shelf prices are lower on the north side of the border.

Leadership Characteristics And Team Outcomes In The Development Of A Marketing Web Page, Garry L. White, Karen H. Smith

Journal of International Technology and Information Management

Team structures are changing under the pressures of e-commerce and globalization. Today teams have to manage the challenges of working across functional boundaries, such as marketing and web development. In such an environment, research in the disciplines of management and psychology have found that shared leadership among team members may be superior to traditional leadership by a single team member, but this notion has not been tested in the contexts of marketing and web development. This paper presents the results of an empirical study showing that teams with shared leadership exhibited better performance and greater member satisfaction than teams with …

Use Of A Fast Information Extraction Method As A Decision Support Tool, Mahmudul Sheikh, Sumali Conlon

Journal of International Technology and Information Management

Ad-hoc extraction of information from documents can ensure the transparency of decisions made by an organization. Different Information Extraction methods have been applied to extract information from various domains. Most widely known methods use manually annotated training documents that require high development time. The automated training methods are not scalable to large application domains. We have developed a semi-automated knowledge-engineering method for building the knowledge-base with minimal efforts. Because our method reduces manual processing of the training data, the development process is very fast. We have developed a prototype application to extract information from the project-reports of the American Recovery …

A Framework For Analyzing Business Model Innovation In Mobile Commerce, Chung-Shing Lee, Jonathan C. Ho

Journal of International Technology and Information Management

The paper develops and tests a framework for evaluating mobile commerce business models and strategies. To study business model innovation in mobile commerce, we analyze the cost, revenue, and growth components of the business model. In addition, we also investigate whether the implementation of the new business model successfully capitalized on the key disruptive attributes of mobile commerce. An analytical framework is developed to guide the empirical study of the two leading mobile commerce companies in Taiwan. The empirical research indicates that the mobile commerce industry in Taiwan has been able to capitalize on many but not all of the …

Lip Movement Exaggerations During Infant Directed Speech, Jordan R. Green, Ignatius S. B. Nip, Erin M. Wilson, Antje Mefferd, Yana Yunusova

Department of Special Education and Communication Disorders: Faculty Publications

Purpose: Although a growing body of literature has indentified the positive effects of visual speech on speech and language learning, oral movements of infant directed speech have rarely been studied. This investigation used 3-dimensional motion capture technology to describe how mothers modify their lip movements when talking to their infants.
Method: Lip movements were recorded from twenty-five mothers as they spoke to their infants and other adults. Lip shapes were analyzed for differences across speaking conditions. The maximum fundamental frequency, duration, acoustic intensity, and first and second formant frequency of each vowel were also measured.
Results: Lip movements were significantly …

A Partial Chromosomal Deletion Caused By Random Plasmid Integration Resulted In A Reduced Virulence Phenotype In Fusarium Graminearum, Thomas K. Baldwin, Iffa Gaffoor, John Antoniw, Corrie Andries, John Guenther, Martin Urban, Heather E. Hallen-Adams, John Pitkin, Kim E. Hammond-Kosack, Frances Trail

Department of Food Science and Technology: Faculty Publications

Fusarium graminearum (teleomorph: Gibberella zeae) is an Ascomycete fungal plant pathogen which infects a range of agriculturally important crops, including wheat, barley, and maize. A random plasmid insertion mutagenesis approach was used to analyze the pathogenicity of the PH-1 strain, for which full genomic information is available. Fungal transformants were initially screened for their ability to infect wheat ears. From a total of 1,170 transformants screened, eight were confirmed to be highly reduced in pathogenicity toward wheat ears and roots. These were designated disease-attenuated F. graminearum (daf) mutants. The in vitro growth rate and appearance of each daf …

Barcoding Bushmeat: Molecular Identification Of Central African And South American Harvested Vertebrates, Mitchell J. Eaton, Greta J. Meyers, Sergios-Orestis Kolokotronis, Matthew S. Leslie, Andrew P. Martin, George Amato

United States Geological Survey: Staff Publications

The creation and use of a globally available database of DNA sequences from a standardized gene region has been proposed as a tool for species identification, assessing genetic diversity and monitoring the legal and illegal trade in wildlife species. Here, we contribute to the Barcode of Life Data System and test whether a short region of the mitochondrial cytochrome c oxidase subunit 1 (COX1) gene would reliably distinguish among a suite of commonly hunted African and South American mammal and reptile species. We used universal primers to generate reference barcode sequences of 645 bp for 23 species from five vertebrate …

Scanning Acoustic Microscopy For Gdl Water Distribution Characterization, Christopher Mcdade

Theses

The objective of this research was to identify and apply possible acoustic imaging techniques for water transport studies in PEM fuel cell diffusion mediums. To accomplish this, a scanning acoustic microscope (SAM) was designed and built along with dedicated control and analysis software to implement all investigative tests and scans. The results of the study were in two parts, acoustic response characterization of the fibrous material and implementation of the developed imaging technique for water saturation distribution characterization. Having used a focused 30MHz centered wide band transducer with focal point FWHM beam diameter of 90 microns the target material ensured …

Improved Strategies For Anti-Money Laundering In Kosovo : [Presentation Given In Late 2010.], Besart Qerimi

Theses

This capstone project report considers the problem of money laundering globally and in Kosovo specifically. Since 1999 in Kosovo there has been an increase of money laundering. To make sure that this problem was addressed in Kosovo the Financial Intelligence Centre (1) has been mandated to investigate and combat money laundering and the associated terrorism. This project emphasizes the definition, phase, trends, methods phases and effects of money laundering. It also explains the role of the national and international organizations and initiatives in the fight against money laundering. This project will help the Ministry of Finance and the development of …

Retention Fastener Preference For Fisher-Price Toy Packaging, Lakeshia Haynes

Theses

"Wrap Rage" continues to be a growing phenomenon as consumers become increasingly frustrated with toy packaging. Consumers have become dissatisfied with the amount of time and effort it takes to remove product from its packaging. To better meet the needs of consumers, toy company Fisher-Price has implemented several improved consumer-friendly package fastener alternatives. The purpose of this study was to test the three most favorable alternative package fastener concepts executed by Fisher-Price. Interviews were conducted to evaluate the amount of time and effort associated with each fastener and to determine which concept was most preferred. The findings of this study …

A Study Of Recent Classification Algorithms And A Novel Approach For Biosignal Data Classification, Eyup Cinar

Theses

Analyzing and understanding human biosignals have been important research areas that have many practical applications in everyday life. For example, Brain Computer Interface is a research area that studies the connection between the human brain and external systems by processing and learning the brain signals called Electroencephalography (EEG) signals. Similarly, various assistive robotics applications are being developed to interpret eye or muscle signals in humans in order to provide control inputs for external devices. The efficiency for all of these applications depends heavily on being able to process and classify human biosignals. Therefore many techniques from Signal Processing and Machine …

Development Of A Platform For Simulating And Optimizing Thermoelectric Energy Systems, John Kreuder

Theses

Thermoelectrics are solid state devices that can convert thermal energy directly into electrical energy. They have historically been used only in niche applications because of their relatively low efficiencies. With the advent of nanotechnology and improved manufacturing processes thermoelectric materials have become less costly and more efficient As next generation thermoelectric materials become available there is a need for industries to quickly and cost effectively seek out feasible applications for thermoelectric heat recovery platforms. Determining the technical and economic feasibility of such systems requires a model that predicts performance at the system level. Current models focus on specific system applications …

The Relationships Between Obesity, Obstructive Sleep Apnea And Commercial Motor Vehicle Operator Performance, Jennifer Ann O'Neil

Theses

Obesity and Obstructive Sleep Apnea will impair Commercial Motor Vehicle operator performance. Obesity will increase the risk of developing serious medical conditions that may cause harm to human health and wellbeing. One condition that can be associated with obesity is known as Obstructive Sleep Apnea. Various symptoms of obstructive sleep apnea will impair a commercial motor vehicle operator's ability to safely maneuver a vehicle. Many commercial motor vehicle collisions have been caused by operator fatigue and have resulted in serious injury and death. Due to unhealthy lifestyles, commercial motor vehicle operators are at a high risk of being obese. Obesity …

Field‐Derived Henry's Law Constants For Polychlorinated Biphenyls In Oceanic Waters, Rosalinda Gioia, Kevin C. Jones, Rainer Lohmann, Luca Nizzetto, Jordi Dachs

Graduate School of Oceanography Faculty Publications

Accurate knowledge of Henry's law constants (K_aw) is very important for fate and transport studies of organic chemicals. Here field‐derived K_aw values for polychlorinated biphenyl (PCB) congeners (PCBs 28, 49, 52, 118, 138, 149, and 153) were determined in the open Atlantic Ocean, at locations where air and seawater were assumed to be at equilibrium. Field‐based K_aw values were derived from air and seawater samples simultaneously collected at these locations, and their relationship with temperature was determined. The average field‐derived K_aw for PCBs 28, 49, 52, 118, and 138 was generally 2–3 times higher …

Unsplit Complex Frequency-Shifted Pml Implementation Using Auxiliary Differential Equations For Seismic Wave Modeling, Wei Zhang, Yang Shen

Graduate School of Oceanography Faculty Publications

The complex-frequency-shifted perfectly matched layer (CFS-PML) technique can efficiently absorb near-grazing incident waves. In seismic wave modeling, CFS-PML has been implemented by the first-order-accuracy convolutional PML technique or second-order-accuracy recursive convolution PML technique. Both use different algorithms than the numerical scheme for the interior domain to update auxiliary memory variables in the PML and thus cannot be used directly with higher-order time-marching schemes. We work with an unsplit-field CFS-PML implementation using auxiliary differential equations (ADEs) to update the auxiliary memory variables. This ADE CFS-PML results in complete first-order differential equations. Thus, the numerical scheme for the interior domain can be …

Parallel Programming Recipes, Thuy C. Nguyenphuc

Master's Projects

Parallel programming has become vital for the success of commercial applications since Moore’s Law will now be used to double the processors (or cores) per chip every technology generation. The performance of applications depends on how software executions can be mapped on the multi-core chip, and how efficiently they run the cores. Currently, the increase of parallelism in software development is necessary, not only for taking advantage of multi-core capability, but also for adapting and surviving in the new silicon implementation. This project will provide the performance characteristics of parallelism for some common algorithms or computations using different parallel languages. …

Security In Peer-To-Peer Sip Voip, Richa Marwaha

Master's Projects

VoIP (Voice over Internet Protocol) is one of the fastest growing technologies in the world. It is used by people all over the world for communication. But with the growing popularity of internet, security is one of the biggest concerns. It is important that the intruders are not able to sniff the packets that are transmitted over the internet through VoIP. Session Initiation Protocol (SIP) is the most popular and commonly used protocol of VoIP. Now days, companies like Skype are using Peer-to-Peer SIP VoIP for faster and better performance. Through this project I am improving an already existing Peer-to-Peer …

Microbial Community Characterization And Pathogen Analysis Within Constructed Wetlands Of Varying Scale Designed For Contaminant Removal, Michael R. Mitzel

Theses and Dissertations (Comprehensive)

Constructed wetlands (CWs) are complex treatment environments, requiring an integrative research approach to improve our understanding of them. The goal of this thesis was to establish an understanding of the functional and structural characteristics of microbial communities within bench-, field- and industrial-scale environmental treatment systems. The impact of pathogenic and/or antibiotic contaminants on these communities based on their functional and structural profiles using community-level physiological profiling (CLPP) and denaturing-gradient gel electrophoresis (DGGE), respectively, was investigated. Under normal operation, bench-, field- and industrial-scale treatment systems were able to produce similarly behaving structural and functional profiles. Increased retention time was consistently associated …