Life Sciences Commons^™

Secondary Structure Prediction Of Long Rna Sequences Based On Inversion Excursions And A Modularized Mapreduce Framework, Daniel Tesfai Yehdego

Open Access Theses & Dissertations

Ribonucleic acid (RNA) molecules and their secondary structures play important roles in many biological processes including gene expression and regulation. The genomes of many viruses are also RNA molecules. Since secondary structures are crucial for RNA functionality, computational predictions of the RNA secondary structures have been widely studied. However, the tremendous demands on computer memory and computing time for complex secondary structures limit the capability of existing thermodynamically based algorithms for structure predictions to handling only short RNA sequences with a few hundred bases. One approach to overcome this limitation is by first cutting long RNA sequences into shorter, non-overlapping …

Sensitivity Analysis Of Streambed Leakance Downstream Of Caballo Reservoir, Derrick Ohara

Open Access Theses & Dissertations

Modeling transient effects of streams near well fields is an important tool for understanding water balance within the Rio Grande Project (Project). The results are known as stream leakage. Stream leakage quantifies the amount of water seeping from a stream, canal and/or drain to/from a well field. Stream leakages near the Canutillo Well field, primary river losses for years 2005 through 2010 along with historical gain/losses and allocations of surface water with the associated agreements were evaluated.

The overall loss rates per mile in the Project for years 2005 to 2010 averaged -0.75 cubic feet per second (cfs). The historical …

Spatial Ecology Of The Trans-Pecos Rat Snake (Bogertophis Subocularis) In The Chihuahuan Desert Of Trans-Pecos Texas, Arturo Rocha

Open Access Theses & Dissertations

The Trans-Pecos Rat Snake (Bogertophis subocularis) is a medium to large rat snake that occurs from south-central New Mexico, south-central Texas, down into the north-central and northeastern states of Mexico. There is paucity in the ecology of B. subocularis to date. Some North American colubrid snakes, such as Thamnophis sirtalis, are the most represented species in thermal ecology and life history studies in all reptiles. There is nothing known on the winter ecological aspects of this species, and very little information regarding its overall ecology. The goal of this study is to determine home range, movement patterns, habitats and utilization …

Impact Of Nutrition Education In High School Students, Leticia Cortez

Open Access Theses & Dissertations

The diet of adolescents is typically high in calories, fat, and saturated fat and often fails to meet the daily recommended amounts of fruits, vegetables, and calcium-rich foods. The frequent consumption of unhealthy diets in combination with the lack of physical activity has resulted in a high prevalence of obesity worldwide. Approximately 17% of adolescents in the United States are obese. Obesity is a common risk factor for the development of chronic disease such as heart disease and diabetes. In the last few decades and along with a high prevalence of obesity there has also been an increased prevalence of …

Mobilizing Subdominant Hiv-Specific Ctls As A Novel Vaccine Strategy, Margaret Christina Costanzo

Open Access Theses & Dissertations

To overcome the extreme antigenic diversity of HIV, there is increasing interest in developing vaccines that target CD8 T cell responses to conserved regions of the viral proteome. Understanding the immunogenic potential of these domains is therefore critical for the success of this vaccine strategy. CD8 T cell responses to conserved domains restricted by the "neutral" and highly prevalent HLA-A2 allele have not been extensively characterized. Here we describe a novel essentially invariant 10-mer epitope in HIV Gag (p2414-23, RTLNAWVKVV (RV10)) in that it is expressed by the majority HIV isolates from all clades. Here we examined the character of …

Generalized Linear Latent Mixed Modeling Of Functional Independent Measures And Patient Outcomes, Maduranga Kasun Dassanayake

Open Access Theses & Dissertations

The Functional Independent Measure (FIM) is one of the most widely accepted functional assessment measures used in the rehabilitation community. Past research studies have investigated the relationship between place of discharge, admission FIM scores or FIM difference scores, and patients' characteristics and found relationships between those variables. However, most of these studies fail to account for the multi-layered multidimensionality of the FIM and the measurement error associated with the FIM items. This study utilizes Generalized Linear Latent Mixed Models (GLLAMM) and Structural Equation Models (SEM) to assess which patient characteristics are associated with FIM difference scores and the structural relationship …

What Is The Role Of Isolation And Disturbance On The Diversity Of Aquatic Invertebrates In Former Ranchlands Of The Northern Chihuahuan Desert?, Gena Esposito

Open Access Theses & Dissertations

The Chihuahuan Desert is considered one of the most diverse deserts in the world and its aquatic systems have been identified as unique and of global importance. Despite this, the Chihuahuan Desert has remained relatively unstudied, especially concerning its aquatic systems and how the extreme desert environment has shaped the diversity of the organisms within them. In this study we examined the effects of isolation and disturbance on macroinvertebrate diversity in both temporary and permanent desert ponds. To examine the effects of isolation and desiccation, macroinvertebrates were collected from a permanent spring (Squaw Spring) and six nearby temporary ponds (tanks) …

The Impact Of Solar Radiation On The Distribution Of The Red Imported Fire Ant, Solenopsis Invicta (Hymenoptera: Formicidae), Audrey Marie Hernando

Open Access Theses & Dissertations

This dissertation investigates the role of solar radiation on Solenopsis invicta, the red imported fire ant. This ant is considered a serious invasive pest in the southern United States. Four Texas cities where fire ants are found were studied: San Antonio, Corpus Christi, Wichita Falls, and the outlier, Lubbock. Shade angles were measured in eight compass directions within plots located along eight transect directions around buildings. Using the shade angle, solar radiation for different times of day and seasons were calculated. All of the cities were on the same precipitation isocline with the exception of Lubbock, Texas. The number of …

A Survey Of Selected Pharmaceuticals And Personal Care Products In A Binational River And Their Effects On A Member Of Its Zooplankton Community, Plationus Patulus (Rotifera), Diana Angelica Martinez Gomez

Open Access Theses & Dissertations

The presence of 9 selected PPCPs (acetaminophen, caffeine, cotinine, codeine, fluoxetine, erythromycin, ciprofloxacin, sulfamethazine, and trimethoprim) was surveyed in water samples collected at four sites along the middle Rio Grande during two flow regimes (irrigation and non-irrigation). Water collection for PPCPs analyses were conducted from August 2010 through September 2011. Three of the sites were located upstream, in, and downstream of the El Paso, TX/Ciudad Juárez, MX metroplex. Site selection was based on their proximity to the metroplex and due to the fact that the Rio Grande in this region is an effluent receiver water system (IBWC, 2011). The fourth …

Validating The Adidas Micoach For Estimating Pace, Distance, And Energy Expenditure During Treadmill Walking And Running, Sean T. Miller

Open Access Theses & Dissertations

The use of accelerometry based physical activity monitors among recreational athletes to meet or exceed recommended physical activity guidelines has grown in popularity. In the interest of capitalizing on this demand, Adidas developed the miCoach Pacer System which allows the user to observe pace, distance, and energy expenditure during walking or running. Purpose. To validate the accuracy of the Adidas miCoach activity monitor in estimating energy expenditure (EE) (kcal/min), pace (min/km), and distance (km) during treadmill walking and running, and for two different sensor configurations. Methods. Nine male and 9 female moderately endurance trained volunteers (mean ± SD age: 28.83 …

Examination Of The Neurochemical Mechanisms That Mediate Nicotine Withdrawal In Adolescent And Adult Rats, Luis Alberto Natividad

Open Access Theses & Dissertations

Introduction: The mechanisms that mediate nicotine withdrawal are presently unclear and age group differences in the neurochemical effects of withdrawal have been largely unexplored. Previous studies in our laboratory demonstrated that adult rats display a decrease in extracellular levels of dopamine in the nucleus accumbens (NAcc) during nicotine withdrawal and this decrease is reduced in adolescent rats (Natividad et al., 2010). The goal of this dissertation was to examine whether these age group differences in dopamine during withdrawal are mediated via excitatory and inhibitory mechanisms that modulate dopamine in the cell body region of the ventral tegmental area (VTA). Methods: …

Assessment Of Carbon Nanoparticle Exposure On Murine Macrophage Function, Raquel M. Suro

Open Access Theses & Dissertations

There is growing concern about the potential cytotoxicity of nanoparticles. Exposure to respirable ultrafine particles (2.5uM) can adversely affect human health and have been implicated with episodes of increased respiratory diseases such as asthma and allergies. Nanoparticles are of particular interest because of their ability to penetrate into the lung and potentially elicit health effects triggering immune responses. Nanoparticles are structures and devises with length scales in the 1 to 100-nanometer range. Black carbon (BC) nanoparticles have been observed to be products of combustion, especially flame combustion and multi-walled carbon nanotubes (MWCNT) have been shown to be found in both …

An Assessment Of Land Cover Change At The Indio Mountains Research Station, Rebecca Anne Escamilla

Open Access Theses & Dissertations

Land cover change is a significant contributor to environmental change on a global scale. In the arid regions of the southwest US, shrub encroachment is one of the most important forms of land cover change. Many factors contribute to shrub encroachment, which can impact structure and function. In the Chihuahuan Desert, mountain ecosystems are known as biodiversity hotspots and are especially susceptible to environmental change making them useful indicators of global change. The overarching goal of this dissertation is to improve i) understanding of land cover change in a Chihuahuan Desert mountain landscape, and ii) how knowledge of land cover …

Jak3/Stat5 Signaling Cascade Represents A Therapeutic Target To Treat Select Hematologic Malignancies, Damaris Rosado

Open Access Theses & Dissertations

Tyrosine kinases are an essential component of cell signal transduction pathways, many of which promote cellular proliferation. However, when a tyrosine kinase is aberrantly activated or its negative regulation is lost, the result can be malignancy. In humans, 90 tyrosine kinases are present and of these, 51 have been linked to a malignancy through mutation or overexpression. Janus kinase 3 (JAK3) is one such kinase that upon hyperactivation, due to a somatic mutation, has been linked to cancer including its substrate, signal transducer and activator of transcription (STAT5). Few studies have investigated the role of JAK3/STAT5 pathways in hematopoietic cancers …

Further Characterization Of The Nodamura Virus Rna2 3'-Terminal Stem Loop Structure And Its Role In Viral Rna Replication, Joshua Frederick

Open Access Theses & Dissertations

Nodamura virus (NoV) is an excellent model system for studying many aspects of the life cycle of positive-strand RNA viruses. NoV's simple genome organization and ability to replicate its genome to high levels in a wide variety of host cells, including plants, yeast, insects and mammals (Ball et al., 1992; Garzon et al., 1978, 1990; Murphy et al., 1970; Price et al., 2005; Scherer & Hurlbut, 1967; Selling et al., 1990; reviewed by Ball & Johnson, 1998), make it a prime model system for studying the basic mechanisms of viral RNA replication. Other positive-strand RNA viruses, including those that are …

The Impact Of Decadal Land Cover Change On The Global Warming Potential Of Beringian Arctic Tundra, David Hwei-Len Lin

Open Access Theses & Dissertations

Arctic terrestrial ecosystems play an important role in the global carbon cycle. If arctic warming continues to rise as projected, large amounts of soil carbon stored in these ecosystems could be released to the atmosphere as carbon dioxide or methane and positively enhance greenhouse warming. Thus, improving understanding of the likely future state and fate of arctic soil carbon, and the carbon uptake potential of arctic terrestrial ecosystems are well recognized research priorities.

At the pan-arctic scale, decadal increases in NDVI (Normalized Difference Vegetation Index), an index of vegetation productivity, have been observed from satellite imagery, indicating a general greening …

Functional Characterization Of P90/Cip2a In Human Lung Cancer, Bo Peng

Open Access Theses & Dissertations

p90/CIP2A is a recently characterized oncoprotein which promotes cancer cell proliferation through the inhibition of c-myc-associated PP2A phosphatase activity, from which it derived the name as cancerous inhibitor of PP2A (CIP2A). Although p90/CIP2A has been found to be overexpressed in various cancer types, from solid tumors to hematological malignancies, the function of this protein is still limited to its ability to regulate the stability of c-myc. The recent study showing p90/CIP2A is able to regulate the phosphorylation of protein kinase B (PKB) in response to the treatment of chemotherapy drugs implied p90/CIP2A may have more functions. In order to investigate …

Implications Of Decade Time Scale Arctic Plant Community Change On Ecosystem Function, Mark Jason Lara

Open Access Theses & Dissertations

Almost half the global soil organic carbon pool is found in northern high latitudes. The majority of this soil carbon is stored in a greenhouse inert state within permafrost. As pronounced warming of high northern latitudes ensues, there is a strong likelihood that this substantial soil organic carbon pool will be mobilized to the atmosphere where it is likely to positively enhance greenhouse warming. Modeling studies suggest this positive feedback could alter future climate states of the Arctic and the globe, and affect how humans may need to adapt to climate change. Accordingly, understanding the patterns and controls and the …

Recent Changes In The Growth And Nutrient Limitation Of Benthic And Pelagic Algae In Arctic Tundra Ponds, Christina Hernandez

Open Access Theses & Dissertations

Arctic ponds are a dominant feature in Barrow, Alaska. Ponds may function as carbon sinks during the growing season from production of photosynthetic organisms like algae; however, little work has been done on this topic. Environmental changes have been occurring in the Arctic stemming from climate change and human perturbations. The focus of this study was to assess a historically studied region for changes in algal primary production that may have been produced due to increases in temperature over the past 40 years and increased human development. Additionally, this study aimed to determine nutrient limitation of algal production in the …

Biological Effects Of Copper On Prosopis Pubescens (Screw Bean Mesquite), Marian Nicte Zappala

Open Access Theses & Dissertations

Phytoremediation is an emerging technology for cleaning industrial and urban contamination (Peuke and Rennenberg, 2005). Many factors including germination rate, biomass changes, biochemical changes, and nutrient changes must be determined in order to utilize a plant for phytoremediation. Our results showed that Prosopis pubescens (Screw bean mesquite) is a hyperaccumulator of copper from copper sulfate and a feasible option to remediate fields with up to 200 ppm of copper sulfate.

Screw bean mesquite seeds are viable even after 30 years of storage. Both copper sulfate and copper nitrate decreased the germination rate of screw bean mesquite seeds. In soil grown …

Systematics Of Leptopelis (Anura: Arthroleptidae) From The Itombwe Plateau, Eastern Democratic Republic Of The Congo, Francisco Portillo

Open Access Theses & Dissertations

Leptopelis, a genus of Central African treefrogs, includes 51 species that live in tropical forests and savannas. Currently, only two species of Leptopelis are known from the poorly explored Itombwe Plateau in eastern Democratic Republic of the Congo (DRC). Itombwe is renowned among conservationists for its rich and endemic amphibian fauna, including: Xenopus itombwensis, Chrysobatrachus cupreonitens, Laurentophryne parkeri, Hyperolius leleupi and at least three species of Arthroleptis. Evolutionary relationships of Itombwe Leptopelis were examined by sequencing two mitochondrial genes (16S: 557 bp [base pairs], cyt b: 620 bp) and one nuclear gene (RAG1: 761 bp). Results recovered strong support for …

Microelement Localization In Leaves Of Populus Spp. And Tolerance Mechanisms To Boron-Salt Toxicity, Daniel Arriaga

Open Access Theses & Dissertations

Phytoremediation has been proposed as a low-cost, environmentally friendly alternative to clean highly contaminated sites. Phytoremediation using trees offer the advantage of metal immobilization (phytostabilization), high hydraulic pumping pressures, produce large plant biomass, absorption of total dissolved salts within their tissue, long life spans, less frequent irrigation and, a massive root system that helps soil attachment. Hybrid poplar varieties are long-lived, perennial, fast growing, and produce a large amount of foliage to harvest. Boron is an essential micronutrient for plants. Certain locations, such as California and Turkey, have suffered from high boron efflux from irrigation waters. It has been identified …

Investigation Of The Membrane Interactions Of Mycobacterium Tuberculosis Secreted Factors Esat-6 And Cfp-10, Joaquin A. De Leon

Open Access Theses & Dissertations

Mycobacterium tuberculosis is the causative agent of the infectious disease tuberculosis, infecting about one-third of human race. Infections are not vast in the United States when compared to many other countries, yet many cases seen in the United States are of those who have immigrated to the United States. The Hispanic/Latino population in the United States contributes to a large fraction of those infected with tuberculosis in the United States. During this study we purified recombinant Mycobacterium tuberculosis secreted factors ESAT-6 and CFP-10 from Escherichia coli. Here we have introduced a method in which we can refold and purify …

Evaluation Of Protection Induced By Dna Vaccine Candidate Against Leishmania Mexicana In Balb/C Mice Model, Rosina Rodarte

Open Access Theses & Dissertations

Background and Significance. The leishmaniases are a diverse group of diseases with four major clinical manifestations: cutaneous, mucocutaneous, visceral, and diffuse. Approximately 21 Leishmania species and 30 sandfly vectors have been implicated in human leishmaniasis. Leishmaniasis is endemic in 88 countries, 72 are developing countries. Currently, 350 million people live in leishmaniasis-endemic areas around the world. The true incidence of the disease is not known. However, the estimated incidence for visceral leishmaniasis is 500,000 cases per year, and for cutaneous and mucocutaneous leishmaniasis 1.5-2 million cases per year. Visceral leishmaniasis causes 70,000 deaths each year. In the Americas region, …

Arachidonic Acid Signaling In Invasive And Non-Invasive Breast Cancer Cells, Debarshi Roy

Open Access Theses & Dissertations

Breast cancer is the second largest cause of cancer-related deaths in women all over the world. Epidemiological studies suggest that the consumption of high-fat diets can promote the incidence of breast cancers in both developed and developing countries. In particular, the lipid-rich diet contains arachidonic acid (AA, a C20:4 polyunsaturated fatty acid), which has been shown to be associated with tumor formation in breast tissues. Nevertheless, the actual mechanism by which AA induces the metastatic transformation and malignancy is not well understood. The goal of my dissertation, therefore, is to identify the molecules and unravel the pathways that participate in …

Characterization Of The Behavioral, Biochemical And Molecular Indices Of Stress Produced By Nicotine Exposure And Withdrawal In Male And Female Rats, Oscar Valentin Torres

Open Access Theses & Dissertations

Introduction: Tobacco use is a major economic and health problem. Particularly concerning is that women consume more tobacco products, have a more difficult time quitting, and are less likely to benefit from cessation therapies than men. As a result, women are at higher risk of developing tobacco-related diseases. Women are generally more susceptible to stress and are more likely to cope with stress by smoking as compared to men. During abstinence, women also experience intense anxiety as compared to men and report that the anxiety-reducing effects of smoking are the main reason for continued use and relapse. Thus, stress produced …

Sustainable Disposal Of Brine, Bijoy Krishna Halder

Open Access Theses & Dissertations

To meet growing water demand, more water is being harvested from nontraditional sources like brackish water from deep underground aquifers. Since these sources contain salts, drinkable water is produced by separating salt and other minerals (TDS, Total Dissolved Solids) from water through a process commonly known as desalination. A typical desalination plant produces 50-60% potable water from brackish water and the remaining water (brine) is disposed in evaporation ponds or by injecting it below the ground surface. To maximize the limited water supply, inland desalination plants have developed technologies to reduce brine production commonly known as zero liquid discharge (ZLD) …

The Effects Of Extended Access To Methamphetamine Self-Administration On Dopaminergic Markers In The Striatum, Joe Luevano

Open Access Theses & Dissertations

Methamphetamine (METH) abuse is a persistent problem in the U.S. and abroad. Escalation of METH use among independent users occurs for a variety of physiological and psychological reasons. Methamphetamine dependence may be attributed to the rewarding effect of this drug via the dopaminergic systems of the central nervous system (CNS). The presence of METH in the CNS increases synaptic release of dopamine. This increase in dopaminergic neurotransmission is thought to be directly attributed to the rewarding effects of METH. Following METH use, compensatory changes have been found to occur in the dopaminergic system during various periods of abstinence. It is …