Browsing by Subject "genetic variation"
Now showing 1 - 5 of 5
Results Per Page
Sort Options
Item Characterization of the Bovine Cathelicidin Gene Family(2012-10-19) Flores, Erin GillenwatersCathelicidins (CATHLs) are small, cationic antimicrobial peptides that establish an early innate immune defense against infections in mammals. Beyond their wide spectrum of antimicrobial activity, these peptides play important roles in wound repair, chemotactic activity, and apoptosis. Thus, comprehensive characterizing of bovine CATHLs could potentially identify underlying inherited differences in innate immunity and disease resistance in cattle. The purpose of the present study was to verify the placement of the CATHL cluster at the distal end of bovine chromosome 22 (BTA22), identify any single nucleotide polymorphisms (SNPs) and insertion-deletion (indel) polymorphisms within the gene family, explore copy number variation, and investigate the functional impact any of these variants may have in overall bovine innate immunity. A framework radiation hybrid map was constructed with 7 markers screened against the bovine 12,000 rad whole genome RH (12K WG-RH) panel, which when compared to the current genome assembly (Btau_4.0) confirmed current gene order. Comparative sequence analysis for 10 domestic cattle breeds representing both Bos taurus taurus and Bos taurus indicus revealed 60 SNPs, 7 of which were nonsynonymous, and 5 indel mutations. Data from array comparative genomic hybridization (aCGH) between four Angus and four Nelore animals showed a 2-fold increase in copy number of the CATHL4 locus, which was verified by quantitative PCR (qPCR) of genomic DNA. Nelore animals showed an approximate 2-fold increase in the CATHL4 gene. Subsequently, the expression of CATHL4 in Nelore neutrophils exhibited a range of 2- to 5-fold increases in CATHL4 gene expression. Finally, a colorimetric bactericidal assay was performed on the neutrophils of the same Angus and Nelore animals previously genotyped for copy number variations (CNVs). After in vitro challenges to Staphylococcus aureus, Salmonella typhimurium, Mannheimia haemolytica, and Pasteurella multocida, the killing capacity of Nelore neutrophils was approximately 20 percent greater than Angus neutrophils for M. haemolytica and 10 percent greater for P. multocida. Characterization of this antimicrobial gene family is central to developing a firm understanding regarding the effects CATHL variation has with respect to bovine innate immunity.Item Ecological significance of the genetic variation in Bouteloua curtipendula (Michx.)Torr.(Texas A&M University, 2005-02-17) Andrea, Tomas de Pisani, MariaThe two most common varieties of the grass Bouteloua curtipendula (Michx.)Torr. in North America use different strategies of clonal growth and have contrasting continental distributions. Variety caespitosa (phalanx form) ranges from central Texas westward to Arizona and California and var. curtipendula (guerrilla form) occurs in a more mesic region over the North American Great Plains. This study sought to determine whether the strategies had an ecological significance and investigated the possible relationship between changes in environmental factors and characteristics of each clonal growth strategy. Varieties showed to be morphologically variable, but the variability did not follow the pattern of the precipitational gradient. The abundance of var. curtipendula was related to soil depth and parent material (limestone types). Abundance of var. caespitosa could not be explained by any environmental factor separately. The performance of clones of the two growth forms in response to changes in resource availability (light and nutrients) and defoliation suggested similarities between the varieties in photosynthetic rate and only showed differences in water potential under extreme conditions. The major differences were related to the proportion of biomass allocated to structures related with seed production versus propagation by rhizomes. Intra-variety genetic variation for several life history traits was detected even with a very small sample size. The caespitose growth form showed more biomass and rate of tiller recruitment after defoliation on average, but responses between genotypes were dissimilar. Varieties also showed levels of plasticity in the allocation to reproductive structures in response to environmental factors. Responses to fire were compared between varieties by experimental burnings with increasing load of artificial fuel. Plants of the two varieties reached similar maximum temperatures although var. caespitosa suffered temperatures considered to be lethal for longer periods of time. Results from this study suggested that, although characteristic of the pattern of clonal growth were not distinctly associated to resource availability or defoliation, distribution of the varieties may be related to a combination of biotic and abiotic factors beyond the factors studied here.Item Genetic analysis of mycobacterium avium subspecies paratuberculosis reveals sequence and epigenetic variation among field isolates(2009-05-15) O'Shea, Brian JamesPrevious research performed in 1999 by Harris et al. has shown that many varieties of ruminants serve as the host species for Mycobacterium avium subspecies paratuberculosis (MparaTb) infections. Gene sequencing has supported the contention that organisms isolated from different hosts harbor different gene sequences; this has been exemplified by Amonsin et al. in 2004 with the sequencing of the mfd (transcription-repair coupling factor) and by Motiwala et al. in 2005 through sequence analysis of phosphatidylethanolaminebinding proteins which reveal a host-specific correlation of isolates. Some contradicting reports from Bannantine et al. from 2003 have further claimed that MparaTb is a monogenic organism based upon sequence data from regions flanking the origin of replication and the 16s rRNA. One of the drawbacks to the techniques implemented in these reports is the extremely restricted region of the bacterial genome that was analyzed; furthermore, only a select number of isolates were analyzed. In the present studies, amplified fragment length polymorphism (AFLP) was used as a tool for a genome scale comparison of MparaTb isolates from differing isolation types as well as a comparison of MparaTb isolates to the genetically similar yet avirulent Mycobacterium avium subspecies avium isolates. AFLP data reveals the MparaTb genome to be much more plastic and polymorphic than previously thought. These polymorphic regions were identified and characterized and are shown to be unique to the organism when compared to an array of Mycobacterial isolates of differing species. These polymorphic regions were also utilized in polymerase chain reaction (PCR) based diagnostic as well as epidemiologic tests. Furthermore, AFLP comparative analysis of intracellular and fecal MparaTb isolates reveals polymorphic regions unique to each isolate type. While these genomic differences are not based upon differences in the genetic code, they are based upon epigenetic modifications such as DNA methylation. These DNA methylation patterns are unique to intracellular MparaTb isolates as opposed to isolates from fecal material. Furthermore, AFLP comparisons of fecal MparaTb isolates that were passaged through the bovine ileum revealed banding pattern differences as compared to the original inoculum.Item Genetic Variation and Evolution of the Size of NBS-LRR-Encoding Gene Family in Cotton and Related Species (Gossypium L.)(2010-07-14) Wu, Yen HsuanMost of genes contained in a genome have been shown to exist in forms of families; however, little is known about their variation and evolution during the course of genome evolution. The present study shows that the numbers of the genes of the NBS-LRR-encoding gene family vary extremely significantly among different lines or cultivars of a species and among related species from the same genus. This suggests that plant genetics and evolution depend on not only gene sequence variation, but also the number of genes in multigene families. This study has further revealed that the variation of number of genes in the gene family in the Gossypium species is affected significantly not only by genome size variation, polyploidization and natural selection, but also by domestication/breeding. There is a positive correlation (P less than or equal to 0.05) between genome size and number of genes in the family, suggesting that species with larger genomes tend to have more NBS-LRR-encoding genes. It was observed that natural polyploids have significantly larger numbers of genes in the family and larger genomes than the artificial polyploids of their putative diploid ancestors. This indicates that polyploidization, perhaps post-polyploidization as well, either led to the loss of the genes in a gene family or slowed the process of gene number increase after polyploidization. It was shown that cultivated cottons have significantly more NBSLRR- encoding genes than wild species at both diploid and polyploidy levels. This result indicates that plant breeding likely allows accumulation of NBS-LRR-encoding genes that potentially provide resistance to pathogens. Therefore, plant breeders have selected not only for favorable alleles and favorable allele combinations, but also for the number of genes. Finally, difference (P less than or equal to 0.001) was found in number of genes in the NBS-LRR-encoding gene family among the species native to different geographical regions, suggesting that natural selection has played an important role in the variation in number of genes in the NBS-LRR-encoding gene family. The gene members that are favorable for fitness at the time are selected and accumulated in the genomes, but those that are not favorable for fitness at the time are lost in natural selection. As this is the first study in the field, further studies remain. These include, but not limited to, the universality of the findings in plants and animals, the universality of the findings in different gene families, genetics of the gene family size variation, relationship between the gene family size variation and phenotypic variation, gene family size variation and breeding, etc. Nevertheless, the findings obtained from this study are sufficient to shed light on many fundamental questions in biology, diversity and complexity of plants and animals.Item Genetic variation in the eastern subterranean termite Reticulitermes flavipes (Isoptera: Rhinotermitidae)(Texas A&M University, 2006-04-12) Benavides, Lucille HThe eastern subterranean termite, Reticulitermes flavipes, is the most widely dispersed termite in North America. The genus Reticulitermes spp. is responsible for 80% of total termite damage caused to urban structures each year. Little is known about the genetic structure of termites, particularly at the colony level. Evidence for what genetically defines a termite colony is a hotly debated topic in current literature due to the implications such findings would have regarding current lawsuits against pest control operations. Information on termite genetic structure is sparse. In this study, the genetic variation and gene flow among Texas populations of R. flavipes at the statewide level and city level was examined. A 324-337 base pairs segment of the mtDNA, AT-rich region was a polymerase chain reaction amplified from 104 different termite specimens from 12 Texas cities. The DNA extracts were then subjected to PCR amplification using specific primers and it was then sequenced. Using the sequence data and appropriate statistical measures it was found that, at the statewide level, nucleotide and haplotypic diversity is low. Gene flow was found to be low on a statewide basis. At the city level nucleotide and haplotypic diversity was high. The findings of this study provide insights into termite genetic structure.