Browsing by Subject "Genetics"
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Item A genetic study of the stormproof boll in Gossypium hirsutum L.(Texas Tech University, 1977-08) Dilbeck, Ray EdwinNot availableItem Advances in applications of modern biotechnology methods in methanogens(2014-08) Williams, Bianca Aleceya; Contreras, Lydia M.Methanogens are autotrophic Archaea that produce methane as a product of their anaerobic metabolism. They are the largest producers of global methane, contributing over 60% of the total methane budget each year. Methane is an extremely potent greenhouse gas, with emissions providing the second-largest contribution to historical global temperature increases after carbon dioxide. Methanogens have become extremely important industrially as because they are used in the production of biofuels, as well as in treating industrial waste for industrial processes. This report will focus on those successful genetic methods and modifications that have been developed for methanogens and how they have started to contribute to understanding methanogen biochemistry.Item An assessment of health educators' likelihood of adopting genomic competencies for the public health workforce(2009-05-15) Chen, Lei-ShihAlthough the completion of the Human Genome Project helps develop efficient treatment/prevention programs, it will raise new and non-trivial public health issues. Many of these issues fall under the professional purview of health educators. Yet, no studies have evaluated if health educators (HEs) are ready to adopt genomic competencies into health promotion. This dissertation addresses this issue by examining three research questions in three separate studies: 1) Why must HEs develop genomic competencies? 2) What are HEs? knowledge of, and attitudes toward genomic competencies? And 3) what is HEs? likelihood of adopting genomic competencies into health promotion? The first theoretical study proposed five arguments supporting the need for HEs to develop their genomic competencies and integrate public health genomics into health promotion. These arguments touched on various dimensions of HEs? professional goals and ranged from professional responsibilities and competencies, to the availability of funding for genomic-related research or interventions and opportunities for future employment. For the second study, a web-based survey was developed and distributed to all members of four major health education organizations. A total of 1,925 HEs? completed the survey and 1,607 responses were utilized in the final analysis. This study indicated that participants had deficient knowledge and unfavorable attitudes toward the CDCproposed genomic competencies. In the third study, a theoretical model was developed to predict HEs? likelihood to incorporate genomic competencies into their practice. Using techniques from Structural Equation Modeling (SEM), the model was tested with the same data of the second study. Findings supported the proposed theoretical model. While genomic knowledge, attitudes, and self-efficacy were significantly associated with HEs? likelihood to incorporate genomic competencies into their practice, attitudes was the strongest predictor of likelihood. In summary, these studies indicated that participating HEs had deficient genomic knowledge, unfavorable attitudes toward a set of CDC-proposed genomic competencies, and low likelihood to adopt genomic competencies into health promotion. Relevant training should be developed and advocated. As the SEM analysis results indicated the survey findings supported the proposed theoretical model, which can be utilized to steer future training for HEs.Item An object-oriented framework to organize genomic data(2009-05-15) Wei, NingBioinformatics resources should provide simple and flexible support for genomics research. A huge amount of gene mapping data, micro-array expression data, expressed sequence tags (EST), BAC sequence data and genome sequence data are already, or will soon be available for a number of livestock species. These species will have different requirements compared to typical biomedical model organisms and will need an informatics framework to deal with the data. In term of exploring complex-intertwined genomic data, the way to organize them will be addressed in this study. Therefore, we investigated two issues in this study: one is an independent informatics framework including both back end and front end; another is how an informatics framework simplifies the user interface to explore data. We have developed a fundamental informatics framework that makes it easy to organize and manipulate the complex relations between genomic data, and allow for query results to be presented via a user friendly web interface. A genome object-oriented framework (GOOF) was proposed with object-oriented Java technology and is independent of any database system. This framework seamlessly links the database system and web presentation components. The data models of GOOF collect the data relationships in order to provide users with access to relations across different types of data, meaning that users avoid constructing queries within the interface layer. Moreover, the module-based interface provided by GOOF could allow different users to access data in different interfaces and ways. In another words, GOOF not only gives a whole solution to informatics infrastructure, but also simplifies the organization of data modeling and presentation. In order to be a fast development solution, GOOF provides an automatic code engine by using meta-programming facilities in Java, which could allow users to generate a large amount of routine program codes. Moreover, the pre-built data layer in GOOF connecting with Chado simplifies the process to manage genomic data in the Chado schema. In summary, we studied the way to model genomic data into an informatics framework, a one-stop approach, to organize the data and addressed how GOOF constructs a bioinformatics infrastructure for users to access genomic data.Item Assessing genetic variation in natal populations of small Canada geese via microsatellite loci(Texas Tech University, 1997-08) Cathey, James C.Traditionally, waterfowl biologists have identified specific groups of Canada geese (Branta canadensis) by the recovery of marked individuals and/or their winter distribution. From winter distributions and field observations of marked birds, small Canada geese in the Central Flyway have been placed into two categories, the Tall Grass Prairie (TGP) and Short Grass Prairie (SGP) populations. These populations nest primarily in the Northwest Territories, Canada. The SGP nest between the Mackenzie River Delta and the Queen Maud Gulf along the Arctic Ocean, whereas the TGP geese nest from eastern Queen Maud Gulf to Baffin and Southampton Islands, and along the west coast of Hudson Bay. The SGP population winters in western Oklahoma, northeastem New Mexico, southeastern Colorado, with the largest portion residing in the panhandle of Texas. The TGP population winters in southeastern Oklahoma, and along the Gulf coast of Texas and Mexico. Although banding and collaring data provide information on the organisms movement, it does not predict potential gene flow, nor does it give the history of a birds genetic make-up. We now have the technology to assess an organism's genetic background. Because Canada geese are philopatric, this behavior increases the potential for populations to become genetically isolated. This project sought to determine whether the genetic structure of individuals corresponds to the TGP and SGP categories defined by field observations. I tried to determine if there were genetic subdivisions among geographically distinct groups. I conducted a search for genetic markers that provide direct rather than implied information regarding breeding groups. This was done by constructing a genomic DNA library and three microsatellite sub-libraries. Polymerase chain reaction (PCR) primers were constructed to amplify each microsatellite locus. For each of the five informative microsatellite loci, 13 natal populations (n = 458) of small Canada geese were assessed for allelic variation.Item Characterization of an ORF in a novel orientation in Escherichia coli(Texas Tech University, 2003-12) Lackey, Melinda K.Evidence has been presented in the literature that demonstrates the expendable nature of the C-terminal region for the proper functioning of TolC in the bacterial cell. Recent sequencing of various microbial genomes demonstrated the presence of 3' overlapping, converging open reading frames involving tolC and its homologues found in other species and genera of bacteria. In this study, we examined the Escherichia coli tolC gene and the 3' overlapping, converging ORF found at the same genetic locus, denoted cloT for tolC in reverse. The expression of c/or was examined using reverse transcriptase PCR to identify the presence of mRNA molecules within the bacterial cell. Amplification of a 120 base pair fragment from total RNA isolated from wild-type E. coli suggested that cloT was transcribed, at least at low levels, in the organism. To corroborate these data, the upstream region of the structural gene was analyzed for the ability to drive transcription of a reporter gene, beta-galactosidase. Activity analysis of this reporter fusion demonstrated the ability of the upstream region of the cloT gene to drive transcription in E. coli. Similarly, we have demonstrated an interaction between the upstream region of cloT and soluble proteins isolated from the cytoplasm of wild-type E. coli. Further experiments were attempted to raise antibodies against a portion of the putative CloT protein using both GST fusion technology and a synthetic peptide. Neither has been fully characterized at time of publication. In addition, attempts to isolate mutations in the unique region of the cloTORF in the chromosome of E. coli were also unsuccessful. Examination of the information known about TolC and its homologues in different genera of bacteria revealed interesting information concerning the C-termini of these proteins. Alignment of the amino acid sequences demonstrated lower identity shared in the C-terminal region of these proteins. In addition, examination of the nucleotide sequences of these homologues indicated the presence of a similar open reading frame sharing a convergent, overlapping relationship with its respective tolC homologue. When combined with published data concerning the expendable nature of the last fifty amino acids of TolC, these data suggest that the presence of a conserved open reading frame in this region may play an important role in the regulation or function of the tolC gene or gene product(s).Item Determination of the genetic basis of seed oil composition and melting point—adaptive quantitative traits—and their fitness effects in Arabidopsis thaliana(2013-12) Pelc, Sandra Elaine; Linder, C. RandalEvidence indicates seed oil melting point is likely an adaptive quantitative trait in many flowering plant species. An adaptive hypothesis suggests selection has changed the melting point of seed oils to covary with germination temperatures because of a trade-off between total energy stores and the rate of energy acquisition during germination under competition. The predicted differences in relative fitness under different temperatures have not yet been tested and little is known about the genetic basis of differences in oil composition. I used Arabidopsis thaliana to: (1) assess the fitness consequences of high and low melting point seeds germinating at different temperatures, (2) assess what genes underlie natural variation in seed oil composition, and (3) consider how these genes may be used to create oils with particular characteristics. To assess the effects of seed oil melting point on timing of seedling emergence and fitness, I competed high and low melting point lines of A. thaliana under cold and warm temperatures. Emergence timing between these lines was not significantly different at either temperature, which comported with warm temperature predictions but not cold temperature predictions. Under all conditions, plants competing against high melting point lines had lower fitness relative to those against low melting point lines, which matched expectations for undifferentiated emergence times. To assess the genetic basis of naturally occurring variation in seed oil melting point, the seed oil compositions of 391 accessions of A. thaliana were used in a genome-wide association study. Twelve genes were tightly linked with SNPs significantly associated with seed oil melting point variation. Seven encoded lipid synthesis enzymes or regulatory products. The remaining 5 encoded products with no clear relation to seed oil melting point. Results suggest selection can alter quantitative trait variation in response to local conditions through a small set of genes. 268 seed-expressed, candidate genes were linked to 103 SNPs associated with A. thaliana seed oil fatty acids. Eight genes were involved in lipid metabolism, and thirty-four encoded regulatory products. I discuss how knowledge of these genes can be used to breed and engineer desirable oil compositions for industry and nutrition.Item Diazepam binding inhibitor and tolerance to ethanol in Drosophila melanogaster(2012-12) Robles, Roseanna Beth; Atkinson, Nigel (Nigel S.); Aldrich, Richard; Duvauchelle, Christine; Mihic, John; Zakon, HaroldTolerance to ethanol is an endophenotype of alcoholism, allowing the study of a complex psychiatric condition using animal models. To identify new genes involved in the acquisition of tolerance, I designed an automated and high-throughput tolerance assay and screened a collection of deficiency mutants for the inability to develop tolerance. The screen yielded several “regions of interest” where more than one overlapping deficiency failed to develop tolerance. One of these regions comprised nine genes, and testing the expression levels of each gene revealed that diazepam binding inhibitor (Dbi) showed grossly increased expression in the deficiency mutant compared to wild type. Another mutant stock, with a P-element transposon inserted downstream of the Dbi gene, both failed to develop tolerance and showed further increased expression of Dbi. There are two insulator binding sites flanking Dbi, and the P-element transposon also contains insulator binding sites. Based on these results, it was hypothesized that an insulator complex kept Dbi expression low in wild type flies and that disrupting the insulator complex allowed aberrantly high expression of Dbi in the mutants. Furthermore, we assumed that induction of Dbi blocked tolerance by making the mutants resistant prior to the first sedation. A UAS-DBI transgene was constructed to over-express Dbi. Induction of the UAS-DBI with a heat shock gal4 driver induced resistance to ethanol sedation; a similar response was observed in the parental control, but the effect was smaller. Although driving UAS-DBI with the neural elav-gal4 driver did not block tolerance, the experimental stock was resistant to ethanol sedation compared to the parental controls, indicating that increased Dbi expression produced “pre-tolerance.” To confirm the theory that insulator disruption was responsible for the increase in Dbi and the resulting no-tolerance phenotype, the P-element in the second mutant was mobilized by introducing a transposase source. These offspring lines were analyzed using qualitative PCR to determine whether the transposon excised precisely, left a portion of the transposon behind, or removed some of the flanking region. A precise excision mutant was identified, but this mutation did not rescue tolerance as predicted. This result might indicate that genetic background was the cause of the no-tolerance phenotype, or it might indicate that the excision was not exactly precise and removed the native insulator binding site, causing the insulator complex to remain disrupted.Item DNA target site recognition and toward gene targeting in mammalian cells by the Ll.LtrB group II intron RNP(2013-05) Hanson, Joseph Haskell; Lambowitz, AlanMobile group II introns insert site-specifically into DNA target sites through a mechanism ("retrohoming") that involves reverse splicing of the intron RNA into the DNA and its subsequent reverse transcription by an intron-encoded protein (IEP) that is associated with the RNA in a ribonucleoprotein (RNP) complex. Characterization of this RNP complex and its retrohoming activities have enabled the development of programmable mobile group II intron gene targeting vectors routinely used in prokaryotic organisms. Building upon recent research by our lab to develop gene targeting in Xenopus laevis and Drosophila melanogaster using the group II intron Ll.LtrB from Lactococcus lactis, I describe work to extend this system to mammalian cells. I demonstrate that group II intron RNPs can be delivered to mammalian cells efficiently and produced in vivo via a CMV/T7 hybrid expression system. Using a robust single-strand annealing assay to detect homologous recombination induced by double-strand breaks (DSBs), I found that group II intron-mediated DSBs are efficiently repaired by mammalian cells. Despite varied approaches, I failed to detect endogenous group II intron-mediated gene targeting in human and mouse cells in culture. Gene expression microarray analysis and in vivo imaging of RNP molecules indicated that group II intron RNPs are sequestered away from the genome and induce host innate immune responses. I also investigated how the C-terminal DNA-binding domain of the Ll.LtrB IEP contributes to DNA target site recognition. Building upon previous mass spectrophotometric analysis of site-specific UV-crosslinking, I used genetic and biochemical analyses to identify potential protein contacts for key target site residues T-23 and T+5. Genetic selection of mutants in a region contacting T+5 led to identification of LtrA variants with increased retrohoming efficiency. My results provide evidence that the DNA-binding domain of a group II intron reverse transcriptase functions in DNA target site recognition and suggest new methods for changing its DNA target specificity and targeting efficiency.Item Evaluation of Immune Response and Performance in Steers of Known Genetic Background Vaccinated and Challenged with Bovine Viral Diarrhea Virus(2011-02-22) Runyan, ChaseThis research was directed at investigating the variation in immune response of cattle when administered a known challenge from Bovine Viral Diarrhea Virus (BVDV) following different Bovine Respiratory Disease (BRD) vaccine treatments. Cattle were assigned vaccine treatments with sire and cow family was stratified across treatments to assess the role genetic differences may impact immune function. The same BVDV strain and challenge technique were used in two trials (2008 and 2009) in Angus-sired yearling steers. Data from these two years were analyzed separately because the cattle were managed and fed differently. Blood antibody Immunoglobulin-G (IgG) titers for IBR, BVD Type 1 and BVD Type 2 were higher for cattle in the Killed vaccine group than the MLV or NON vaccinated groups (P < 0.05) in both years. In the 2008 study, average daily gain (ADG) was higher for cattle from the Killed vaccine group (P < 0.05) for the 28 d following BVDV challenge, but no cattle were classified as morbid based on rectal temperature. In the 2009 study, differences in rectal temperatures were observed, and a total of 35 of 93 having over 40.0 degrees C (28 in the first 14 d following challenge). Cattle in the MLV vaccine group had lower overall mean temperatures, with no animals having rectal temperatures over 40 degrees C 14 d following viral challenges. Differences in rectal temperature were also observed due to sire. Differences in feed intake also occurred due to treatment, day, treatment ? day interaction, and maternal-grandsire. The MLV vaccine group maintained more constant levels of intake as compared to Killed and NON vaccinated cattle at days 5 to 12. Although large differences in titers following BVDV challenge were observed, the relationships of this immune response with animal health and performance appears very complex.Item Evolution of 12S rRNA gene in pocket gophers (Genus: Geomys)(Texas Tech University, 1997-12) Jolley, Ted W.Pocket gophers are known for their fossorial lifestyle, small isolated populations, and low fecundity. These characteristics make pocket gophers an ideal group for examining rate heterogeneity and sequence divergence in light of recent hypotheses concerning metabolic-rate and body size. To test these hypotheses, the mitochondrial 12S ribosomal (rRNA) gene was sequenced from individuals representing 10 species of the genus Geomys. In addition, specimens of Cratogeomys castanops. Thomomvs bottae. T^ umbrinus. Dipodomvs philHpsii. and Pedetes capensis were examined as outgroups. Specifically, the goals of this study were to: (1) determine if heterogeneity existed in rates of sequence divergence between fossorial and nonfossorial rodents, (2) determine intrageneric nucleotide sequence variation at the 12S rRNA gene, and (3) determine if the 12S rRNA gene contains phylogenetic signal to resolve the phylogenetic relationships within Geomys. The overall levels of 12S rRNA sequence divergence observed (average 3.5, range 0.6-7.5) support a low level of divergence within Geomvs. with the overall transition/transversion ratio lower than that observed in other mammalian groups. Relative rate tests did not detect significant overall levels of rate heterogeneity within and among Geomvs and outgroup taxa, nontheless certain taxa did show rate heterogeneity when compared to other members within group. The resultant 12S rRNA gene phylogenies provided strong phylogenetic signal and consistently supported several relationships within species and subspecies of Geomvs.Item Functional characteristics of genes involved in brassinosteroid signaling in cotton(Texas Tech University, 2003-12) Sun, YanCotton fibers are highly elongated single celled trichomes that grow from the seed integument. Elongation of fiber cells begins almost after ovule fertilization and continues for approximately 20 days. In this study, I have shown that BR signaling is necessary for cotton fiber initiation and elongation, using in vitro cultured cotton ovule with Brassinosteroids (BR) and brassinazole (Brz, BR biosynthesis inhibitor). BRs are polyhydroxylated sterol derivatives of plant origin that are required for normal plant development. Several Arabidopsis genes that encode critical components of this pathway have been identified through genetic screening. BRM encodes a membrane-bound leucine-rich receptor-like kinase that apparently acts as the BR receptor. BIN2, which acts downstream of BRM in this pathway, encodes a GSK3/SHAGGY-like kinase that down-regulates BR signaling. To understand the role of cotton orthologous genes in fiber development, cotton ESTs similar to the Arabidopsis BRM and BIN2 genes were identified. These ESTs were used to clone the corresponding full-length GhBRM and GhBIN2 cDNAs. The GhBRM was cloned from a cotton cDNA library and then amplified from cotton genomic DNA. This 3561 bp gene contains no introns and encodes a protein with 1187 amino acids. Database analyses shows that the GhBRM protein has all the distinct domains characteristic of BRM. Four GhBIN2 cDNAs were also cloned. They all include a coding sequence of 1146 base pairs in length and encode derived proteins of 381 amino acids. Sequence comparison with mammalian GSK3p and Drosophila GSK3/SHAGGY-like kinase showed that GhBIN2 proteins share many conservative regions with these two GSK3/SHAGGY-like kinases. Analysis of the expression patterns of the GhBRM and GhBIN2s genes using quantitative real-time PCR showed that they are expressed throughout cotton plants, including leaves, buds, hypocotyls, roots, sepals, ovules, bolls, and fibers. To identify the functions of these genes, gene constructs that express GhBRM and GhBIN2 under control of a CaMV 35S promoter were developed. Expression of the GhBRM transgene in the dwarf bri1-5 mutant Arabidopsis plants restored them to normal height. Expression analysis showed that the heights of the transgenic plants were significantly correlated with the GhBRH expression level (r = 0.97). These results strongly suggest that the GhBRH gene encodes a functional BR receptor protein. Conversely, expression of the GhBIN2 transgene in wildtype Arabidopsis plants resulted in severe stunting similar to strong BR deficient or insensitive mutants. Expression analysis showed that the heights of the transgenic plants were inversely correlated with these GhBlN2 expression levels (the average correlation level r= -0.90). These results indicate that the GhBlN2 genes function as negative regulators of BR signal transduction pathway. These results confirm that the GhBRM and GhBIN2 cDNAs encode proteins that are capable of functioning in the BR signaling pathway. BR signal transduction pathway could provide the basis for genetic modification of fiber development.Item Functional characterization of transcriptional inhibitory domains in the C/EBP-epsilon basic region/leucine zipper transcription factor(Texas Tech University, 2003-08) Li, YaminC/EBPE is a member of the CCAAT/enhancer binding protein (C/EBP) family of transcription factors and is primarily expressed in neutrophils. Multiple functional domains were previously identified in the C/EBPe polypeptide including a regulatory domain (RD or RDI) that negatively regulates the activity of C/EBPe. Within the RD a five amino acid motif (the regulatory domain motif (RDM)) is conserved in three other C/EBP family members and is critical for the inhibitory function of the RD. Interestingly the RDM is similar to the recognition sequence for the small ubiquitin-like modifier protein (SUMO) and attachment of SUMO to the RDM can activate C/EBPe. The goal of this study was to explore the molecular mechanisms by which the RD controls C/EBPe activity. These experiments may provide important information about general transcriptional regulatory mechanisms as RD-like elements, and SUMO attachment sites, exist in inhibitory domains of a large number of transcriptional regulators. Two models were designed to explain the mechanism of the function of the RD. One model proposes that intra-molecular interactions exist between the RD and its linked activation domain (AD), thereby blocking access of the AD to components of the transcriptional machinery. In this model, the attachment of SUMO to the RDM releases the AD and activates C/EBPe. Physical interactions between the RD and AD were not detected in either a mammalian two-hybrid assay or a direct interaction assay. The validity of this first model was also assessed by examining the activation domain specificity of the RD. The C/EBPe RD was capable of inhibiting linked ADs from three different classes, suggesting that the RD is unlikely to function according to model one. The second model assumes the RD functions by recruiting as yet unknown inhibitory RDM binding factor(s) (RDM-BF). In this model, SUMO attachment would displace the RDM-BFs thereby releasing the inhibitory effect of the RD. The first candidate RDM-BF tested was the family of proteins with histone deacetylase (HDAC) activity as these proteins are classically associated with co-repressor activity. Although the activity of C/EBPe was increased in the presence of the general HDAC inhibitor Trichostatin A, this effect was not dependent on the integrity of the RDM. These results indicate that C/EBPe may recruit HDACs through a domain separate from the RDM. In conclusion, the AD and RD of C/EBPe appear not to directly interact, however, additional candidate RDM-BFs must be identified and examined to determine whether the RDM functions by recruiting accessory, inhibitory proteins.Item Genetic compatibility of Rana areolata with southwestern members of the Rana pipiens complex: (Anura : Ranidae)(Texas Tech University, 1968-08) Cuellar, Hector SaulNot availableItem Genetic structure, heterozygosity, and energetic patterns in wintering mallard and American wigeon populations on the southern High Plains of Texas(Texas Tech University, 1991-08) Rhodes, Olin EugeneThe objectives of this study were (1) to estimate the relative Wahlund effect observed within and among groups of mallards during migration into the wintering grounds of the Southern High Plains (SHP), and evaluate the relative accumulation of genetic information in the wintering population of mallards that migrate onto the SHP; (2) to determine if lipid reserves or body masses of mallards are correlated to multilocus genetic variation; (3) to determine if carcass component reserves of wintering American wigeon (Anas americana) are affected by demographic or environmental variables; and (4) to determine if carcass component reserves of wintering American wigeon are correlated to multilocus genetic variation. Mallards (n=325) and American wigeon (n=643) were collected from the SHP of Texas from 15 October 1988 to 15 March 1989. Lipid and body masses were estimated for mallards. Body mass and masses of carcass components (lipid, protein, mineral, and water) were estimated for American wigeon. Mallards and American wigeon were surveyed electrophoretically for genetic variation at 30 and 25 loci, respectively. Mallards and American wigeon had high levels of genetic variation compared to estimates for waterfowl or avian species in general. The genetic information obtained for wintering mallards exhibited a deficiency of heterozygotes (11.7%), which is indicative of the presence of a mixture of genetically heterogeneous populations in the wintering sample. Mallards carrying significant amounts of new genetic information arrived into the wintering area until at least the middle of December. Mallard populations may be structured genetically over their breeding range to a greater extent than has been previously thought. Multilocus genetic variation was correlated negatively with body mass and carcass component reserves in mallards and American wigeon of different sex and age groups. This may indicate that birds with different genetic characteristics have different metabolic efficiencies or growth potentials. The relationships detected between genetic and functional characteristics in these wintering mallards and American wigeon are the first documented for any waterfowl species. Carcass components of American wigeon varied significantly over the wintering period, and overwinter changes in carcass component reserves were different among birds of various sex and age groups. American wigeon of different sexes and ages maintain fat and protein reserves of proportionally different sizes, and use those reserves at different rates.Item Genetics of plasma cytokine variation in healthy baboons and humans(2005) Proffitt, John Michael; Freeland-Graves, Jeanne H.The goal of this project was to investigate the genetic regulation of plasma cytokine variation in healthy baboons and humans. The first objective was to estimate the heritabilities of plasma levels of inflammatory cytokines in healthy baboons. In Study I, levels of the inflammatory cytokines TNF-α, GM-CSF, IL-1β, and IL-6, as well as sTNFR1, and sTNFR2 were measured in 370 related baboons. All of the traits exhibited significant evidence for genetic regulation. The heritabilities ranged from 61% for TNF-α to 14% for sTNFR1. The second objective was to identify chromosomal regions governing the production of resistin in healthy baboons. In Study II, resistin levels were measured in 416 related baboons. Variation in the plasma concentration of resistin was significantly linked to chromosome 18, between the markers D18S475 and D18S172 on the cytoband 18q12 (LOD = 4.0). The third objective of this study was to locate quantitative trait loci (QTLs) that affect circulating levels of plasma TNF-α and IL-1β levels in healthy humans. Study III examined plasma levels of TNF-α and IL-1β in a population of Caucasian Americans from the Midwestern United States. Quantitative trait loci were identified for TNF-α and IL-1β (LOD = 3.0 and LOD = 4.0, respectively) on chromosome 18 between markers ATA82B02 and D18S1371. The fourth objective was to detect QTLs affecting plasma levels of CRP, and to investigate its association with obesity phenotypes in healthy humans. Study IV revealed that chromosome 12 harbors a QTL regulating circulating CRP levels between markers D12S375 and D12S1052 (LOD = 4.1). CRP was genetically correlated with parameters of adiposity. The results from these baboon and human studies suggest that circulating cytokine levels in healthy animals are under significant genetic control. Chromosomes 12 and 18 appear to contain genetic differences that influence inflammation. Future work should aim to resolve the specific genetic elements through fine mapping and the positional candidate gene approach.Item Influence of corn hybrids and water stress on yield and nutritive value(2009-05) Montgomery, Randall; Xu, Wenwei; Thorvilson, Harlan G.; Wester, David B.; Allen, Vivien G.Silage corn (Zea mays) in Texas has increased from 16,000 ha harvested in 1985 to 53,000 ha harvested in 2005. All corn in the Texas High Plains is irrigated with water from the Ogallala Aquifer. Due to the declining water level of the Ogallala Aquifer and rising energy costs, corn silage producers need new hybrids that require less water and respond to improved crop management practices. As the dairy industry continues to grow in West Texas, producers must supply a high-quality, high-yielding corn forage that meets the nutritional demands of the dairy industry. The objective of this study was to compare the responses in regards to grain yield, forage yield and quality of five Texas Agricultural Experiment Station (TAES) corn hybrids and three widely grown commercial hybrids (Garst 8288, P31B13, and DKC66-80) under full and limited irrigation treatments. This experiment was conducted in 2005 and 2006, at Halfway, TX and Etter, TX. There were two irrigation treatments (well-watered and drought-stressed) at Etter and Halfway in both years. Drought stress was imposed by reducing the amount of irrigation water by one-half compared to well-watered plots from V10 to R3 growth stages. Plots were two-rows 5.5 m long and spaced 1 m apart at Halfway and 0.76 m apart at Etter. After planting, plots were thinned to 66,947 plants/ha at Etter and 57,383 plants/ha in Halfway. Data was collected on grain yield, silage yield, plant height, ear height, days to pollen, neutral detergent fiber (NDF), acid detergent fiber (ADF), crude protein and numerous other forage quality traits. Whole plant corn samples were collected and sub-samples were analyzed by Dairy One Forage Laboratory (Ithaca, NY) using Near Infrared Reflectance Spectroscopy (NIRS). The basic experimental design for this analysis was a randomized complete block design with two blocks (locations); irrigation treatments (100ET and 50ET) represented the main plot factor of a split-plot arrangement, and hybrid was a subplot factor. No three-way interactions were observed among year, irrigation, and hybrid for any of the variables analyzed. Additionally, interactions between irrigation and hybrid, and between irrigation and year, were not present for any of the variables analyzed. Effects of hybrids depended on the year of the experiment (year X hybrid interaction) for percentage ADF, NDF, TDN, and DM. For grain yield, per plant fresh weight (FW plant-1), DTP, PHT and EHT, differences among hybrids were independent of other factors included in this study. Thus, differences among hybrids were averaged over each yr and effects of hybrid and irrigation treatment were examined. Differences among hybrids were observed for grain yield (kg ha-1), FW plant-1, DTP, PHT, and EHT. When analyzing grain yield, the commercial check P31B13 (8703 kg ha-1) was the highest yielding hybrid with the exception of C3A654 x B110 (7800 kg ha-1) and DKC66-80 (8044 kg ha-1). In terms of FW plant-1, S1W x CML343 yielded a greater fresh weight per plant than any other hybrids except DKC66-80, while C3A654 x B110 yielded the least fresh weight per plant. Also, S1W x CML343 was the latest maturing hybrid when compared to all others and took an average of 80 d to anthesis (DTP). In terms of plant height, S2B73 x NC300 was a taller hybrid than Tx205 x B110 (230.6) and C3A654 x B110 (210.3) as it averaged 244.4 cm, while, C3A654 x B110 was statistically the shortest when compared to all other hybrids as it measured just over 210 cm on average. Drought stress (50% ET irrigation) did affect both ADF and NDF in terms of forage quality. Both cell wall (NDF) and cell wall minus hemicelluloses (ADF) were higher in hybrids subjected to water stress than hybrids irrigated at 100% ET. Irrigation level did not affect percentage CP and TDN. Grain yield was reduced about 50% by the low irrigation treatment compared with full irrigation. Surprisingly, there were no statistical differences found in the forage yield (FW plant-1) or in DTP with the imposition of drought. Effects of year and hybrid interacted with each other for ADF, NDF, TDN and DM. For DM, hybrids were similar (P > 0.1560) in 2005 and differed (P < 0.0001) in 2006. However, for ADF, NDF and TDN, hybrids differed in each year. In future studies the integration of brown mid-rib hybrids should be made a priority. Some hybrids from this study did show promise and should be considered for future studies as well. Although S1W x CML343 lacked the quality traits that some of the other hybrids, it should not be ruled out on that premise alone. It did appear to be one of the higher yielding hybrids and should be considered for future studies. While C3A654 x B110 did appear to produce higher quality forage, it also had the shortest plants and might lack the overall forage production when being considered for future studies. Also, SPG3 x B110 appeared to have quality traits that would be very desirable and at the same time may include some higher yielding traits and should be used in potential studies. A major limitation in this study was the inclusion of only two blocks, although the two locations did serve as valid blocks. More research and detailed analysis must be performed in order to select for high yielding, high producing corn forage that might potentially use less water. This study may help to serve as a reference to future researches.Item Isolation and characterization of a Pseudomonas aeruginosa gene, ptxR, which positively regulates exotoxin A production(Texas Tech University, 1997-05) Colmer, Jane AnnProduction of exotoxin A, the most toxic of the virulence factors produced by the opportunistic pathogen Pseudomonas aeruginosa, is a complicated, highly regulated process involving several genes. In this study, we describe the isolation and characterization of two new regulatory genes for toxA expression, ptxR and ptxS. The presence of extra copies of ptxR in PA01 results in a fivefold increase in exotoxin A activity. Subcloning, complementation, nucleotide sequence analyses, and T7 expression experiments revealed that the ptxR open reading frame (ORE) encodes a 34 kDa protein. Computer analysis for amino acid homology revealed that the product of ptxR (RxR) belongs to the LysR family of transcriptional activators and contains a putative helix-turn-helix DNA binding motif. Transcriptional studies using RNA analysis and a toxAlacZ fusion disclosed that ptxR enhances both toxA and regA transcription. These results suggest ptxR acts through regA to enhance toxA expression. Further studies confirmed that the presence of a 2.1 kbp fragment 5' of ptxR reduced the enhancement in exotoxin A by threefold. Nucleotide sequence analysis and expression experiments revealed that this fragment carries an ORE, ptxS, encoding a 38 kDa protein, RxS. Computer analysis of the amino acid sequence indicated that RxS belongs to the GalR-LacI family of repressors. The presence of a helix-turn-helix motif suggests a DNA binding function for PtxS. Additional experiments, using ptxRlacZ fusions, provided evidence that ptxS affects ptxR expression directly. The presence of three potential GaIR binding sites in the ptxR upstream region suggests that RxS might interfere with pfxP function at the transcriptional level by binding to its upstream region. We have also examined ptxR expression and the effect of ptxR on toxA expression throughout the growth cycle of Pseudomonas aeruginosa strains PA01 and PA103 using toxAlacZ chromosomal integrates and the ptxRlacZ fusion plasmid. These experiments suggest that while the enhancement in toxA transcription by ptxR continues at later stages of the growth cycle, ptxS expression declines; and, that ptxR expression in Pseudomonas aeruginosa is iron-independent.Item Parallelization Methods for the Distribution of High-Throughput Bioinformatics Algorithms(2011-05) Rees, Eric; Youn, Eunseog; Dowd, Scot E.; San Francisco, MichaelThe development of high-throughput bioinformatics technologies has caused a massive influx of biological data over the course of the past decade. During this same span of time, computational hardware has also been rapidly increasing in speed while decreasing in price, multi-core processors have become standard in home and office environments, and distributed and cloud based computing has become affordable and readily available to researchers with implementations such as Amazon’s S3, Microsoft’s Azure, Google’s App Engine, and the 3Tera Cloud. Bioinformatics software tools such as BLAST, a tool for finding local alignments between a set of unknown genetic sequences versus a set of known genetic sequences, have simple interfaces and few installation requirements often so biologists can use them easily in the laboratory without needing an in-depth knowledge of how computer systems work. This, however, is rarely the case for distributed implementations of bioinformatics tools which often require the user to first set up and configure the underlying program that will handle the distribution, such as the Message Passing Interface (MPI). Once the underlying distribution algorithm is chosen, many of the software tools require the user to then configure the program to work with their chosen method and, in some cases, write the necessary source code to link the program with the underlying service. These are difficult steps for most computer scientists and are near impossible for the average biologist. By constructing a modularized set of methods that can connect to, broadcast to, and read from a multicast created by the methods, future bioinformatics software developers will be able to construct the underlying message passing system without requiring the end-user, often a biologist, to set up and configure one of their own. Using these multicast methods will allow any program the ability to seek out and track any nodes on the network that will be used in the distributed system. This communication method allows the program to easily scale up and down depending on available nodes without direct user intervention to alter the size of the system. This system is then tested by creating a program that connects NCBI’s Basic Local Alignment Search Tool to the multicast system to allow the BLAST algorithm to then be distributed across multiple nodes. This new system will demonstrate how future programs could then connect stand alone tools, such as BLAST, to the multicast system to create programs that will execute on a distributed system and automatically scale depending on the network size without altering the tools source code.Item Phylogeography of the cottonmouth, Agkistrodon piscivorus, using AFLP and venom protein profiles.(2011-05-25T14:32:04Z) Strickland, Jason L.; Strickland, Jason; Ammerman, Loren K.; Ross, Linda; Maxwell, Terry C.; Parkinson, Christopher L.; Angelo State University. Department of Biology.The objective of this study was to examine population structure in cottonmouths (Agkistrodon piscivorus) using Amplified Fragment Length Polymorphism (AFLP) and compare genetic and venom protein profiles in Texas. AFLP profiles using 622 fragments were generated for 105 individuals to understand the level of variation within Agkistrodon. In Texas, there was a significant lack of gene flow detected and support for the isolation of Concho Valley individuals. Cottonmouths showed the greatest genetic variation when compared to other Agkistrodon species but there was not complete support for two species of cottonmouths as currently proposed. RP-HPLC was used to examine venom protein profiles in 86 Texas cottonmouths. Relative peak heights were analyzed using PCA and the MANOVA demonstrated separation of populations based on profiles (p<0.001). Genetic and venom variation did not follow the same pattern indicating that there may be other selection pressures acting on the venom proteins.