Digital Commons Network^™

Universal Swine Influenza Antigen And Vaccine, Zhao Wang

Electronic Theses and Dissertations

Swine influenza A viruses pose a serious concern for global health and worldwide swine industry considering their evasion from vaccine-induced immune responses. Formulation of effective influenza vaccines can be complicated by both antigenic shift to a different subtype of hemagglutinin (HAs) and antigenic drift within a particular HA subtype. To address these concerns, we employed a systematic approach to determine the antigenic determinants of swine influenza A viruses by focusing on H1 and H3 subtypes. In parallel, we used a cross-disciplinary approach including structural biology and modeling, virology, and immunology to identify swine influenza A virus-derived HA fusion intermediates broadly …

A Pcr/Sequencing Technique To Identify Species And Genotypes Of Haemonchus From Mixed Trichostrongyle Egg Dna Recovered From Livestock Fecal Samples, Pratiksha Khanal

Electronic Theses and Dissertations

Six primer pairs, each with a pair of genus-specific and universal second internal transcribed spacer (ITS2) primers were evaluated to amplify and sequence the ITS2 region of nuclear ribosomal DNA to identify the species and genotypes of Haemonchus from livestock fecal samples containing mixtures of trichostrongyle nematode eggs. Based upon the use of universal ITS2 primers on Haemonchus adults, the ITS2 region has been shown to contain three fixed single-nucleotide differences between H. placei and H. contortus. It is clinically useful to identify the species and genotypes of Haemonchus infecting livestock, but it has not been possible in fecal …

The Colomoto Interactive Notebook: Accessible And Reproducible Computational Analyses For Qualitative Biological Networks, Aurelien Naldi, Celine Hernandez, Nicolas Levy, Gautier Stoll, Pedro T. Monteiro, Claudine Chaouiya, Tomáš Helikar, Andrei Zinovyev, Laurence Calzone, Sarah Cohen-Boulakia, Denis Thieffry, Loic Pauleve

Department of Biochemistry: Faculty Publications

Analysing models of biological networks typically relies on workflows in which different software tools with sensitive parameters are chained together,many times with additional manual steps. The accessibility and reproducibility of such workflows is challenging, as publications often overlook analysis details, and because some of these tools may be difficult to install, and/or have a steep learning curve. The CoLoMoTo Interactive Notebook provides a unified environment to edit, execute, share, and reproduce analyses of qualitative models of biological networks. This framework combines the power of different technologies to ensure repeatability and to reduce users’ learning curve of these technologies. The framework …

The Role Of Prrx1 And Snai2 As Master Regulators Of Fibroblast Identity, Huda A. Alzahrani

Masters Theses

Mammalian development involves a complex system of regulatory signals and reactions, leading to the creation of distinct tissues with specific structures and functions controlled by various gene expression profiles. Tissue-specific gene expression is by controlled specific combinations of transcription factors and cofactors that dictate cell differentiation via activation and repression of genes in mammalian cells.

Whole genome microarray analyses of fibroblasts have revealed candidate genes that may serve as master regulators of fibroblast identity, such as Prrx1 and Snai2, that activate downstream genes such as Bmp3, Twist, Shox2, Cfos, Slug, Sema3A, Spp1, and Col1a1. A previous study showed that Prrx1 …

Quantitation Without Calibration: Response Profile As An Indicator Of Target Amount, Mrittika Debnath

Graduate Research Theses & Dissertations

Quantitative assessment of biomarkers is essential in numerous contexts from decision-making in clinical situations to food quality monitoring to the interpretation of life-science research findings. However, appropriate quantitation techniques are not as widely addressed as detection methods. One of the major challenges in biomarker’s quantitation is the need to have a calibration for correlating a measured signal to a target amount. The step complicates the methodologies and makes them less sustainable. In this work, we addressed the issue via a new strategy: relying on the position of response profile rather than absolute signal for assessment of a target nucleic acid’s …

Development Of Biclustering Techniques For Gene Expression Data Modeling And Mining, Juan Xie

Electronic Theses and Dissertations

The next-generation sequencing technologies can generate large-scale biological data with higher resolution, better accuracy, and lower technical variation than the arraybased counterparts. RNA sequencing (RNA-Seq) can generate genome-scale gene expression data in biological samples at a given moment, facilitating a better understanding of cell functions at genetic and cellular levels. The abundance of gene expression datasets provides an opportunity to identify genes with similar expression patterns across multiple conditions, i.e., co-expression gene modules (CEMs). Genomescale identification of CEMs can be modeled and solved by biclustering, a twodimensional data mining technique that allows clustering of rows and columns in a gene …

Embryological Studies On Trichloris (Poaceae, Chloridoideae), Geraldina Alicia Richard, María Carolina Cerino, Beatriz G. Galati, Eliana De Luján Exner, José Francisco Pensiero

Turkish Journal of Botany

The present study provides information on the development of the female and male gametophytes and seed ontogeny characteristics for Trichloris, and it discusses their taxonomic significance to the family Poaceae. Trichloris species are characterized by having 2?3 stamens per floret, tetrasporangiate anthers, a monocotyledonous development of the anther wall, a single middle layer of common origin with the tapetum, fibrous thickening in the cell walls of the endothecium, and a secretory tapetum. These characteristics are constant within Poaceae. The possession of bitegmic and tenuinucellate ovules, laterally positioned antipodals prior to their degeneration, a free exocarp, and an epiblast in the …

Identification Of Qtl Modifying The Activity Of The Tcb1-S Locus And Characterization And Sequencing Of Two Plutonium-Beryllium Induced Reduced Gametophyte Transmission Mutants In Maize, Merritt Bryer Burch

Electronic Theses and Dissertations

This thesis is split into two independent projects both involving the male gametophyte generation of maize. The first project looks at how pollen interacts with the female gametophyte to reduce its transmission in cross-incompatible reactions controlled by the unilateral cross-incompatibility system, teosinte crossing barrier 1. The second project explores two plutonium-beryllium induced male gametophyte mutants and attempts to uncover their genetic basis.

Identification of QTL Modifying the Activity of the Tcb1-s Locus
Teosinte crossing barrier 1 (Tcb1) is a unilateral cross-incompatibility system present in maize that provides a pre-zygotic pistil barrier to plants carrying Tcb1-s (strong allele) from pollen …

Novel Computational Methods For Sequencing Data Analysis: Mapping, Query, And Classification, Xinan Liu

Theses and Dissertations--Computer Science

Over the past decade, the evolution of next-generation sequencing technology has considerably advanced the genomics research. As a consequence, fast and accurate computational methods are needed for analyzing the large data in different applications. The research presented in this dissertation focuses on three areas: RNA-seq read mapping, large-scale data query, and metagenomics sequence classification.

A critical step of RNA-seq data analysis is to map the RNA-seq reads onto a reference genome. This dissertation presents a novel splice alignment tool, MapSplice3. It achieves high read alignment and base mapping yields and is able to detect splice junctions, gene fusions, and circular …

Ultra-Fast And Memory-Efficient Lookups For Cloud, Networked Systems, And Massive Data Management, Ye Yu

Theses and Dissertations--Computer Science

Systems that process big data (e.g., high-traffic networks and large-scale storage) prefer data structures and algorithms with small memory and fast processing speed. Efficient and fast algorithms play an essential role in system design, despite the improvement of hardware. This dissertation is organized around a novel algorithm called Othello Hashing. Othello Hashing supports ultra-fast and memory-efficient key-value lookup, and it fits the requirements of the core algorithms of many large-scale systems and big data applications. Using Othello hashing, combined with domain expertise in cloud, computer networks, big data, and bioinformatics, I developed the following applications that resolve several major …

Comparative Study Of Growth Patterns In Seven Strains Of Japanese Quail Using Nonlinear Regression Modeling, Hadi Farajiarough, Mohammad Rokouei, Ali Maghsoudi, Mahmoud Ghazaghi

Turkish Journal of Veterinary & Animal Sciences

The aim of this study was to compare the growth pattern of seven strains of Japanese quail including Wild, Italian Speckled, Tuxedo, Scarlett, English white, White button, and A&M Texas by nonlinear growth functions including Gompertz, Richards, logistic, Lopez, and Weibull functions. The body weights of the unselected randomly bred populations of these strains were measured weekly from 1 to 42 days of age and then used to fit functions. The fitness of each function was assessed by statistics including the mean square error, Akaike information criterion, Bayesian information criterion, and adjusted coefficient of determination. The results showed that Gompertz …

Discovery Of Piperlongumine Derivatives As Anti-Leukemic And Anti-Prostate Cancer Agents, Yi Liao

Wayne State University Dissertations

Piperlongumine (PL) is an electrophilic anti-cancer natural product. Through non-covalent or covalent interactions with cellular targets, PL inactivates multiple oncogenic pathways and suppresses key components of cellular anti-oxidant/anti-electrophile defense systems. These actions result in pleiotropic anticancer effects and are expected to be effective to heterogeneous acute myeloid leukemia (AML) and prostate cancer (PCa). We applied two approaches to enhance the anticancer potency of PL: 1) To design PL-histone deacetylase inhibitor hybrid drugs (PL-HDACis; e.g., 1-58), and 2) To dimerize PL pharmacophore to generate a dimeric PL (DiPL) warhead that is suitable for further conjugation (e.g., 5-17). Both 1-58 and 5-17 …

Community Structure And Epizootic Infection Prevalence Of Northern Wisconsin Anurans, Kayla Christine Watters

Browse all Theses and Dissertations

Amphibian populations are declining globally at historically rapid rates, and while a multitude of factors have contributed to amphibian population declines, emerging infectious diseases, such as chytridiomycosis and ranavirus have been linked to a large proportion of the reported amphibian mass mortality events. Distribution and infection prevalence data for chytridiomycosis and ranavirus are lacking, and effective surveillance is crucial. This project aims to describe anuran richness, relative abundance, habitat occupancy, and community structure and to identify the chytridiomycosis and ranavirus infection prevalence rates of the anuran population at Dairymen's Inc. Wood frogs, spring peepers, boreal chorus frogs, northern leopard frogs, …

Poultry Industry, Allen Szalanski

Entomology and Plant Pathology Faculty Publications and Presentations

Cimicids, and particularly the Common bed bug, Cimex lectularius L., can infest poultry houses and cause severe cutaneous reactions in the birds as wellas other clinical effects. This chapter discusses some cimicids that have been documented as pests of poultry, including: the Mexican chicken bug, Haematosiphon inodorus (Duges); the Brazilian chicken bug, Ornithocoris toledoi Pinto; the related species, Ornithcorus pallidus Usinger; and and the Tropical bed bug, Cimex hemipterus (F.).

The Effects Of Temperature On Batrachochytrium Dendrobatidis Resistance And Heart Rate In The Polymorphic Eastern Red-Backed Salamanders, Plethodon Cinereus, Joseph Alan Demarchi

Masters Theses

No abstract provided.

Climate Metric Coherence: Stationarity Of The Relationships Between North Pacific Climate Indices And Ecological Processes In The Gulf Of Alaska, Michael Opiekun

Theses and Dissertations

The Pacific Decadal Oscillation (PDO) has been used to characterize the dominant basin-scale climate variability, in the North Pacific. The PDO index has been correlated to Pacific salmon (Oncorhynchus spp.) population dynamics in the Gulf of Alaska (GOA) during the late 1900s, but the stationarity of the statistical relationships between salmon production and the basin-scale index (and between the regional physical processes and the basin-scale index) has not been quantified. A change in the relationship between the PDO and salmon catches has been noted during the late 1980s, motivating further investigation of variability in climate and ecosystem properties during this …

Cytoprotective Effect Of A Functional Antipollutant Blend Through Reducing B[A] P-Induced Intracellular Oxidative Stress And Uva Exposure, Gi̇zem Örs, Sultan Gülçe İz

Turkish Journal of Biology

Benzo[a]pyrene (B[a]P) is a ubiquitous environmental pollutant that reacts with skin and induces intracellular oxidative stress through reactive oxygen species (ROS) accumulation. The antipollution properties of natural extracts, especially including antioxidants, for inhibiting ROS in cells are gaining importance, in addition to the anticancer effects attributed to them. In this study, a commercial functional antipollutant blend of plant extracts consisting of ellagic acid standardized Punica granatum peel extract, Sambucus nigra fruit extract, Prunus cerasus seed extract, and hydrolyzed wheat protein with high antioxidant properties and UV damage-protective properties attributed to each one was investigated. The cytoprotective effect of this functional …

Assembly And Trafficking Of The Cystic Fibrosis Transmembrane Conductance Regulator And Associated Proteins, Zhihui Zhang

Theses and Dissertations--Chemistry

Cystic Fibrosis (CF) is an autosomal recessive genetic disease that leads to severe malfunction in many organs, but particularly the lungs. The primary cause of this malfunction is the decrease of the airway surface liquid layer on the lung epithelium. The lack of hydration leads to mucus build up on the epithelial lining, leading to blockage of airways. The underlying cause of CF is the dysfunction of the cystic fibrosis transmembrane conductance regulator (CFTR), which results from mutations in the protein. Almost 90% of CF patients are caused by the deletion of the phenylalanine at position 508 of CFTR, which …

Study Of The Mechanism Of Action For Ru(Ii) Polypyridyl Complexes As Potential Anticancer Agents, Yang Sun

Theses and Dissertations--Chemistry

Application of chemotherapeutic agents in current cancer treatment has been limited by adverse effects as poor selectivity results in systemic toxicity; most chemotherapy approaches also experience inherited or acquired drug resistance which lead to reduced treatment outcome. Research efforts have focused on the discovery of novel chemotherapies that overcome the limitations mentioned above. Ru(II) polypyridyl complexes with anti-cancer properties have been extensively studied as traditional cytotoxic agents and photodynamic therapy agents due to their photophysical and photochemical characteristics.

Most research has focused on the design of Ru(II) polypyridyl complexes that have affinities to nucleic acids as inspired by the classic …

Hidden Diversity In Aquatic Habitats: Lessons From Cryptic Species In Microscopic Invertebrates (Rotifera), Azar Kordbacheh

Open Access Theses & Dissertations

Speciation is a continuous and adaptive process by which lineages are diverged into multiple groups, and species are the product of this process. Taxonomy is the study of relationship between organisms, classifying and naming them, and one of the taxonomical challenges is delimiting species boundaries. Species delimitation can be controversial because biologists do not agree on species concepts and approaches for defining species boundaries. One of the well-known species concepts is the Biological Species Concept that requires studying reproductive barriers among populations. Investigating strength of reproductive isolation among populations is not always practical in the wild. Therefore, many biologists have …

The Structural And Functional Study Of The Human Mitochondrial Hsp60 Chaperonin In Neurodegenerative Diseases, Jinliang Wang

Open Access Theses & Dissertations

Proteins are essential elements that are responsible for a variety of cellular activities within organisms, including catalyzing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells and organisms, and transporting molecules. After protein synthesis in the ribosome, the unfolded protein need to fold into their unique compact structures so that they can perform their full biological functions. The biologically active structure of a protein is referred to the native-state of the protein with biological activity. The process of protein folding is one of the most important and challenging research topics of contemporary biochemistry, especially for its central role …

It Takes Two: Evidence For Reduced Sexual Conflict Over Parental Care In A Biparental Canid, Christopher J. Schell, Julie K. Young, Elizabeth V. Lonsdorf, Jill M. Mateo, Rachel M. Santymire

United States Department of Agriculture Wildlife Services: Staff Publications

In biparental systems, sexual conflict over parental investment predicts that the parent providing care experiences greater reproductive costs. This inequality in parental contribution is reduced when offspring survival is dependent on biparental care. However, this idea has received little empirical attention. Here, we determined whether mothers and fathers differed in their contribution to care in a captive population of coyotes (Canis latrans). We performed parental care assays on 8 (n = 8 males, 8 females) mated pairs repeatedly over a 10-week period (i.e., 5–15 weeks of litter age) when pairs were first-time breeders (2011), and again as experienced …

Spatial Distribution And Dietary Niche Breadth Of The Leopard Panthera Pardus (Carnivora: Felidae) In The Northeastern Himalayan Region Of Pakistan, Faraz Akrim, Tariq Mahmood, Muhammad Sajid Nadeem, Shaista Andleeb, Siddiqa Qasim

Turkish Journal of Zoology

Knowledge of a predato's diet is important for understanding its ecology and for predicting its influence on the dynamics of prey populations. We investigated the spatial distribution and diet composition of the leopard (Panthera pardus) in the northeastern Himalayan region of Pakistan. We used molecular scatology technique to identify scats of common leopard collected from the field. The leopard was recorded at 30 different surveyed sites with an elevational range between 757-1891 m a.s.l. Its diet comprised 17 prey species, including both wild and domestic prey. Frequency of occurrence of wild prey was approximately 35% of the total leopard diet, …

Mesostigmata Mites (Acari: Parasitiformes) Associated With Birds And Their Nests From, Mohamed Waleed Negm, Azza Abdelgawad Mohamed, Hosam Mohamed Khalil El-Gepaly, Safaa Mohamed Abdelaziz

Turkish Journal of Zoology

A survey of gamasid mites (Arachnida: Acari: Mesostigmata) associated with domestic and wild birds in Egypt was conducted. In total, 16 species within 10 families were collected from 22 bird species. The most abundant species belonged to the genera Dermanyssus Dugès (Dermanyssidae), Ornithonyssus Sambon, and Steatonyssus Kolenati (both Macronyssidae). Among various birds examined, the distribution and occurrence of mites were recorded. Taxonomic remarks about the morphology of the collected mites are presented to facilitate species discrimination for non-acarologists. Steatonyssus longipes Radovsky & Yunker, 1963, previously described as a new species from the Egyptian slit-faced bat, Nycteris thebaica Geoffroy (Chiroptera), is …

Three New Records From Phylinae (Hemiptera: Heteroptera: Miridae) For The Turkish Fauna, Gülten Yazici, Erol Yildirim

Turkish Journal of Zoology

This study was conducted in the Erzurum province of Turkey during 2009-2014. The species Criocoris crassicornis (Hahn, 1834), Europiella artemisiae (Becker, 1864), and Paredrocoris pectoralis Reuter, 1878 were recorded for the first time from Turkey. The important taxonomic characters are described and photographs or illustrations are provided.

Many Paths Toward Discovery: A Module For Teaching How Science Works, Rebecca M. Price, Kathryn E. Perez

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

Improving students' understanding of how science works requires explicit instruction. Here, we test the efficacy of a module based on two previously published activities (the "Cube Puzzle" and the case study "Asteroids and Dinosaurs") that teach how science works to college science majors. Students also use the How Science Works Flowchart from Understanding Science (http://undsci.berkeley. edu/) to reflect on these activities. To assess the efficacy of this module, we asked students to illustrate the process of science before and after the intervention. After the intervention, students' diagrams were significantly more complex and nonlinear. Students also incorporated more social aspects of …

Oceanic, Latitudinal, And Sex-Specific Variation In Demography Of A Tropical Deepwater Snapper Across The Indo-Pacific Region, Ashley J. Williams, C. Wakefield, Stephen J. Newman, Elodie Vourey, Francisco J. Abascal, Tuikolongahau Halafihi, Jeremie Kaltavara, Simon J. Nicol

Fisheries Research Articles

Deepwater tropical fisheries provide an important source of income and protein to Pacific and Indian Ocean coastal communities who are highly dependent on fish for food security. The development of quantitative assessments and management strategies for these deepwater fisheries has been hindered by insufficient biological and fisheries data. We examine the age-specific demography of the pygmy ruby snapper Etelis carbunculus, an important target species in tropical deepwater fisheries, across 90° of longitude and 20° of latitude in the Pacific and Indian Oceans. Our results show that growth of E. carbunculus varies significantly between oceans and sexes and across latitudes …

The Age Structure Of A Population Of Aedes Provocans (Diptera: Culicidae) In Southwestern Ontario, Stephen M. Smith, Richard M. Kurtz

The Great Lakes Entomologist

In a previous paper it was shown that an eastern-Ontario population of the early-spring mosquito Aedes provocans had an atypical age structure: the adult-female population aged rapidly and synchronously, achieving an advanced gonotrophic age in an unusually brief period of time. The present study examined the age structure of Ae. provocans near Waterloo, in south-western Ontario, at a site at which adult emergence occurred over a wider, more variable period and at which the preferred nectar sources for young adults were much less abundant. In Waterloo, the adult-female population aged more slowly and much less synchronously than in eastern Ontario. …

Aphid Prey Of Passaloecus Cuspidatus (Hymenoptera: Sphecidae), John M. Fricke

The Great Lakes Entomologist

Provisioning activity of Passaloecus cuspidatus extended from 29 May through 6 August 1987. Eighty trap-nests contained 281 provisioned cells containing 9,618 aphids. The average number of aphids per cell was 34.2 and the average number of cells provisioned per day was 0.73. Passaloecus cuspidatus stored the following aphids as provisions: Cinaria sp., Euceraphis sp., Macrosiphum euphorbiae, Myzus sp., Myzus cerasi, Myzus monardae, and Sitobium avenae. The number of aphids provisioned per cell was inversely related to aphid size. The number of aphids provisioned per cell varied signifI­cantly (9-74).

Emerging Infectious Disease And The Imperiled Relict Leopard Frog, Anthony Wayne Waddle

UNLV Theses, Dissertations, Professional Papers, and Capstones

The disease chytridiomycosis, caused by the aquatic fungal pathogen Batrachochytrium dendrobatidis (Bd), has emerged as a major contributing factor for worldwide amphibian declines. Although relatively recently described, the impacts from the disease this pathogen causes have been definitively tied to amphibian declines, including some that occurred decades ago. In some cases, declines of individual species occurred with little documentation and are thus poorly understood. The relict leopard frog (Rana onca = Lithobates onca) has experienced such a decline and by the latter part of the 20th century only occurred in two general areas in southern Nevada. Recent research has found …