+publisher:"Texas A&M University" +contributor:("Womack, James")

Texas A&M University

1. Jones, Brittany. Genetic and Phylogenetic Studies of Toll-Like Receptor 5 (TLR5) in River Buffalo (Bubalus Bubalis).

Degree: PhD, Veterinary Microbiology, 2012, Texas A&M University

URL: http://hdl.handle.net/1969.1/148100

► River buffalo are economically important to many countries and only recently has their genome been explored for the purpose of mapping genetic variation in traits… (more)

▼ River buffalo are economically important to many countries and only recently has their genome been explored for the purpose of mapping genetic variation in traits of economic and biologic interest. The purpose of this research is to characterize the genetic and evolutionary profile of Toll-like receptor 5 (TLR5), which mediates the mammalian innate immune response to bacterial flagellin. This study is comprised of three parts: 1) generating a radiation hybrid (RH) map of river buffalo chromosome 5 (BBU5) where the TLR5 gene is located and building a comparative map with homologous cattle chromosomes; 2) conducting a single-nucleotide polymorphism (SNP) survey of the TLR5 gene to reveal variation within river buffalo and other species; and 3) performing an evolutionary study by inferring phylogenetic trees of TLR5 across multiple taxa and determining the possible evolutionary constraints within the TLR5 coding region. River buffalo chromosome 5 is a bi-armed chromosome with arms corresponding to cattle chromosomes 16 and 29. A BBU5 RH map was developed using the previously published river buffalo RH mapping panel and cattle-derived markers. The RH map developed in this study became an integral part of the first river buffalo whole genome RH map. Genetic variation of the TLR5 gene was evaluated in a small domestic herd of river buffalo. Sequencing of the TLR5 coding region and partial associated 5'- and 3'-untranslated regions yielded 16 novel SNPs. Six SNPs were identified as non-synonymous with one predicted to potentially code for a functionally altered product. For the evolutionary study of the TLR5 coding region, phylogenetic trees were inferred based on TLR5 variation across multiple orders and another for artiodactyla. Species that are closely related to river buffalo appear to have undergone negative selection in TLR5 while those that diverged from river buffalo earlier may be retaining alleles that river buffalo are removing from the population. In conclusion, putative chromosomal rearrangements were identified between river buffalo and cattle, the variation that was uncovered in the TLR5 coding region could potentially lead to differential immunity across species, and there appears be some evolutionary flexibility in the DNA sequence of the TLR5 coding region. Advisors/Committee Members: Womack, James E (advisor), Derr, James (committee member), Skow, Loren (committee member), Holman, Patricia (committee member).

Subjects/Keywords: radiation hybrid (RH) mapping; phylogenetics; single-nucleotide polymorphism (SNP); toll-like receptor 5 (TLR5); innate immunity; river buffalo

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APA (6^th Edition):

Jones, B. (2012). Genetic and Phylogenetic Studies of Toll-Like Receptor 5 (TLR5) in River Buffalo (Bubalus Bubalis). (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/148100

Chicago Manual of Style (16^th Edition):

Jones, Brittany. “Genetic and Phylogenetic Studies of Toll-Like Receptor 5 (TLR5) in River Buffalo (Bubalus Bubalis).” 2012. Doctoral Dissertation, Texas A&M University. Accessed February 28, 2021. http://hdl.handle.net/1969.1/148100.

MLA Handbook (7^th Edition):

Jones, Brittany. “Genetic and Phylogenetic Studies of Toll-Like Receptor 5 (TLR5) in River Buffalo (Bubalus Bubalis).” 2012. Web. 28 Feb 2021.

Vancouver:

Jones B. Genetic and Phylogenetic Studies of Toll-Like Receptor 5 (TLR5) in River Buffalo (Bubalus Bubalis). [Internet] [Doctoral dissertation]. Texas A&M University; 2012. [cited 2021 Feb 28]. Available from: http://hdl.handle.net/1969.1/148100.

Council of Science Editors:

Jones B. Genetic and Phylogenetic Studies of Toll-Like Receptor 5 (TLR5) in River Buffalo (Bubalus Bubalis). [Doctoral Dissertation]. Texas A&M University; 2012. Available from: http://hdl.handle.net/1969.1/148100

Texas A&M University

2. Halley-Schultz, Yvette A. A Draft De Novo Genome Assembly and Mitochondrial Population Genomics for the Northern Bobwhite (Colinus Virginianus).

Degree: PhD, Genetics, 2015, Texas A&M University

URL: http://hdl.handle.net/1969.1/156517

► Wild populations of northern bobwhites (Colinus virginianus; hereafter bobwhite) have declined across most of their historic U.S. range, and despite their importance as an experimental… (more)

▼ Wild populations of northern bobwhites (Colinus virginianus; hereafter bobwhite) have declined across most of their historic U.S. range, and despite their importance as an experimental wildlife model for ecotoxicology studies, no bobwhite draft genome assembly has emerged. Herein, we present the first bobwhite draft de novo genome assembly, with more than 90% of the assembled bobwhite genome captured within < 40,000 final scaffolds (N50 = 45.4 Kb) despite evidence for approximately 3.22 heterozygous polymorphisms per Kb. Moreover, three annotation analyses produced evidence for > 14,000 unique genes and proteins. Bobwhite analyses of divergence with the chicken (Gallus gallus) and zebra finch (Taeniopygia guttata) genomes revealed many extremely conserved gene sequences, and evidence for lineage-specific divergence of noncoding regions. Coalescent models for reconstructing the demographic history of the bobwhite and the scarlet macaw were concordant with how opposing natural selection strategies (i.e., skewness in the r-/K-selection continuum) would be expected to shape genome diversity and the effective population sizes in these species. Using genomic tools and resources developed via the draft genome assembly, we evaluated the concordance of population inferences and conclusions resulting from the analysis of short mitochondrial fragments (i.e., partial or complete D-Loop nucleotide sequences) versus complete mitogenome sequences for 53 bobwhites representing six ecoregions across TX and OK (USA). Median joining (MJ) haplotype networks demonstrated that analyses performed using small mitochondrial fragments were insufficient for estimating the true (i.e., complete) mitogenome haplotype structure, corresponding levels of divergence, and maternal population history of our samples. Notably, discordant demographic inferences were observed when mismatch distributions of partial (i.e., partial D-Loop) versus complete mitogenome sequences were compared, with the reduction in mitochondrial genomic information content observed to encourage spurious inferences in our samples. A probabilistic approach to variant prediction for the complete bobwhite mitogenomes revealed 344 segregating sites corresponding to 347 total mutations, including 49 putative nonsynonymous single nucleotide variants (SNVs) distributed across 12 protein coding genes. Evidence of gross heteroplasmy was observed for 13 bobwhites, with 10 of the 13 heteroplasmies involving one moderate to high frequency SNV. Haplotype network and phylogenetic analyses for the complete bobwhite mitogenome sequences revealed two divergent maternal lineages (dXY = 0.00731; FST = 0.849; P < 0.05), thereby supporting the potential for two putative subspecies. However, the diverged lineage (n = 103 variants) almost exclusively involved bobwhites geographically classified as Colinus virginianus texanus, which is discordant with the expectations of previous geographic subspecies designations. Tests of adaptive evolution for functional divergence (MKT), frequency distribution… Advisors/Committee Members: Seabury, Christopher M (advisor), Murphy, William J (committee member), Criscitiello, Michael F (committee member), Womack, James E (committee member).

Subjects/Keywords: Genomics; Genetics; northern bobwhite

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APA (6^th Edition):

Halley-Schultz, Y. A. (2015). A Draft De Novo Genome Assembly and Mitochondrial Population Genomics for the Northern Bobwhite (Colinus Virginianus). (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/156517

Chicago Manual of Style (16^th Edition):

Halley-Schultz, Yvette A. “A Draft De Novo Genome Assembly and Mitochondrial Population Genomics for the Northern Bobwhite (Colinus Virginianus).” 2015. Doctoral Dissertation, Texas A&M University. Accessed February 28, 2021. http://hdl.handle.net/1969.1/156517.

MLA Handbook (7^th Edition):

Halley-Schultz, Yvette A. “A Draft De Novo Genome Assembly and Mitochondrial Population Genomics for the Northern Bobwhite (Colinus Virginianus).” 2015. Web. 28 Feb 2021.

Vancouver:

Halley-Schultz YA. A Draft De Novo Genome Assembly and Mitochondrial Population Genomics for the Northern Bobwhite (Colinus Virginianus). [Internet] [Doctoral dissertation]. Texas A&M University; 2015. [cited 2021 Feb 28]. Available from: http://hdl.handle.net/1969.1/156517.

Council of Science Editors:

Halley-Schultz YA. A Draft De Novo Genome Assembly and Mitochondrial Population Genomics for the Northern Bobwhite (Colinus Virginianus). [Doctoral Dissertation]. Texas A&M University; 2015. Available from: http://hdl.handle.net/1969.1/156517

Texas A&M University

3. Dobson, Lauren K. Sequencing the Genome of the North American Bison.

Degree: PhD, Genetics, 2015, Texas A&M University

URL: http://hdl.handle.net/1969.1/155759

► American bison (Bison bison) is a well-known iconic species with a history and legacy intertwined with the Plains of North America. Unfortunately, the American colonization… (more)

▼ American bison (Bison bison) is a well-known iconic species with a history and legacy intertwined with the Plains of North America. Unfortunately, the American colonization of North America in the late 1800’s resulted in the almost complete destruction of the American bison and subsequent population bottleneck. Bison were also faced with forced hybridization of domestic cattle genetics (Bos taurus), through failed experiments of some ranchers to produce a hardier beef animal for the greatplains. The hybridization of domestic cattle into bison presents challenges in the management and conservation of American bison today, primarily because it is difficult to differentiate between hybrid cattle-bison and purebred bison within a population. Whole genome sequencing provides the next step in advancing bison management and conservation. A 2.82-Gb de novo reference assembly of the American bison genome was produced using approximately 75X coverage, utilizing both mate pair and pair-end sequencing. Illumina, Inc. and 454 Life Sciences Technologies raw sequence reads were mapped to both nuclear and mitochondrial sequences of the domestic cattle reference UMD3.1 (Ensembl GCA_000003055.3), in order to detect genetic variants, including single nucleotide variants (SNVs) and insertion and deletions (INDELs). An additional 14 re-sequenced bison genomes were also aligned to the UMD3.1 domestic cattle reference sequence to identify genomic variants. These variants were determined and annotated to examine their effect on gene structure and function in bison. With the completed de novo plains bison reference genome sequence a comparison of historic and modern bison sequences identified genomic variants and were compared across bison populations. Historic bison samples that predate cattle and bison introgression were sequenced and conserved genomic regions between historic and current bison were identified. Identified variants between modern and historic bison provided an outline of the genetic architecture of bison that existed before the population bottleneck. This genomic analysis of North American bison provides insight into the genetic history, taxonomy, and inheritance of important genetic traits in bison that have allowed them to not only survive but thrive in their recovery from this population bottle neck that occurred 130 years ago. Advisors/Committee Members: Derr, James N (advisor), Womack, James E (committee member), Raudsepp, Terje (committee member), Dindot, Scott N (committee member), Riley, David G (committee member).

Subjects/Keywords: bison genome sequencing

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Dobson, L. K. (2015). Sequencing the Genome of the North American Bison. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/155759

Chicago Manual of Style (16^th Edition):

Dobson, Lauren K. “Sequencing the Genome of the North American Bison.” 2015. Doctoral Dissertation, Texas A&M University. Accessed February 28, 2021. http://hdl.handle.net/1969.1/155759.

MLA Handbook (7^th Edition):

Dobson, Lauren K. “Sequencing the Genome of the North American Bison.” 2015. Web. 28 Feb 2021.

Vancouver:

Dobson LK. Sequencing the Genome of the North American Bison. [Internet] [Doctoral dissertation]. Texas A&M University; 2015. [cited 2021 Feb 28]. Available from: http://hdl.handle.net/1969.1/155759.

Council of Science Editors:

Dobson LK. Sequencing the Genome of the North American Bison. [Doctoral Dissertation]. Texas A&M University; 2015. Available from: http://hdl.handle.net/1969.1/155759

Texas A&M University

4. Chen, Junfeng. Bovine Nk-Lysins: Genomic Expansion and Functional Diversification.

Degree: PhD, Genetics, 2016, Texas A&M University

URL: http://hdl.handle.net/1969.1/156854

► NK-lysin is a cationic antimicrobial peptide (AMP) of the host innate immune system and active against a broad spectrum of targets, including bacteria, viruses, fungi… (more)

▼ NK-lysin is a cationic antimicrobial peptide (AMP) of the host innate immune system and active against a broad spectrum of targets, including bacteria, viruses, fungi and cancer cells. NK-lysin has been well-studied in humans and pigs, in which each genome contains a single copy of NK-lysin. However, the bovine genome has received much less attention with only one study, in which two 405-bp Bo-lysin fragments with 94% nucleotide identity were detected among four experimental donors. These two sequences likely represent two different bovine NK-lysin genes. The purpose of the present study was to characterize the gene number and the genomic organization of bovine NK-lysins and their roles in host resistance to pathogens, including pathogens involved in bovine respiratory diseases (BRD). Two overlapping BAC clones (CH240-372P1 and CH240-27G22) covering the whole bovine NK-lysin region were sequenced by PacBio (Seattle, WA) and the assembled supercontig revealed four NK-lysin genes on cattle chromosome 11. NK2A, NK2B and NK2C are tandemly arrayed as three copies in 30 ~ 35 Kb segments, located 41.8 Kb upstream of NK1. All four genes are functional, albeit with differential tissue expression. NK1, NK2A and NK2B exhibited the highest expression in intestine Peyer’s patch while NK2C was expressed almost exclusively in lung. Four peptides corresponding to the functional helices 2 & 3 of each gene product were synthesized. Circular dichroism (CD) spectroscopy demonstrated that peptides adopted a more helical secondary structure upon binding to an anionic model membrane, and a liposome leakage assay suggested that these peptides disrupt the model membrane. To test the potential role in host response to BRD pathogens, we analyzed RNA-seq data to determine expression of each NK-lysin gene in bronchial lymph node and lung in healthy animals and animals challenged with BRD pathogens. The expression of some NK-lysins, especially NK2C, was significantly elevated in most of the challenged animals, indicating potential functions in BRD resistance. Antimicrobial effects of the synthetic peptides against Escherichia coli, Staphylococcus aureus, Pasteurella multocida and Mannheimia haemolytica were further confirmed with bacterial killing assays, and their lytic influences on cell membranes were confirmed by transmission electron microscopy (TEM). Advisors/Committee Members: Womack, James E (advisor), Lawhon, Sara D (committee member), Riggs, Penny (committee member), Skow, Loren (committee member), Schroeder, Friedhelm (committee member).

Subjects/Keywords: Antimicrobial peptides; NK-lysin; gene family expansion; copy number variation; bovine respiratory diseases; RNA-seq

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Chen, J. (2016). Bovine Nk-Lysins: Genomic Expansion and Functional Diversification. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/156854

Chicago Manual of Style (16^th Edition):

Chen, Junfeng. “Bovine Nk-Lysins: Genomic Expansion and Functional Diversification.” 2016. Doctoral Dissertation, Texas A&M University. Accessed February 28, 2021. http://hdl.handle.net/1969.1/156854.

MLA Handbook (7^th Edition):

Chen, Junfeng. “Bovine Nk-Lysins: Genomic Expansion and Functional Diversification.” 2016. Web. 28 Feb 2021.

Vancouver:

Chen J. Bovine Nk-Lysins: Genomic Expansion and Functional Diversification. [Internet] [Doctoral dissertation]. Texas A&M University; 2016. [cited 2021 Feb 28]. Available from: http://hdl.handle.net/1969.1/156854.

Council of Science Editors:

Chen J. Bovine Nk-Lysins: Genomic Expansion and Functional Diversification. [Doctoral Dissertation]. Texas A&M University; 2016. Available from: http://hdl.handle.net/1969.1/156854

Texas A&M University

5. Dobson, Lauren K. Sequencing the Genome of the North American Bison.

Degree: PhD, Genetics, 2015, Texas A&M University

URL: http://hdl.handle.net/1969.1/186954

► American bison (Bison bison) is a well-known iconic species with a history and legacy intertwined with the Plains of North America. Unfortunately, the American colonization… (more)

▼ American bison (Bison bison) is a well-known iconic species with a history and legacy intertwined with the Plains of North America. Unfortunately, the American colonization of North America in the late 1800’s resulted in the almost complete destruction of the American bison and subsequent population bottleneck. Bison were also faced with forced hybridization of domestic cattle genetics (Bos taurus), through failed experiments of some ranchers to produce a hardier beef animal for the greatplains. The hybridization of domestic cattle into bison presents challenges in the management and conservation of American bison today, primarily because it is difficult to differentiate between hybrid cattle-bison and purebred bison within a population. Whole genome sequencing provides the next step in advancing bison management and conservation. A 2.82-Gb de novo reference assembly of the American bison genome was produced using approximately 75X coverage, utilizing both mate pair and pair-end sequencing. Illumina, Inc. and 454 Life Sciences Technologies raw sequence reads were mapped to both nuclear and mitochondrial sequences of the domestic cattle reference UMD3.1 (Ensembl GCA_000003055.3), in order to detect genetic variants, including single nucleotide variants (SNVs) and insertion and deletions (INDELs). An additional 14 re-sequenced bison genomes were also aligned to the UMD3.1 domestic cattle reference sequence to identify genomic variants. These variants were determined and annotated to examine their effect on gene structure and function in bison. With the completed de novo plains bison reference genome sequence a comparison of historic and modern bison sequences identified genomic variants and were compared across bison populations. Historic bison samples that predate cattle and bison introgression were sequenced and conserved genomic regions between historic and current bison were identified. Identified variants between modern and historic bison provided an outline of the genetic architecture of bison that existed before the population bottleneck. This genomic analysis of North American bison provides insight into the genetic history, taxonomy, and inheritance of important genetic traits in bison that have allowed them to not only survive but thrive in their recovery from this population bottle neck that occurred 130 years ago. Advisors/Committee Members: Derr, James N (advisor), Womack, James E (committee member), Raudsepp, Terje (committee member), Dindot, Scott N (committee member), Riley, David G (committee member).

Subjects/Keywords: bison genome sequencing

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Dobson, L. K. (2015). Sequencing the Genome of the North American Bison. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/186954

Chicago Manual of Style (16^th Edition):

Dobson, Lauren K. “Sequencing the Genome of the North American Bison.” 2015. Doctoral Dissertation, Texas A&M University. Accessed February 28, 2021. http://hdl.handle.net/1969.1/186954.

MLA Handbook (7^th Edition):

Dobson, Lauren K. “Sequencing the Genome of the North American Bison.” 2015. Web. 28 Feb 2021.

Vancouver:

Dobson LK. Sequencing the Genome of the North American Bison. [Internet] [Doctoral dissertation]. Texas A&M University; 2015. [cited 2021 Feb 28]. Available from: http://hdl.handle.net/1969.1/186954.

Council of Science Editors:

Dobson LK. Sequencing the Genome of the North American Bison. [Doctoral Dissertation]. Texas A&M University; 2015. Available from: http://hdl.handle.net/1969.1/186954

Texas A&M University

6. Mattison, Ashley Jean. The Genetic Basis of Grain Traits in Sorghum.

Degree: PhD, Genetics, 2017, Texas A&M University

URL: http://hdl.handle.net/1969.1/165815

► Crop production must increase by 70% by 2050 in order to meet the expected requirements for population growth. While previous research has resulted in genetic… (more)

▼ Crop production must increase by 70% by 2050 in order to meet the expected requirements for population growth. While previous research has resulted in genetic improvement of the grain output in major cereal crops such as Zea mays and Oryza sativa, much less investment has been made to improve the grain yield of Sorghum bicolor, a drought-tolerant grain and forage crop native to Africa. Multiple genetic and environmental factors influence grain yield making it challenging to identify the pathways determining the amount of grain produced. In this dissertation, variation in grain yield, grain weight and grain number per plant, panicle architecture traits, and grain composition were measured in three different RIL populations. Several quantitative trait loci (QTL) for grain number and weight that act independently to modify grain yield were identified. QTL for for grain composition, stem hollowing, and nutrient remobilization were identified, a subset of which aligned with QTL for grain weight. A QTL on LG01 was identified for both grain weight and grain number in the BTx642 x Tx7000 recombinant inbred lines (RIL) population; however, the tradeoff between grain weight and grain number resulted in no increase in grain yield. In the BTx623 x IS3620c population, a QTL was identified in the same region on LG01 for grain yield and grain number. These results suggest that two tightly linked genes influencing grain weight and grain number are located in this region of LG01. Sorghum is a photoperiod-sensitive short-day plant with critical photoperiods ranging from 11-14 hours. When grain sorghum was introduced into more temperate climates, breeders selected for earlier flowering times to optimize grain yield. Six maturity loci, Ma₁-Ma₆, were identified that modify flowering time. When recessive, Ma₁– Ma₆ result in an earlier flowering phenotype in long days. Four of the six maturity genes, Ma₁, Ma₃, Ma₅ and Ma₆, have previously been map-based cloned and identified. In this study, Ma₂ was fine mapped, sequenced, and identified as Sobic.002G302700, a gene encoding a zinc finger transcription factor. The identified SNP in 80M creates a stop codon causing a loss of function of Ma₂. Advisors/Committee Members: Mullet, John E (advisor), Shippen, Dorothy E (committee member), Rooney, William L (committee member), Womack, James C (committee member).

Subjects/Keywords: sorghum; genetics; plant science; quantitative traits

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Mattison, A. J. (2017). The Genetic Basis of Grain Traits in Sorghum. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/165815

Chicago Manual of Style (16^th Edition):

Mattison, Ashley Jean. “The Genetic Basis of Grain Traits in Sorghum.” 2017. Doctoral Dissertation, Texas A&M University. Accessed February 28, 2021. http://hdl.handle.net/1969.1/165815.

MLA Handbook (7^th Edition):

Mattison, Ashley Jean. “The Genetic Basis of Grain Traits in Sorghum.” 2017. Web. 28 Feb 2021.

Vancouver:

Mattison AJ. The Genetic Basis of Grain Traits in Sorghum. [Internet] [Doctoral dissertation]. Texas A&M University; 2017. [cited 2021 Feb 28]. Available from: http://hdl.handle.net/1969.1/165815.

Council of Science Editors:

Mattison AJ. The Genetic Basis of Grain Traits in Sorghum. [Doctoral Dissertation]. Texas A&M University; 2017. Available from: http://hdl.handle.net/1969.1/165815

Texas A&M University

7. Downey-Slinker, Erika Diane. Studies of Immunogenetic Variation in Cattle.

Degree: PhD, Genetics, 2016, Texas A&M University

URL: http://hdl.handle.net/1969.1/156836

► Genetic selection for animal health and disease resistance has been limited, likely due to the challenges of performing controlled studies with an industry relevant phenotype.… (more)

▼ Genetic selection for animal health and disease resistance has been limited, likely due to the challenges of performing controlled studies with an industry relevant phenotype. Studies in large populations of animals of unknown relationship pose challenges for genome wide association studies of disease resistance. The aims of this project were to characterize variation in the bovine major histocompatibility complex (BoLA), a specific region of the bovine genome known be critical for development of immune response, and then investigate individual variation in host immunity to a specific viral pathogen of cattle, bovine viral diarrhea virus (BVDV). Cattle “homozygous” for BoLA were identified from approximately 2,000 head of Holstein calves in large genome wide association studies. Cattle were genotyped on the Illumina BovineHD SNP chip and PHASED for the characterization of BoLA haplotypes. Among 160 “homozygous” animals, we identified 38 different haplotype groups. The 38 haplotype groups maintained the structure predicted by earlier studies that identified 50K SNP haplotypes, but demonstrated that more diversity is present among these 38 BoLA haplotype groups than was indicated by the 50K haplotypes. Among the 1,221 SNPs genotyped on the HD chip were 230 SNPs with no calls in at least one of the 160 homozygous animals. The no call SNPs are located predominately in regions predicted to contain copy number variation, and no call SNPs appear to likely mark regions of polymorphic structural variation otherwise undetected in the SNP defined haplotypes. This structural variation may be important for future genome association studies. Cattle diseases are often difficult to diagnose due to presentation with different disease phenotypes, ranging from subclinical to lethal. Likewise, immune response to vaccination is also variable and may be related to individual differences in disease susceptibilities. To evaluate individualized response to BVDV vaccination, we evaluated protection afforded by commercial vaccines against a BVDV challenge. The results from the BVDV challenge study indicate that measuring antibody titer as a response to BVDV vaccination may not be predictive of a protective immune response. Rectal temperature alone for health classification missed up to 50% of animals with subclinical disease. Variation in host immunity appears to underlie the response to pathogens and likely to vaccination as well. Host differences in immunity between Bos indicus and Bos taurus cattle were evaluated subsequent to BVDV vaccination. Differences in baseline immune cell counts were observed. Indicine cattle had higher white blood cell counts primarily influenced by the 2-fold higher neutrophil levels. Response to vaccination was primarily observed as an innate immune response with an increase in neutrophils. The largest change was in neutrophil response observed in the taurine calves. Immunosuppression from the modified live vaccination was greater in the indicine calves compared to taurine calves. However, a combination of… Advisors/Committee Members: Skow, Loren C (advisor), Herring, Andy D (advisor), Dindot, Scott V (committee member), Mwangi, Waithaka (committee member), Womack, James E (committee member).

Subjects/Keywords: bovine; MHC; vaccine; disease

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Downey-Slinker, E. D. (2016). Studies of Immunogenetic Variation in Cattle. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/156836

Chicago Manual of Style (16^th Edition):

Downey-Slinker, Erika Diane. “Studies of Immunogenetic Variation in Cattle.” 2016. Doctoral Dissertation, Texas A&M University. Accessed February 28, 2021. http://hdl.handle.net/1969.1/156836.

MLA Handbook (7^th Edition):

Downey-Slinker, Erika Diane. “Studies of Immunogenetic Variation in Cattle.” 2016. Web. 28 Feb 2021.

Vancouver:

Downey-Slinker ED. Studies of Immunogenetic Variation in Cattle. [Internet] [Doctoral dissertation]. Texas A&M University; 2016. [cited 2021 Feb 28]. Available from: http://hdl.handle.net/1969.1/156836.

Council of Science Editors:

Downey-Slinker ED. Studies of Immunogenetic Variation in Cattle. [Doctoral Dissertation]. Texas A&M University; 2016. Available from: http://hdl.handle.net/1969.1/156836

Texas A&M University

8. Fagundes De Avila, Felipe. Comparative Mapping of the Alpaca Genome.

Degree: PhD, Biomedical Sciences, 2014, Texas A&M University

URL: http://hdl.handle.net/1969.1/153632

► The development of gene maps constitutes a key feature for understanding genome architecture and comparative evolution. The genomes of some livestock species such as cattle,… (more)

▼ The development of gene maps constitutes a key feature for understanding genome architecture and comparative evolution. The genomes of some livestock species such as cattle, horses and pigs, have received considerable attention over the years due to their economic importance. In contrast, though camelids are gaining worldwide popularity as production and companion animals, cytogenetics and genome mapping in these species lag far behind those of other mammals. One of the reasons for the scarce body of knowledge regarding the camelid genome is their particularly difficult karyotype for analysis. All six extant camelid species have a diploid number of 74 chromosomes; the gross morphological similarities shared by many of the autosomes, combined with the relatively small size of some chromosome pairs, present serious challenges for identifying individual chromosomes using conventional cytogenetic techniques. The Alpaca Genome Project includes whole genome sequencing, radiation hybrid (RH) mapping and human-camel comparative chromosome painting (Zoo-FISH). However, there is no common platform that aligns various maps and precisely assigns them to individual chromosomes. Therefore, the goal of this research project was to construct a cytogenetic map for the alpaca genome by fluorescence in situ hybridization (FISH) of large insert clones from the alpaca CHORI-246 genomic BAC library. The BACs were selected based on the available Zoo-FISH, RH and sequence map data to target evolutionarily conserved genes and to get uniform distribution of markers throughout the alpaca genome. Candidate genes for traits of interest such as various congenital and reproduction-related disorders, as well as for phenotypic traits such as fiber color and texture, were also selected for mapping. A total of 230 markers were mapped to the 36 alpaca autosomes and the sex chromosomes; moreover, comparative mapping showed exceptional conservation of both gene synteny and order between alpaca and dromedary camel chromosomes. The cytogenetic map of the alpaca genome is a platform that effectively integrates the whole genome sequence and the radiation hybrid map with cytogenetic data, thus facilitating the discovery of genes of interest and providing tools for studying chromosome evolution and for clinical cytogenetics by means of a collection of chromosome-specific markers for camelids. Advisors/Committee Members: Raudsepp, Terje (advisor), Riggs, Penny (advisor), Chowdhary, Bhanu P (committee member), Womack, James E (committee member), Murphy, William J (committee member).

Subjects/Keywords: alpaca; camelid; cytogenetics; molecular cytogenetics; genome; FISH; BAC library; translocation; minute chromosome.

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APA (6^th Edition):

Fagundes De Avila, F. (2014). Comparative Mapping of the Alpaca Genome. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/153632

Chicago Manual of Style (16^th Edition):

Fagundes De Avila, Felipe. “Comparative Mapping of the Alpaca Genome.” 2014. Doctoral Dissertation, Texas A&M University. Accessed February 28, 2021. http://hdl.handle.net/1969.1/153632.

MLA Handbook (7^th Edition):

Fagundes De Avila, Felipe. “Comparative Mapping of the Alpaca Genome.” 2014. Web. 28 Feb 2021.

Vancouver:

Fagundes De Avila F. Comparative Mapping of the Alpaca Genome. [Internet] [Doctoral dissertation]. Texas A&M University; 2014. [cited 2021 Feb 28]. Available from: http://hdl.handle.net/1969.1/153632.

Council of Science Editors:

Fagundes De Avila F. Comparative Mapping of the Alpaca Genome. [Doctoral Dissertation]. Texas A&M University; 2014. Available from: http://hdl.handle.net/1969.1/153632

Texas A&M University

9. Doan, Ryan. The Identification and Characterization of Copy Number Variants in the Bovine Genome.

Degree: PhD, Genetics, 2013, Texas A&M University

URL: http://hdl.handle.net/1969.1/151022

► Separate domestication events and strong selective pressures have created diverse phenotypes among existing cattle populations; however, the genetic determinants underlying most phenotypes are currently unknown.… (more)

Subjects/Keywords: Genetic variants; epigenetics; regulatory elements; cattle; copy number variants

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APA (6^th Edition):

Doan, R. (2013). The Identification and Characterization of Copy Number Variants in the Bovine Genome. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/151022

Chicago Manual of Style (16^th Edition):

Doan, Ryan. “The Identification and Characterization of Copy Number Variants in the Bovine Genome.” 2013. Doctoral Dissertation, Texas A&M University. Accessed February 28, 2021. http://hdl.handle.net/1969.1/151022.

MLA Handbook (7^th Edition):

Doan, Ryan. “The Identification and Characterization of Copy Number Variants in the Bovine Genome.” 2013. Web. 28 Feb 2021.

Vancouver:

Doan R. The Identification and Characterization of Copy Number Variants in the Bovine Genome. [Internet] [Doctoral dissertation]. Texas A&M University; 2013. [cited 2021 Feb 28]. Available from: http://hdl.handle.net/1969.1/151022.

Council of Science Editors:

Doan R. The Identification and Characterization of Copy Number Variants in the Bovine Genome. [Doctoral Dissertation]. Texas A&M University; 2013. Available from: http://hdl.handle.net/1969.1/151022

Texas A&M University

10. Busch, Catherine Michelle. Mapping a Gene Responsible for Natural Resistance to Rift Valley Fever Virus in Inbred Rats.

Degree: PhD, Genetics, 2015, Texas A&M University

URL: http://hdl.handle.net/1969.1/155679

► The Rift Valley Fever virus (RVFV) presents an epidemic and epizootic threat in sub-Saharan Africa, Egypt, and the Arabian Peninsula, and has recently gained attention… (more)

▼ The Rift Valley Fever virus (RVFV) presents an epidemic and epizootic threat in sub-Saharan Africa, Egypt, and the Arabian Peninsula, and has recently gained attention as a potential weapon of bioterrorism due to its ability to infect both livestock and humans. Inbred rat strains show similar characteristic responses to the disease as humans and livestock, making them a suitable model species. Previous studies had shown differences among various inbred rat strains in susceptibility to RVFV hepatic disease, including a higher susceptibility of Wistar-Furth (WF) rats compared to a more resistant Lewis (LEW) strain. Further study revealed that this resistance trait follows the pattern of a dominant gene inherited in Mendelian fashion. A congenic WF.LEW strain resistant to infection with RVFV was derived from the susceptible WF and resistant LEW strains, and a subsequent genome scan revealed two prospective regions for the location of the gene, one on chromosome 3 and the other on chromosome 9. Subsequently, this study employed the methods of backcrossing, genotyping, viral challenges, gene expression studies, and sequencing to define a practicable region of interest and to further identify a viable candidate gene and prospective mechanism by which resistance is conferred. A program of backcrossing WF.LEW rats to WF rats, genotyping offspring using SNPs and microsatellites, and subsequently challenging N1 litters with RVFV was used to determine that the ~2Mb region on the distal end of chromosome 3 contains the gene conferring resistance. The use of genetic markers to detect recombination in further backcross generations resulted in the identification of two recombinants in this newly established region of interest. Through RVFV challenges, the recombinants narrowed the prospective region of chromosome 3 to ~500Kb containing 20 genes. Comparative qPCR analysis of all 20 genes combined with comparative sequencing studies of the entire region between susceptible WF/NHsd rats and resistant WF.LEW rats facilitated the identification of candidate gene Rtel1 and a proposed mechanism by which resistance is conferred, which will potentially become the basis for developing new preventive measures against the virus. Advisors/Committee Members: Womack, James E (advisor), Kraemer, Duane C (committee member), Skow, Loren C (committee member), Welsh, Jane (committee member).

Subjects/Keywords: Rift Valley Fever Virus; rats; gene mapping

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APA (6^th Edition):

Busch, C. M. (2015). Mapping a Gene Responsible for Natural Resistance to Rift Valley Fever Virus in Inbred Rats. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/155679

Chicago Manual of Style (16^th Edition):

Busch, Catherine Michelle. “Mapping a Gene Responsible for Natural Resistance to Rift Valley Fever Virus in Inbred Rats.” 2015. Doctoral Dissertation, Texas A&M University. Accessed February 28, 2021. http://hdl.handle.net/1969.1/155679.

MLA Handbook (7^th Edition):

Busch, Catherine Michelle. “Mapping a Gene Responsible for Natural Resistance to Rift Valley Fever Virus in Inbred Rats.” 2015. Web. 28 Feb 2021.

Vancouver:

Busch CM. Mapping a Gene Responsible for Natural Resistance to Rift Valley Fever Virus in Inbred Rats. [Internet] [Doctoral dissertation]. Texas A&M University; 2015. [cited 2021 Feb 28]. Available from: http://hdl.handle.net/1969.1/155679.

Council of Science Editors:

Busch CM. Mapping a Gene Responsible for Natural Resistance to Rift Valley Fever Virus in Inbred Rats. [Doctoral Dissertation]. Texas A&M University; 2015. Available from: http://hdl.handle.net/1969.1/155679

11. Wright, Bradley Allen. Reciprocal cross differences in Brahman-Hereford F2 cows: reproductive and maternal traits.

Degree: MS, Animal Breeding, 2007, Texas A&M University

URL: http://hdl.handle.net/1969.1/4978

► Data from 75 F2 Brahman-Hereford cows of four specific breed combinations, F2 HB (produced by F1 HB sires x F1 HB dams, where Ã¢ÂÂHBÃ¢ÂÂ refers… (more)

▼ Data from 75 F2 Brahman-Hereford cows of four specific breed combinations, F2 HB (produced by F1 HB sires x F1 HB dams, where Ã¢ÂÂHBÃ¢ÂÂ refers to cattle sired by Hereford bulls and out of Brahman cows), F2 BH (produced by F1 BH sires x F1 BH dams), HB x BH and BH x HB, were evaluated for maternal performance at the Texas A&M Research Center near McGregor. Differences between breed combinations were analyzed for calf crop born (CCB), calf crop weaned (CCW), calf survival (CS), birth weight (BW), weaning weight (WW), and cow weight at palpation (PW). The adjusted means for F2 HB, F2 BH, HB x BH, and BH x HB were 0.84 ÃÂ± 0.06, 0.57 ÃÂ± 0.07, 0.82 ÃÂ± 0.06, and 0.62 ÃÂ± 0.08, respectively, for CCW. F2 HB cows had a 0.27 ÃÂ± 0.09 higher percent calf crop weaned than F2 BH cows (P < 0.01) and a 0.22 ÃÂ± 0.11 higher percent calf crop weaned than BH x HB cows (P < 0.05). HB x BH cows had a 0.25 ÃÂ± 0.08 higher percent calf crop weaned than F2 BH (P < 0.01) and a 0.20 ÃÂ± 0.10 higher percent calf crop weaned than BH x HB cows (P < 0.05). As 6-year-olds, the adjusted means for cow weight at palpation for F2 HB, F2 BH, HB x BH, and BH x HB cows were 523.65 ÃÂ± 20.49 kg, 602.61 ÃÂ± 23.63 kg, 492.84 ÃÂ± 16.98 kg, and 515.93 ÃÂ± 22.96 kg, respectively. Averaged across all ages, HB x BH cows weighed 56.59 ÃÂ± 15.29 kg less than F2 BH cows (P < 0.001) and 41.11 ÃÂ± 18.92 kg less than BH x HB cows (P < 0.05). Also, F2 HB cows weighed 40.45 ÃÂ± 17.68 kg less than F2 BH cows (P < 0.05). In this herd, HB-sired cows had higher reproductive efficiency than BH-sired cows. Also, HB-sired cows tended to be lighter than BH-sired cows. Although these differences existed, exact causes could not be determined primarily due to confounding between the birth year of the cow and the sire breed of the cow. Advisors/Committee Members: Sanders, James O. (advisor), Herring, Andy D. (committee member), Womack, James E. (committee member).

Subjects/Keywords: Reciprocal differences; F2 Brahman-Hereford cows; Reproductive efficiency

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APA (6^th Edition):

Wright, B. A. (2007). Reciprocal cross differences in Brahman-Hereford F2 cows: reproductive and maternal traits. (Masters Thesis). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/4978

Chicago Manual of Style (16^th Edition):

Wright, Bradley Allen. “Reciprocal cross differences in Brahman-Hereford F2 cows: reproductive and maternal traits.” 2007. Masters Thesis, Texas A&M University. Accessed February 28, 2021. http://hdl.handle.net/1969.1/4978.

MLA Handbook (7^th Edition):

Wright, Bradley Allen. “Reciprocal cross differences in Brahman-Hereford F2 cows: reproductive and maternal traits.” 2007. Web. 28 Feb 2021.

Vancouver:

Wright BA. Reciprocal cross differences in Brahman-Hereford F2 cows: reproductive and maternal traits. [Internet] [Masters thesis]. Texas A&M University; 2007. [cited 2021 Feb 28]. Available from: http://hdl.handle.net/1969.1/4978.

Council of Science Editors:

Wright BA. Reciprocal cross differences in Brahman-Hereford F2 cows: reproductive and maternal traits. [Masters Thesis]. Texas A&M University; 2007. Available from: http://hdl.handle.net/1969.1/4978

12. Flores, Erin Gillenwaters. Characterization of the Bovine Cathelicidin Gene Family.

Degree: PhD, Genetics, 2012, Texas A&M University

URL: http://hdl.handle.net/1969.1/ETD-TAMU-2011-08-9812

► Cathelicidins (CATHLs) are small, cationic antimicrobial peptides that establish an early innate immune defense against infections in mammals. Beyond their wide spectrum of antimicrobial activity,… (more)

▼ Cathelicidins (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. Advisors/Committee Members: Womack, James E. (advisor), Derr, James N. (committee member), Long, Charles R. (committee member), Riggs, Penny K. (committee member).

Subjects/Keywords: antimicrobial peptides; cathelicidins; cattle; genetic variation

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APA (6^th Edition):

Flores, E. G. (2012). Characterization of the Bovine Cathelicidin Gene Family. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/ETD-TAMU-2011-08-9812

Chicago Manual of Style (16^th Edition):

Flores, Erin Gillenwaters. “Characterization of the Bovine Cathelicidin Gene Family.” 2012. Doctoral Dissertation, Texas A&M University. Accessed February 28, 2021. http://hdl.handle.net/1969.1/ETD-TAMU-2011-08-9812.

MLA Handbook (7^th Edition):

Flores, Erin Gillenwaters. “Characterization of the Bovine Cathelicidin Gene Family.” 2012. Web. 28 Feb 2021.

Vancouver:

Flores EG. Characterization of the Bovine Cathelicidin Gene Family. [Internet] [Doctoral dissertation]. Texas A&M University; 2012. [cited 2021 Feb 28]. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-2011-08-9812.

Council of Science Editors:

Flores EG. Characterization of the Bovine Cathelicidin Gene Family. [Doctoral Dissertation]. Texas A&M University; 2012. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-2011-08-9812

13. Dindot, Scott Victor. The development of a bovine interspecies model for the analysis of genomic imprinting in normal and nuclear transfer derived fetuses.

Degree: PhD, Genetics, 2004, Texas A&M University

URL: http://hdl.handle.net/1969.1/1161

► The advent of somatic cell nuclear transfer in cattle has provided the opportunity for researchers to generate genetically identical animals as well as animals that… (more)

▼ The advent of somatic cell nuclear transfer in cattle has provided the opportunity for researchers to generate genetically identical animals as well as animals that possess precise genetic modifications for agriculture and biomedical purposes. However, in spite of the revolutionary impact this technology presents, problems remain which hinder the production of healthy animals on a consistent basis. Research on cloned mice implicates improper reprogramming of epigenetic modifications and genomic imprinting for the low pregnancy rates and high incidence of abnormalities that are manifested in cloned animals; however, a systematic and comprehensive analysis of nuclear reprogramming in cloned cattle remains undone. The purpose of this research is to assess and characterize the patterns of genomic imprinting in normal and nuclear transfer derived bovine fetuses. To facilitate the identification of imprinted genes in the bovine, a Bos gaurus/Bos taurus interspecies model has been incorporated to maximize the genetic heterozygosity that exists between the alleles of putative imprinted genes for allelic discrimination and parental inheritance. The sequence of twenty-six genes, previously reported as imprinted in mice and humans, was analyzed in Bos gaurus (Gaur) and Bos taurus (Angus) cattle for the presence of single nucleotide polymorphisms (SNP). SNPs were detected in the Gene trap locus 2 (GTL2), Insulin like growth factor 2 (IGF2), Wilms tumor 1 (WT1) and the X chromosome inactivation specific transcript (XIST). Allelic expression analysis in interspecies hybrids indicated maternal genomic imprinting at the IGF2 and XIST loci, paternal genomic imprinting at the GTL2 locus and no imprinting at the WT1 locus. Analysis in cloned hybrids indicated fidelity of allelic expression at the IGF2 and GTL2 loci, however disruption of imprinting was observed at the XIST locus in the placenta of clones. These results are the largest identification of imprinted genes in the bovine and the first identification of the disruption of an imprinted gene in an animal derived from somatic cell nuclear transfer. Advisors/Committee Members: Derr, James (advisor), Piedrahita, Jorge (advisor), Davis, George (committee member), Womack, James (committee member), Skow, Loren (committee member).

Subjects/Keywords: imprinting; epigenetics; bovine; cloning; nuclear transfer

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APA (6^th Edition):

Dindot, S. V. (2004). The development of a bovine interspecies model for the analysis of genomic imprinting in normal and nuclear transfer derived fetuses. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/1161

Chicago Manual of Style (16^th Edition):

Dindot, Scott Victor. “The development of a bovine interspecies model for the analysis of genomic imprinting in normal and nuclear transfer derived fetuses.” 2004. Doctoral Dissertation, Texas A&M University. Accessed February 28, 2021. http://hdl.handle.net/1969.1/1161.

MLA Handbook (7^th Edition):

Dindot, Scott Victor. “The development of a bovine interspecies model for the analysis of genomic imprinting in normal and nuclear transfer derived fetuses.” 2004. Web. 28 Feb 2021.

Vancouver:

Dindot SV. The development of a bovine interspecies model for the analysis of genomic imprinting in normal and nuclear transfer derived fetuses. [Internet] [Doctoral dissertation]. Texas A&M University; 2004. [cited 2021 Feb 28]. Available from: http://hdl.handle.net/1969.1/1161.

Council of Science Editors:

Dindot SV. The development of a bovine interspecies model for the analysis of genomic imprinting in normal and nuclear transfer derived fetuses. [Doctoral Dissertation]. Texas A&M University; 2004. Available from: http://hdl.handle.net/1969.1/1161

14. Baradji, Issa. The Role of Apical Membrane Antigen-1 in Erythrocyte Invasion by the Zoonotic Apicomplexan Babesia microti.

Degree: PhD, Veterinary Microbiology, 2010, Texas A&M University

URL: http://hdl.handle.net/1969.1/ETD-TAMU-2008-08-68

► Babesia microti is a tickborne hemoprotozoan parasite that causes the disease babesiosis in humans. Babesia microti Apical Membrane Antigen-1 (AMA-1) is a micronemal protein suspected… (more)

▼ Babesia microti is a tickborne hemoprotozoan parasite that causes the disease babesiosis in humans. Babesia microti Apical Membrane Antigen-1 (AMA-1) is a micronemal protein suspected to play a role in erythrocyte invasion. To investigate interaction between AMA-1 and the host cell, the ectodomain region of the B. microti ama-1 gene was cloned into an expression vector, expressed as a histidine-tagged fusion protein, and used to probe red blood cell membrane proteins in far Western blot assays. The B. microti ama-1 ectodomain, which excludes the signal peptide and the transmembrane region of the open reading frame, was amplified from a cloned gene sequence. The AMA-1 ectodomain is a membrane bound polypeptide that extends into the extracellular space and is most likely to interact or initiate interaction with the host red blood cell surface receptor(s). The amplicon was ligated into a protein expression vector to produce a 58.1 kDa recombinant His-tagged fusion protein, which was confirmed by Western blot analysis. The recombinant B. microti AMA-1 fusion protein was enriched on nickel affinity columns and then used to probe mouse, human and horse red blood cell membrane proteins in far Western blot assays. Babesia microti AMA-1 consistently reacted strongly with a protein migrating at 49 kDa. A similar reaction occurred between the B. microti AMA-1 and horse red blood cell membrane proteins, suggesting that similar interacting proteins of this size are shared by red blood cells from the three species. The B. microti AMA-1 may bind to red blood cell membrane sialic-acid groups, as shown for other Babesia spp. This may explain the signal at the 49 kDa position observed between B. microti AMA-1 and red blood cell membrane proteins from three different species. Further studies may determine if the binding epitopes of the red blood cell binding partner at this position vary and contribute to the specificity of each parasite AMA-1 for their respective host cells. Advisors/Committee Members: Holman, Patricia J. (advisor), Ball, Judith M. (committee member), Magill, Clint C. (committee member), Womack, James E. (committee member).

Subjects/Keywords: Babesia microti; Apical Membrane Antigen-1; AMA-1; erythrocyte; parasite ligand; red blood cell; receptor; protein-protein interaction

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APA (6^th Edition):

Baradji, I. (2010). The Role of Apical Membrane Antigen-1 in Erythrocyte Invasion by the Zoonotic Apicomplexan Babesia microti. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/ETD-TAMU-2008-08-68

Chicago Manual of Style (16^th Edition):

Baradji, Issa. “The Role of Apical Membrane Antigen-1 in Erythrocyte Invasion by the Zoonotic Apicomplexan Babesia microti.” 2010. Doctoral Dissertation, Texas A&M University. Accessed February 28, 2021. http://hdl.handle.net/1969.1/ETD-TAMU-2008-08-68.

MLA Handbook (7^th Edition):

Baradji, Issa. “The Role of Apical Membrane Antigen-1 in Erythrocyte Invasion by the Zoonotic Apicomplexan Babesia microti.” 2010. Web. 28 Feb 2021.

Vancouver:

Baradji I. The Role of Apical Membrane Antigen-1 in Erythrocyte Invasion by the Zoonotic Apicomplexan Babesia microti. [Internet] [Doctoral dissertation]. Texas A&M University; 2010. [cited 2021 Feb 28]. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-2008-08-68.

Council of Science Editors:

Baradji I. The Role of Apical Membrane Antigen-1 in Erythrocyte Invasion by the Zoonotic Apicomplexan Babesia microti. [Doctoral Dissertation]. Texas A&M University; 2010. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-2008-08-68

15. Fritz, Krista L. Analysis of Haplotype Structure in the Bovine Major Histocompatibility Complex.

Degree: PhD, Genetics, 2011, Texas A&M University

URL: http://hdl.handle.net/1969.1/ETD-TAMU-2009-12-7304

► The goal of this project was to identify and characterize polymorphic markers spanning regions of the bovine major histocompatibility complex (BoLA) to analyze patterns of… (more)

Subjects/Keywords: Major Histocompatibility Complex; cattle; haplotypes

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APA (6^th Edition):

Fritz, K. L. (2011). Analysis of Haplotype Structure in the Bovine Major Histocompatibility Complex. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/ETD-TAMU-2009-12-7304

Chicago Manual of Style (16^th Edition):

Fritz, Krista L. “Analysis of Haplotype Structure in the Bovine Major Histocompatibility Complex.” 2011. Doctoral Dissertation, Texas A&M University. Accessed February 28, 2021. http://hdl.handle.net/1969.1/ETD-TAMU-2009-12-7304.

MLA Handbook (7^th Edition):

Fritz, Krista L. “Analysis of Haplotype Structure in the Bovine Major Histocompatibility Complex.” 2011. Web. 28 Feb 2021.

Vancouver:

Fritz KL. Analysis of Haplotype Structure in the Bovine Major Histocompatibility Complex. [Internet] [Doctoral dissertation]. Texas A&M University; 2011. [cited 2021 Feb 28]. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-2009-12-7304.

Council of Science Editors:

Fritz KL. Analysis of Haplotype Structure in the Bovine Major Histocompatibility Complex. [Doctoral Dissertation]. Texas A&M University; 2011. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-2009-12-7304

16. Brannan, Jaime Lynette. Transcriptional Profiling of Immune Responses in Cattle Experimentally Infested with Amblyomma americanum ticks.

Degree: PhD, Genetics, 2013, Texas A&M University

URL: http://hdl.handle.net/1969.1/151106

► Infestation of cattle by Lone Star ticks, Amblyomma americanum, leads to damage of hides intended for leather, weight loss, infertility, and potentially death of cattle,… (more)

▼ Infestation of cattle by Lone Star ticks, Amblyomma americanum, leads to damage of hides intended for leather, weight loss, infertility, and potentially death of cattle, which contribute to production losses for farmers. Public concerns regarding chemical residues in food and the environment necessitate development of chemical-free alternative tick controls, such as breeding for tick-resistant phenotypes and developing anti-tick vaccines. Thus, the goal of this study was elucidation of mechanisms that mediate immune responses in cattle infested with A. americanum using gene expression techniques. Methods for isolation of total RNA from bovine tick bite-site biopsies and blood leukocytes were optimized to provide RNA suitable for gene expression studies. Tick bite-site biopsies (6 mm) and blood leukocytes were collected from a total of 13 calves (N=6, Group 4 and N=7, Group 5 calves) during experimental tick infestations to determine A. americanum tick-susceptible and -resistant phenotypes. Microarray experiments compared gene expression in tick bite-sites from tick-susceptible, moderately tick-resistant, and highly tick-resistant calves. A total of 35 genes were profiled in tick bite-site biopsies and 12 genes were evaluated in blood leukocytes via gene-specific qRT-PCR assays, and analyzed for each phenotype and for each group of calves as a whole. Analysis of microarray data revealed differential expression of IL-1R-mediators among the three cattle phenotypes. Expression profiles generated by qRT-PCR for TLR-mediating genes such as TLR2, TLR4, CD14, and MyD88 suggest that a MyD88-dependent signaling pathway may mediate the development of acquired immunity in cattle infested with Lone Star ticks. Additionally, increased expression for IL12, IFNgamma, and TNFalpha suggests that a Th1-type cell-mediated reaction may be activated, whereas increased expression of IL6, IL10, and IGHG1 supports the involvement of a Th2-type humoral-mediated response at tick bite-sites in cattle infested with at A. americanum. Regression analyses identified strong correlations between factors involved in pattern recognition in tick bite-site biopsies, including associations between TLR4 and IL1alpha, and between IL1alpha and IL1RN. In conclusion, this dissertation reports optimal methodology for gene expression studies in tick-infested cattle and provides preliminary data concerning the underlying mechanisms associated with the immune response in Lone Star tick-infested cattle. Advisors/Committee Members: Holman, Patricia J (advisor), Womack, James E (advisor), Riggs, Penny K (committee member), Tizard, Ian R (committee member), Pruett, John H (committee member).

Subjects/Keywords: gene expression; qRT-PCR; Amblyomma americanum; tick-resistance; cattle

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APA (6^th Edition):

Brannan, J. L. (2013). Transcriptional Profiling of Immune Responses in Cattle Experimentally Infested with Amblyomma americanum ticks. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/151106

Chicago Manual of Style (16^th Edition):

Brannan, Jaime Lynette. “Transcriptional Profiling of Immune Responses in Cattle Experimentally Infested with Amblyomma americanum ticks.” 2013. Doctoral Dissertation, Texas A&M University. Accessed February 28, 2021. http://hdl.handle.net/1969.1/151106.

MLA Handbook (7^th Edition):

Brannan, Jaime Lynette. “Transcriptional Profiling of Immune Responses in Cattle Experimentally Infested with Amblyomma americanum ticks.” 2013. Web. 28 Feb 2021.

Vancouver:

Brannan JL. Transcriptional Profiling of Immune Responses in Cattle Experimentally Infested with Amblyomma americanum ticks. [Internet] [Doctoral dissertation]. Texas A&M University; 2013. [cited 2021 Feb 28]. Available from: http://hdl.handle.net/1969.1/151106.

Council of Science Editors:

Brannan JL. Transcriptional Profiling of Immune Responses in Cattle Experimentally Infested with Amblyomma americanum ticks. [Doctoral Dissertation]. Texas A&M University; 2013. Available from: http://hdl.handle.net/1969.1/151106

17. Boggs, Rene' Michelle. MicroRNA expression in canine mammary cancer.

Degree: PhD, Veterinary Microbiology, 2008, Texas A&M University

URL: http://hdl.handle.net/1969.1/85979

► MicroRNAs (miRNAs) play a vital role in differentiation, proliferation and tumorigenesis by binding to messenger RNAs (mRNA) and inhibiting translation. To initiate an investigation into… (more)

Subjects/Keywords: breast cancer; RT-PCR; miRNA; canine; genetics

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APA (6^th Edition):

Boggs, R. M. (2008). MicroRNA expression in canine mammary cancer. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/85979

Chicago Manual of Style (16^th Edition):

Boggs, Rene' Michelle. “MicroRNA expression in canine mammary cancer.” 2008. Doctoral Dissertation, Texas A&M University. Accessed February 28, 2021. http://hdl.handle.net/1969.1/85979.

MLA Handbook (7^th Edition):

Boggs, Rene' Michelle. “MicroRNA expression in canine mammary cancer.” 2008. Web. 28 Feb 2021.

Vancouver:

Boggs RM. MicroRNA expression in canine mammary cancer. [Internet] [Doctoral dissertation]. Texas A&M University; 2008. [cited 2021 Feb 28]. Available from: http://hdl.handle.net/1969.1/85979.

Council of Science Editors:

Boggs RM. MicroRNA expression in canine mammary cancer. [Doctoral Dissertation]. Texas A&M University; 2008. Available from: http://hdl.handle.net/1969.1/85979

18. Moody, Jessica Ashley. Epigenetic modifications and conserved, non-coding DNA play a role in regulation of type IV collagen gene expression.

Degree: PhD, Veterinary Microbiology, 2009, Texas A&M University

URL: http://hdl.handle.net/1969.1/ETD-TAMU-2839

► Type IV collagens are components of basement membranes throughout the body and are involved in maintenance of the structural integrity of tissues as well as… (more)

▼ Type IV collagens are components of basement membranes throughout the body and are involved in maintenance of the structural integrity of tissues as well as cellular differentiation, growth, and adhesion. Members of this collagen family are uniquely arranged in pairs in a head-to-head orientation and share a proximal promoter region. The COL4A5-COL4A6 gene pair is involved in numerous human diseases and cancer metastasis. For these reasons, defining the mechanisms that regulate collagen gene expression is of specific interest. To study type IV collagens, an in vitro model system was characterized. Comparative genomics was utilized to identify conserved, non-coding DNA in COL4A5 and COL4A6. These sequences were transfected into cell lines differing in type IV collagen expression and tested for the ability to regulate transcription of a reporter gene. Each cell line was also treated with the epigenetic modifying agents, 5-Aza and TSA. The effects on type IV collagen expression were determined. The COL4A5-COL4A6 promoter region was extensively characterized using ChIP analysis; antibodies against RNAPII, acetylated histone H3, and H3K9me2 were used. Additionally, bisulfite sequencing was carried out on each cell line to determine the methylation status of CpG dinucleotides in the promoter. Cell lines differing in expression of COL4A5 and COL4A6 were identified: 1) SCC-25 keratinocytes and HEK-293 cells transcribed both COL4A5 and COL4A6, 2) HT-1080 cells selectively activated COL4A5, and 3) SK-N-SH neuroblastoma cells did not express either gene. In SK-N-SH cells, histone modifications were shown to facilitate formation of condensed chromatin to prevent transcription initiation; repression was independent of DNA methylation. Activation of COL4A5 and COL4A6 in SCC-25 and HEK-293 cells involved acetylation of histones, although differences between the two cell types were seen. In addition, conserved, non-coding sequences were shown to affect transcription of a reporter gene; these sequences may be interacting with the transcription machinery to modulate collagen expression. Finally, repression of COL4A6 in HT-1080 cells appeared to be mediated through DNA methylation of the promoter; selective activation of COL4A5 may involve conserved, non-coding DNA. In summary, epigenetic modifications as well as conserved sequences are intimately involved in regulation of type IV collagen gene expression. Advisors/Committee Members: Murphy, Keith E. (advisor), Kier, Ann B. (committee member), Long, Charles R. (committee member), Weston, Porter W. (committee member), Womack, James E. (committee member).

Subjects/Keywords: type IV collagen; regulation

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APA (6^th Edition):

Moody, J. A. (2009). Epigenetic modifications and conserved, non-coding DNA play a role in regulation of type IV collagen gene expression. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/ETD-TAMU-2839

Chicago Manual of Style (16^th Edition):

Moody, Jessica Ashley. “Epigenetic modifications and conserved, non-coding DNA play a role in regulation of type IV collagen gene expression.” 2009. Doctoral Dissertation, Texas A&M University. Accessed February 28, 2021. http://hdl.handle.net/1969.1/ETD-TAMU-2839.

MLA Handbook (7^th Edition):

Moody, Jessica Ashley. “Epigenetic modifications and conserved, non-coding DNA play a role in regulation of type IV collagen gene expression.” 2009. Web. 28 Feb 2021.

Vancouver:

Moody JA. Epigenetic modifications and conserved, non-coding DNA play a role in regulation of type IV collagen gene expression. [Internet] [Doctoral dissertation]. Texas A&M University; 2009. [cited 2021 Feb 28]. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-2839.

Council of Science Editors:

Moody JA. Epigenetic modifications and conserved, non-coding DNA play a role in regulation of type IV collagen gene expression. [Doctoral Dissertation]. Texas A&M University; 2009. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-2839

Texas A&M University

19. Salih, Hanni. An updated object oriented bovine QTL viewer and genome-wide bovine meta-analysis.

Degree: PhD, Genetics, 2009, Texas A&M University

URL: http://hdl.handle.net/1969.1/ETD-TAMU-2969

► Waves of bovine genomic data have been produced as a result of the bovine genome sequencing projects. In addition to the massive amounts of genomic… (more)

▼ Waves of bovine genomic data have been produced as a result of the bovine genome sequencing projects. In addition to the massive amounts of genomic sequence, significant annotation including single nucleotide polymorphisms, sequence tagged sites and haplotype blocks have been produced by the Bovine HapMap Project. Furthermore, many agriculturally significant traits in cattle such as milk yield and carcass weight are measured on a quantitative scale and have been genetically mapped as quantitative trait loci (QTL). QTL data can be used to generate another form of bovine annotation linking phenotype to genotype. However, it is impossible for humans to be able to analyze genomic scale data without computer based tools. Bioinformatic tools have been shown to greatly increase productivity and improve efficiency when dealing with large data sets. My dissertation presents an integrated, extensible database that houses SNPs, STSs, haplotypes, and QTL. The database is presented to researchers through a restructured, object oriented Bovine QTL Viewer that displays multiple levels of bovine annotation synergistically. Evaluation of use of the viewer was performed using a survey based approach and measured quantitatively. In addition, the QTL data from the database was used to analyze the frequency of gene ontology (GO) annotations within QTL regions. QTL regions were divided into 8 trait based groups. GO terms were counted within each category of QTL and in non- QTL regions of the genome. Top level GO term frequencies were generated from the counts and these frequencies were compared between QTL and non-QTL portions of the genome. Furthermore, specific sets of GO terms believed to be related to QTL categories were also used to determine if QTL regions were enriched for genes annotated with such GO terms. As a result, we determined that gene density varied significantly across QTL regions and that many QTL categories showed GO term frequency differences that could be related to the trait’s biology. Furthermore, our selected GO term sets were shown to be significantly enriched in some QTL categories. Advisors/Committee Members: Adelson, David (advisor), Womack, James (advisor), Elsik, Christine (committee member), Furuta, Richard (committee member).

Subjects/Keywords: Bovine; Genome-Wide; QTL

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APA (6^th Edition):

Salih, H. (2009). An updated object oriented bovine QTL viewer and genome-wide bovine meta-analysis. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/ETD-TAMU-2969

Chicago Manual of Style (16^th Edition):

Salih, Hanni. “An updated object oriented bovine QTL viewer and genome-wide bovine meta-analysis.” 2009. Doctoral Dissertation, Texas A&M University. Accessed February 28, 2021. http://hdl.handle.net/1969.1/ETD-TAMU-2969.

MLA Handbook (7^th Edition):

Salih, Hanni. “An updated object oriented bovine QTL viewer and genome-wide bovine meta-analysis.” 2009. Web. 28 Feb 2021.

Vancouver:

Salih H. An updated object oriented bovine QTL viewer and genome-wide bovine meta-analysis. [Internet] [Doctoral dissertation]. Texas A&M University; 2009. [cited 2021 Feb 28]. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-2969.

Council of Science Editors:

Salih H. An updated object oriented bovine QTL viewer and genome-wide bovine meta-analysis. [Doctoral Dissertation]. Texas A&M University; 2009. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-2969

Texas A&M University

20. Knox, Anna Lavonne. The incidence of tropheryma whipplei in the population of the Brazos Valley region of Texas.

Degree: MS, Laboratory Animal Medicine, 2009, Texas A&M University

URL: http://hdl.handle.net/1969.1/ETD-TAMU-3184

► An epidemiological study of the bacteria Tropheryma whipplei was conducted in the Brazos Valley region of Texas; specifically in the cities of College Station and… (more)

Subjects/Keywords: Tropheryma whipplei

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APA (6^th Edition):

Knox, A. L. (2009). The incidence of tropheryma whipplei in the population of the Brazos Valley region of Texas. (Masters Thesis). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/ETD-TAMU-3184

Chicago Manual of Style (16^th Edition):

Knox, Anna Lavonne. “The incidence of tropheryma whipplei in the population of the Brazos Valley region of Texas.” 2009. Masters Thesis, Texas A&M University. Accessed February 28, 2021. http://hdl.handle.net/1969.1/ETD-TAMU-3184.

MLA Handbook (7^th Edition):

Knox, Anna Lavonne. “The incidence of tropheryma whipplei in the population of the Brazos Valley region of Texas.” 2009. Web. 28 Feb 2021.

Vancouver:

Knox AL. The incidence of tropheryma whipplei in the population of the Brazos Valley region of Texas. [Internet] [Masters thesis]. Texas A&M University; 2009. [cited 2021 Feb 28]. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-3184.

Council of Science Editors:

Knox AL. The incidence of tropheryma whipplei in the population of the Brazos Valley region of Texas. [Masters Thesis]. Texas A&M University; 2009. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-3184

Texas A&M University

21. Santani, Avni Bhawan. Genomic analysis of the horse Y chromosome.

Degree: PhD, Genetics, 2005, Texas A&M University

URL: http://hdl.handle.net/1969.1/1494

► Stallion fertility is of significant economic importance in the multibillion dollar equine industry. Presently, the underlying genetic causes of infertility in stallions are unknown. Analysis… (more)

▼ Stallion fertility is of significant economic importance in the multibillion dollar equine industry. Presently, the underlying genetic causes of infertility in stallions are unknown. Analysis of the human genome has shown that in more than 25% of cases, male infertility is associated with deletions/rearrangements in the Y chromosome. Presently there is no gene map for the Y chromosome in the horse. Therefore, the primary aim of this study is to build a detailed physical map of the chromosome with a long-term aim to identify and analyze Y-specific factors affecting fertility in stallions. To materialize this, we constructed the first radiation hybrid and FISH map of the euchromatic region of the horse Y chromosome. This basic map was used to obtain Y-specific BAC clones that provided new STS markers from the end sequences. Chromosome walking provided 73 BACs comprising 7 contigs that were built across the euchromatic region using 124 markers for content mapping. The results were validated by restriction fingerprinting and Fiber FISH. The map is presently the most informative among the domestic species and second to only human and mouse Y chromosome maps. The construction of this map will pave the way for isolation and functional characterization of genes critical for normal male fertility and reproduction and will in the future lead to the development of a diagnostic test to facilitate early identification of deletions/rearrangements on the Y chromosome of potentially affected foals/stallions. The second part of the study comprised the first extended investigation to assess genetic variation in the horse Y chromosome. Approximately 4.5Mb of the euchromatic region was screened for polymorphic microsatellite markers. Of the 27 markers that were characterized and screened for polymorphism in 14 breeds of the domestic horse and eight extant equids, only one was polymorphic in the domestic horse, suggesting a low level of genetic variation on the chromosome. However, 21 of the markers showed noteworthy variation (on average four alleles/marker) among the eight equids. These markers will be vital in future studies aimed at elucidating the genetic relationships between the various equids through phylogenetic analysis. Advisors/Committee Members: Chowdhary, Bhanu (advisor), Varner, Dickson (committee member), Womack, James (committee member), Skow, Loren (committee member).

Subjects/Keywords: Y; map; microsatellites; contig

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APA (6^th Edition):

Santani, A. B. (2005). Genomic analysis of the horse Y chromosome. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/1494

Chicago Manual of Style (16^th Edition):

Santani, Avni Bhawan. “Genomic analysis of the horse Y chromosome.” 2005. Doctoral Dissertation, Texas A&M University. Accessed February 28, 2021. http://hdl.handle.net/1969.1/1494.

MLA Handbook (7^th Edition):

Santani, Avni Bhawan. “Genomic analysis of the horse Y chromosome.” 2005. Web. 28 Feb 2021.

Vancouver:

Santani AB. Genomic analysis of the horse Y chromosome. [Internet] [Doctoral dissertation]. Texas A&M University; 2005. [cited 2021 Feb 28]. Available from: http://hdl.handle.net/1969.1/1494.

Council of Science Editors:

Santani AB. Genomic analysis of the horse Y chromosome. [Doctoral Dissertation]. Texas A&M University; 2005. Available from: http://hdl.handle.net/1969.1/1494

Texas A&M University

22. Ramlachan, Nicole. Organization of the class I region of the bovine major histocompatibility complex (BoLA) and the characterization of a class I frameshift deletion (BoLA-Adel) prevalent in feral bovids.

Degree: PhD, Genetics, 2006, Texas A&M University

URL: http://hdl.handle.net/1969.1/3197

► The major histocompatibility complex (MHC) is a genomic region containing genes of immunomodulatory importance. MHC class I genes encode cell-surface glycoproteins that present peptides to… (more)

▼ The major histocompatibility complex (MHC) is a genomic region containing genes of immunomodulatory importance. MHC class I genes encode cell-surface glycoproteins that present peptides to circulating T cells, playing a key role in recognition of self and non-self. Studies of MHC loci in vertebrates have examined levels of polymorphism and molecular evolutionary processes generating diversity. The bovine MHC (BoLA) has been associated with disease susceptibility, resistance and progression. To delineate mechanisms by which MHC class I genes evolved to function optimally in a species like cattle, it is necessary to study genomic organization of BoLA to define gene content, and investigate characteristics of expressed class I molecules. This study describes development of a physical map of BoLA class I region derived from screening two BAC libraries, isolating positive clones and confirming gene content, order and chromosomal location through PCR, novel BAC end sequencing techniques, and selected BAC shotgun cloning and/or sequencing and FISH analysis. To date, this is the most complete ordered BAC array encompassing the BoLA class I region from the class III boundary to the extended class I region. Characterization of a frameshift allele exhibiting trans-species polymorphism in Bos and Bison by flow cytometry, real-time RT-PCR, 1D and 2D gel analysis is also described. This frameshift allele encodes an early termination signal within the antigen recognition site (ARS) of exon 3 of the BoLA BSA-Adel class I gene predicting a truncated class I protein that is soluble. An ability to assess MHC diversity in populations and provision of animals with defined MHC haplotypes and genetic content for experimental research is necessary in developing a basis upon which to build functional studies to elucidate associations between haplotype and disease in bovids. The BoLA class I region is immunologically important for disease association studies in an economically important species. This study provides knowledge of gene content and organization within the class I MHC region in cattle, providing a template for more detailed analysis and elucidation of complex disease associations through functional genomics and comparative analysis, as well as evolution of the MHC in bovids to optimize a populationÂs immune response. Advisors/Committee Members: Skow, Loren (advisor), Chowdhary, Bhanu (committee member), Womack, James (committee member), Miranda, Rajesh (committee member).

Subjects/Keywords: MHC; BoLA; class I; immunogenetics; comparative genomics; bovine

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APA (6^th Edition):

Ramlachan, N. (2006). Organization of the class I region of the bovine major histocompatibility complex (BoLA) and the characterization of a class I frameshift deletion (BoLA-Adel) prevalent in feral bovids. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/3197

Chicago Manual of Style (16^th Edition):

Ramlachan, Nicole. “Organization of the class I region of the bovine major histocompatibility complex (BoLA) and the characterization of a class I frameshift deletion (BoLA-Adel) prevalent in feral bovids.” 2006. Doctoral Dissertation, Texas A&M University. Accessed February 28, 2021. http://hdl.handle.net/1969.1/3197.

MLA Handbook (7^th Edition):

Ramlachan, Nicole. “Organization of the class I region of the bovine major histocompatibility complex (BoLA) and the characterization of a class I frameshift deletion (BoLA-Adel) prevalent in feral bovids.” 2006. Web. 28 Feb 2021.

Vancouver:

Ramlachan N. Organization of the class I region of the bovine major histocompatibility complex (BoLA) and the characterization of a class I frameshift deletion (BoLA-Adel) prevalent in feral bovids. [Internet] [Doctoral dissertation]. Texas A&M University; 2006. [cited 2021 Feb 28]. Available from: http://hdl.handle.net/1969.1/3197.

Council of Science Editors:

Ramlachan N. Organization of the class I region of the bovine major histocompatibility complex (BoLA) and the characterization of a class I frameshift deletion (BoLA-Adel) prevalent in feral bovids. [Doctoral Dissertation]. Texas A&M University; 2006. Available from: http://hdl.handle.net/1969.1/3197

Texas A&M University

23. Peoples, Michael D 1978-. Identification and Characterization of Bovine Pol III Promoters to Express a Short-Hairpin RNA.

Degree: MS, Genetics, 2010, Texas A&M University

URL: http://hdl.handle.net/1969.1/148456

► The use of molecular biology as a means to advance agriculture has proven beneficial in many fields. However, the development lentiviral vectors that utilize a… (more)

▼ The use of molecular biology as a means to advance agriculture has proven beneficial in many fields. However, the development lentiviral vectors that utilize a livestock promoter to express short hairpin RNA (shRNA) has been limited to date. The goal of this research project was to develop and characterize lentiviral bovine Pol III mir30 shRNA expression vectors for future use in livestock research. The bovine Pol III promoter (7sk, U6-2, or H1) was inserted directly upstream of a mir30 shRNA expression sequence in the lentiviral vector pNef-GT. A transient luciferase knockdown assay in human embryonic kidney (HEK) 293T cells was used to compare the functionality of these vectors. The bPol III mir30 shRNA expression vector was co-transfected with the pGL3 luciferase expression vector and the renilla expression vector pLB at a ratio of 5:10:1 respectively. The vectors were allowed 48 hrs to produce their respective products before luciferase activity was measured with the Stop-n-Glo Assay (Promega). Each bPol III promoter was able to express a functional shRNA resulting in a reduction of luciferase activity greater than 68 percent. The bH1 and bU6-2 Luc shRNA vectors were the most effective vectors when transfected with >76 percent (p-value <0.05) reduced luciferase activity. To confirm that these promoters were functional after integration into a bovine genome, recombinant lentivirus was made from these vectors. These particles were then used to transduce a bovine kidney (MDBK) cell line that expressed luciferase. After transduction, transgenic cells were selected by the addition of the antibiotic, Geneticin to the culture media until a population of 100 percent bPol III expression cells were observed for two passages and luciferase activity was measured. The 7sk promoter was the most effective bPol III promoter that reduced luciferase activity in these cells by 72 percent (p-value <0.05), while the bU6-2 and bH1 were moderately effective at reducing luciferase levels (37 percent, 46 percent respectively). These experiments were the first to quantify the bovine Pol III promoter function after integration into a bovine genome. While variability was observed, for livestock based research, the b7sk lentiviral vector appears to be the best choice to express a shRNA from the genome of a bovine genome. Advisors/Committee Members: Westhusin, Mark (advisor), Long, Charles (committee member), Womack, James (committee member).

Subjects/Keywords: bovine Pol III promoters; rLentivirus; shRNA; RNAi

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APA (6^th Edition):

Peoples, M. D. 1. (2010). Identification and Characterization of Bovine Pol III Promoters to Express a Short-Hairpin RNA. (Masters Thesis). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/148456

Chicago Manual of Style (16^th Edition):

Peoples, Michael D 1978-. “Identification and Characterization of Bovine Pol III Promoters to Express a Short-Hairpin RNA.” 2010. Masters Thesis, Texas A&M University. Accessed February 28, 2021. http://hdl.handle.net/1969.1/148456.

MLA Handbook (7^th Edition):

Peoples, Michael D 1978-. “Identification and Characterization of Bovine Pol III Promoters to Express a Short-Hairpin RNA.” 2010. Web. 28 Feb 2021.

Vancouver:

Peoples MD1. Identification and Characterization of Bovine Pol III Promoters to Express a Short-Hairpin RNA. [Internet] [Masters thesis]. Texas A&M University; 2010. [cited 2021 Feb 28]. Available from: http://hdl.handle.net/1969.1/148456.

Council of Science Editors:

Peoples MD1. Identification and Characterization of Bovine Pol III Promoters to Express a Short-Hairpin RNA. [Masters Thesis]. Texas A&M University; 2010. Available from: http://hdl.handle.net/1969.1/148456

Texas A&M University

24. Schroeder, James William. Assessing the possibility of a functionally discontinuous biological paradigm.

Degree: MA, Philosophy, 2007, Texas A&M University

URL: http://hdl.handle.net/1969.1/4804

► This project sets as its goal the development of an Intelligent Design paradigm that makes falsifiable predictions. According to Karl Popper, such falsifiability is a… (more)

▼ This project sets as its goal the development of an Intelligent Design paradigm that makes falsifiable predictions. According to Karl Popper, such falsifiability is a key component of scientific theories. To accomplish this, two hypothetical historical narratives are first outlined based on guided processes and the design points they predict. A biochemical approach to characterizing organisms then defines a protein's global functional limits as determining the set of amino acids that allow it to successfully perform its functions in any situation. The local functional limits restrict this potential substitution set to only those proteins viable within an individual genetic background. Proteins are referred to as the first-order of specified complexity because a protein's gene is the fundamental unit of inheritance. Other orders of specified complexity are described culminating in the organism level, which is the fundamental unit of selection. Each phylogenetic tree within the two intelligent design scenarios is founded by an original group or archetype. The descendants of this archetype are known as the archetype's genus. Speciation events within the genus are brought about by a slow process called co-adapted drift that creates distinct species through functional incompatibilities. A theory of natural selection is developed that attempts to characterize the relationship between the gene and the organism. Natural selection in this sense is described as a preservation mechanism that selects against deleterious phenotypes instead of selecting for beneficial ones. Finally, a practical methodology is developed that begins by determining the history of a gene in a given species by the symmetrical causal relationships of the alleles and the species allelic distribution. The original alleles in this species and their local functional limits are then compared with those of analogous genes in similar species to determine if these species were functionally compatible at that time. The two Intelligent Design paradigms predict patterns of incompatibilities, or design points, where guided actions were involved. This is a falsifiable prediction that raises the status of these paradigms in a Popperian sense. Advisors/Committee Members: Sansom, Roger B. (advisor), Bradley, Walter L. (committee member), Womack, James E. (committee member).

Subjects/Keywords: Assessing; Possibility; Functionally; Discontinuous; Biological; Paradigm

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APA (6^th Edition):

Schroeder, J. W. (2007). Assessing the possibility of a functionally discontinuous biological paradigm. (Masters Thesis). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/4804

Chicago Manual of Style (16^th Edition):

Schroeder, James William. “Assessing the possibility of a functionally discontinuous biological paradigm.” 2007. Masters Thesis, Texas A&M University. Accessed February 28, 2021. http://hdl.handle.net/1969.1/4804.

MLA Handbook (7^th Edition):

Schroeder, James William. “Assessing the possibility of a functionally discontinuous biological paradigm.” 2007. Web. 28 Feb 2021.

Vancouver:

Schroeder JW. Assessing the possibility of a functionally discontinuous biological paradigm. [Internet] [Masters thesis]. Texas A&M University; 2007. [cited 2021 Feb 28]. Available from: http://hdl.handle.net/1969.1/4804.

Council of Science Editors:

Schroeder JW. Assessing the possibility of a functionally discontinuous biological paradigm. [Masters Thesis]. Texas A&M University; 2007. Available from: http://hdl.handle.net/1969.1/4804

Texas A&M University

25. Callicott, Ralph J. Characterization and Mapping of the Gene Conferring Resistance to Rift Valley Fever Virus Hepatic Disease in WF.LEW Rats.

Degree: PhD, Genetics, 2010, Texas A&M University

URL: http://hdl.handle.net/1969.1/ETD-TAMU-2008-12-196

► Rift Valley Fever Virus is a plebovirus that causes epidemics and epizootics in sub-Saharan African countries but has expanded to Egypt and the Arabian Peninsula.… (more)

Subjects/Keywords: Lewis; Wistar-Furth; SSLP; SNP; Rift Valley Fever Virus; resistance; congenic; substrain

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APA (6^th Edition):

Callicott, R. J. (2010). Characterization and Mapping of the Gene Conferring Resistance to Rift Valley Fever Virus Hepatic Disease in WF.LEW Rats. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/ETD-TAMU-2008-12-196

Chicago Manual of Style (16^th Edition):

Callicott, Ralph J. “Characterization and Mapping of the Gene Conferring Resistance to Rift Valley Fever Virus Hepatic Disease in WF.LEW Rats.” 2010. Doctoral Dissertation, Texas A&M University. Accessed February 28, 2021. http://hdl.handle.net/1969.1/ETD-TAMU-2008-12-196.

MLA Handbook (7^th Edition):

Callicott, Ralph J. “Characterization and Mapping of the Gene Conferring Resistance to Rift Valley Fever Virus Hepatic Disease in WF.LEW Rats.” 2010. Web. 28 Feb 2021.

Vancouver:

Callicott RJ. Characterization and Mapping of the Gene Conferring Resistance to Rift Valley Fever Virus Hepatic Disease in WF.LEW Rats. [Internet] [Doctoral dissertation]. Texas A&M University; 2010. [cited 2021 Feb 28]. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-2008-12-196.

Council of Science Editors:

Callicott RJ. Characterization and Mapping of the Gene Conferring Resistance to Rift Valley Fever Virus Hepatic Disease in WF.LEW Rats. [Doctoral Dissertation]. Texas A&M University; 2010. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-2008-12-196

Texas A&M University

26. Bell, Rebecca Jane. Genetics of x-linked and autosomal recessive hereditary nephropathy in the domestic dog.

Degree: PhD, Veterinary Microbiology, 2009, Texas A&M University

URL: http://hdl.handle.net/1969.1/ETD-TAMU-2125

► Although typically thought of as a beloved companion or indispensable aide, the domestic dog (Canis lupus familiaris) has emerged as an excellent model for the… (more)

▼ Although typically thought of as a beloved companion or indispensable aide, the domestic dog (Canis lupus familiaris) has emerged as an excellent model for the study of human hereditary diseases. Many hereditary diseases of the dog have nearly identical clinical presentations as those of the human and are, most often, caused by mutations in the same genes. One such disease is hereditary nephropathy; an inherited glomerular disease in the domestic dog that is similar to Alport syndrome of the human. Both diseases are caused by mutations in the type IV collagens genes, and the disease has nearly identical pathology and clinical presentations in the dog and human. By studying this disease in the dog, our laboratory hopes to increase understanding of the disease so that information that can be applied to both the human and the dog. Reported here is 1) the development of a genomic based test to determine genotypes of mixed breed dogs in a colony presenting with X-linked hereditary nephropathy, 2) the determination of patterns of X-chromosome inactivation in normal dogs and dogs that are carriers of Xlinked hereditary nephropathy, 3) the design of a synthetic COL4A5 cDNA to be used for gene therapy treatment of dogs with X-linked hereditary nephropathy, 4) the investigation of type IV collagen gene expression changes in normal dogs and those affected with X-linked and autosomal recessive hereditary nephropathy, and 5) the discovery of the mutation causative for autosomal recessive hereditary nephropathy in the English Cocker Spaniel. Utilization of the colony of dogs affected with X-linked hereditary nephropathy (for which the causative mutation was previously identified) allowed for comparisons of type IV collagen gene expression to English Cocker Spaniels with autosomal recessive hereditary nephropathy. These data were critical to identification of the gene harboring the causative mutation for autosomal recessive hereditary nephropathy. Sequencing was performed to identify the mutation. With the ability to test for carriers of this disease, it is our hope that breeders will use it to to maintain the desired traits in the ECS while simultaneously eliminating the production of affected offspring. Advisors/Committee Members: Murphy, Keith E. (advisor), Lees, George E. (committee member), Long, Charles R (committee member), Womack, James E (committee member).

Subjects/Keywords: canine genetics; hereditary nephropathy; Alport syndrome

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APA (6^th Edition):

Bell, R. J. (2009). Genetics of x-linked and autosomal recessive hereditary nephropathy in the domestic dog. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/ETD-TAMU-2125

Chicago Manual of Style (16^th Edition):

Bell, Rebecca Jane. “Genetics of x-linked and autosomal recessive hereditary nephropathy in the domestic dog.” 2009. Doctoral Dissertation, Texas A&M University. Accessed February 28, 2021. http://hdl.handle.net/1969.1/ETD-TAMU-2125.

MLA Handbook (7^th Edition):

Bell, Rebecca Jane. “Genetics of x-linked and autosomal recessive hereditary nephropathy in the domestic dog.” 2009. Web. 28 Feb 2021.

Vancouver:

Bell RJ. Genetics of x-linked and autosomal recessive hereditary nephropathy in the domestic dog. [Internet] [Doctoral dissertation]. Texas A&M University; 2009. [cited 2021 Feb 28]. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-2125.

Council of Science Editors:

Bell RJ. Genetics of x-linked and autosomal recessive hereditary nephropathy in the domestic dog. [Doctoral Dissertation]. Texas A&M University; 2009. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-2125

Texas A&M University

27. Wahl, Jacquelyn Marie Bell. Genetics of merle patterning in the domestic dog and gene transcript profiling and immunobiology of dermatomyositis in the shetland sheepdog.

Degree: PhD, Veterinary Microbiology, 2009, Texas A&M University

URL: http://hdl.handle.net/1969.1/ETD-TAMU-2840

► Since its domestication, the dog has served in many roles, from protector, guide, hunter, and best friend, to model organism. Every role in which the… (more)

▼ Since its domestication, the dog has served in many roles, from protector, guide, hunter, and best friend, to model organism. Every role in which the dog serves is important; however, this work highlights the importance of the dog as a model organism for study of human hereditary diseases. Roughly half of the 450 hereditary diseases found in the dog have clinical presentations similar to those found in the human. Included in these are auditory-pigmentation conditions and skin diseases for which the dog is a working model. Described herein are studies of the merle coat pattern and dermatomyositis. Through research on these topics, important information can be obtained that can be used to help both the dog and the human. Merle is a pattern of coloring observed in the coat of the domestic dog and is characterized by patches of diluted pigment. Dogs heterozygous or homozygous for the merle locus exhibit a wide range of auditory and ophthalmologic abnormalities. Linkage disequilibrium was identified for a microsatellite marker with the merle phenotype in the Shetland Sheepdog. This region of the human genome contains SILV, a gene important in mammalian pigmentation. Therefore, this gene was evaluated as a candidate for merle patterning. A short interspersed element insertion at the boundary of intron 10/exon 11 was found, and this insertion segregates with the merle phenotype in multiple breeds. These data show that SILV is responsible for merle patterning and is associated with impaired function of the auditory and ophthalmologic systems. Dermatomyositis (DM) is an inflammatory disease of the skin and muscle that occurs most often in the rough collie and Shetland Sheepdog. Gene transcript profiles were generated for affected and normal skin using a canine-specific oligonucleotide array. Two-hundred and eight-five gene transcripts, many of which are involved in immune function, were found to be differentially regulated in these tissues. Also reported are western blot, immunohistochemistry, and immunofluorescence analyses. While our work suggests that canine DM is a disease that may be immune mediated, it did not detect the production of specific disease-associated autoantibodies. Advisors/Committee Members: Murphy, Keith E. (advisor), Kier, Ann B (committee member), Rees, Christine A. (committee member), Womack, James E (committee member).

Subjects/Keywords: Merle; Canine Genetics

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Wahl, J. M. B. (2009). Genetics of merle patterning in the domestic dog and gene transcript profiling and immunobiology of dermatomyositis in the shetland sheepdog. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/ETD-TAMU-2840

Chicago Manual of Style (16^th Edition):

Wahl, Jacquelyn Marie Bell. “Genetics of merle patterning in the domestic dog and gene transcript profiling and immunobiology of dermatomyositis in the shetland sheepdog.” 2009. Doctoral Dissertation, Texas A&M University. Accessed February 28, 2021. http://hdl.handle.net/1969.1/ETD-TAMU-2840.

MLA Handbook (7^th Edition):

Wahl, Jacquelyn Marie Bell. “Genetics of merle patterning in the domestic dog and gene transcript profiling and immunobiology of dermatomyositis in the shetland sheepdog.” 2009. Web. 28 Feb 2021.

Vancouver:

Wahl JMB. Genetics of merle patterning in the domestic dog and gene transcript profiling and immunobiology of dermatomyositis in the shetland sheepdog. [Internet] [Doctoral dissertation]. Texas A&M University; 2009. [cited 2021 Feb 28]. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-2840.

Council of Science Editors:

Wahl JMB. Genetics of merle patterning in the domestic dog and gene transcript profiling and immunobiology of dermatomyositis in the shetland sheepdog. [Doctoral Dissertation]. Texas A&M University; 2009. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-2840

Texas A&M University

28. Rossetti, Carlos Alberto. Host and pathogen transcriptional profiles of acute Brucella melitensis infection.

Degree: PhD, Veterinary Microbiology, 2009, Texas A&M University

URL: http://hdl.handle.net/1969.1/ETD-TAMU-1636

► The parallel gene expression profiles of Brucella melitensis and the host have not been elaborated. In this study, I analyze and discuss the transcriptional profiles… (more)

▼ The parallel gene expression profiles of Brucella melitensis and the host have not been elaborated. In this study, I analyze and discuss the transcriptional profiles of B. melitensis invasive-associated genes, the expression profile of intracellular B. melitensis and B. melitensis-infected non-phagocytic cells in the first 12 h post-infection (PI), and the in vivo temporal global transcriptome of both B. melitensis and the infected bovine host in the first 4 h PI. The initial study found that B. melitensis at late-log phase of growth were more invasive in non-phagocytic cells than at early-log or stationary growth phase. Microarray-based studies identified 454 Brucella genes differentially expressed between the most and the least invasive growth phases. Additionally, B. melitensis strains with transposon interrupted in loci BMEII0380 (acrA) and BMEI1538 (hypothetical protein) were found to be deficient in internalization compare with the wild-type strain. A second experiment was designed with the goal of characterizing host and pathogen transcriptome in parallel. For detecting intracellular Brucella gene expression, a combined protocol consisting of a linear amplification of sense-stranded RNA biased to pathogen transcripts to the previously enriched host:pathogen RNA mixed sample, was developed. RNA samples were hybridized on human and Brucella cDNA microarrays, which analysis revealed a common down-regulation transcriptional profile at 4 h PI that was reverse at 12 h PI. The integrity of B. melitensis virB operon and the expression of host MAPK1 were confirmed as critical for early B. melitensis intracellular survival and replication in non-phagocytic cells. Finally, a temporal morphological and molecular characterization of the initial B. melitensis:bovine host interaction using a calf ileal loop model was performed. B. melitensis was isolated from intestinal Peyer’s patches as soon as 15 min and from systemic blood after 30 min postintra luminal inoculation. Microarray results revealed a common transcriptional profile in Brucella, but two different transcriptional profiles were identified in the host in the first 4 h PI. The importance of differentially expressed biological processes, pathways and individual genes in the initial Brucella pathogenesis is discussed. Advisors/Committee Members: Adams, L. Garry (advisor), Thomas, Terry L. (committee member), Tsolis, Renee M. (committee member), Womack, James E. (committee member).

Subjects/Keywords: Brucella; Bovine; Gene expression; Microarrays

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Rossetti, C. A. (2009). Host and pathogen transcriptional profiles of acute Brucella melitensis infection. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/ETD-TAMU-1636

Chicago Manual of Style (16^th Edition):

Rossetti, Carlos Alberto. “Host and pathogen transcriptional profiles of acute Brucella melitensis infection.” 2009. Doctoral Dissertation, Texas A&M University. Accessed February 28, 2021. http://hdl.handle.net/1969.1/ETD-TAMU-1636.

MLA Handbook (7^th Edition):

Rossetti, Carlos Alberto. “Host and pathogen transcriptional profiles of acute Brucella melitensis infection.” 2009. Web. 28 Feb 2021.

Vancouver:

Rossetti CA. Host and pathogen transcriptional profiles of acute Brucella melitensis infection. [Internet] [Doctoral dissertation]. Texas A&M University; 2009. [cited 2021 Feb 28]. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-1636.

Council of Science Editors:

Rossetti CA. Host and pathogen transcriptional profiles of acute Brucella melitensis infection. [Doctoral Dissertation]. Texas A&M University; 2009. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-1636

Texas A&M University

29. Taylor, Kristen Hawkins. Genetic analyses of bovine CARD15, a putative disease resistance gene.

Degree: PhD, Genetics, 2004, Texas A&M University

URL: http://hdl.handle.net/1969.1/219

► Through a binding partner the CARD15 gene activates NF-kB, a molecule with a role in the initiation of the inflammatory immune response. The gene is… (more)

▼ Through a binding partner the CARD15 gene activates NF-kB, a molecule with a role in the initiation of the inflammatory immune response. The gene is highly conserved in both structure and function in human and mouse and has recently been implicated as a disease resistance gene in Crohn's disease and Blau Syndrome in human. The gene's relationship to disease and its conservation between species suggests that it may also have a conserved role in bovine disease resistance. To elucidate the potential role of bovine CARD15 in disease resistance, the gene was characterized in cattle. Bovine CARD15 is located 4.2 cR5000 telomeric to ADCY7 on chromosome 18. It spans ~30 kb and is comprised of 12 exons, 11 of which are coding. Bovine CARD15 is expressed in many tissues, but is most abundant in peripheral blood leukocytes. An extensive comparative analysis between the bovine, mouse and human CARD15 genes revealed high levels of inter-species conservation in sequence, genomic structure and protein domains. Conserved putative regulatory motifs were identified in the three species comparison of the 5'UTR, 3'UTR and the intronic sequences flanking exons. Additionally, diverse regulatory motifs were identified in each of the species indicating an evolutionary divergence in the mechanisms of regulation of gene expression. To assess the extent of genetic diversity within bovine CARD15, 41 individuals from nine breeds representing two subspecies were sequenced and screened for polymorphisms. Thirty-six single nucleotide polymorphisms (SNPs) were identified including 26 within the gene transcript. Haplotypes were estimated for each individual and parsimonious SNP sets were identified with which the multi-locus Bos taurus and Bos indicus haplotypes may be reconstructed. There was a significantly higher rate of substitutions within Bos indicus than in Bos taurus. A significantly higher rate of nonsynonymous to synonymous substitutions was found in Bos taurus indicating that positive Darwinian selection is acting on the gene within this subspecies. Association analyses were performed between these SNP loci and haplotypes with Johne's disease. No overwhelming evidence for a simple causal relationship was detected. Assays are provided to screen populations of cattle for variation in the CARD15 gene. Advisors/Committee Members: Womack, James E. (advisor), Derr, James N. (committee member), Adams, L. Garry (committee member), Roussel, Allen J. (committee member).

Subjects/Keywords: CARD15; NOD2; bovine; disease resistance; Crohn's; Johne's

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Taylor, K. H. (2004). Genetic analyses of bovine CARD15, a putative disease resistance gene. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/219

Chicago Manual of Style (16^th Edition):

Taylor, Kristen Hawkins. “Genetic analyses of bovine CARD15, a putative disease resistance gene.” 2004. Doctoral Dissertation, Texas A&M University. Accessed February 28, 2021. http://hdl.handle.net/1969.1/219.

MLA Handbook (7^th Edition):

Taylor, Kristen Hawkins. “Genetic analyses of bovine CARD15, a putative disease resistance gene.” 2004. Web. 28 Feb 2021.

Vancouver:

Taylor KH. Genetic analyses of bovine CARD15, a putative disease resistance gene. [Internet] [Doctoral dissertation]. Texas A&M University; 2004. [cited 2021 Feb 28]. Available from: http://hdl.handle.net/1969.1/219.

Council of Science Editors:

Taylor KH. Genetic analyses of bovine CARD15, a putative disease resistance gene. [Doctoral Dissertation]. Texas A&M University; 2004. Available from: http://hdl.handle.net/1969.1/219

Texas A&M University

30. Cox, Melissa Luanne. Identification of a mutation in COL4A5 causative for X-linked Alport syndrome in the domestic dog and analysis of gene expression in the kidneys of affected and nonaffected siblings.

Degree: PhD, Genetics, 2004, Texas A&M University

URL: http://hdl.handle.net/1969.1/244

► The domestic dog, Canis lupus familiaris, plays many roles in the lives of humans. Additionally, the dog is recognized for its potential as a model… (more)

▼ The domestic dog, Canis lupus familiaris, plays many roles in the lives of humans. Additionally, the dog is recognized for its potential as a model for many human hereditary diseases. Thus, the genetics and genomics of the dog are being studied extensively in order to facilitate its use as a model, as well as to help the dog for its own sake. As part of this research effort, our laboratory has added type I markers (i.e., the acidic and basic keratins, c-kit, type I and IV collagens, and the gene encoding uromodulin) to the emerging map of the canine genome. The mapping of genes, particularly those in large gene families such as the collagens, is valuable because it rapidly increases the density of gene loci on the map and provides insight regarding conservation of synteny between the dog and other mammals. The major focus of work reported here is the genetics of X-linked Alport syndrome (XLAS), a terminal renal disease that affects the human and the dog. The disease results from mutations in COL4A5, a type IV collagen gene. Reported here are the 1) sequencing and mapping of the canine cDNA encoding uromodulin, 2) mapping of the type I and type IV collagen genes, 3) sequencing of the full-length cDNA of canine COL4A5, 4) identification of a 10 bp deletion in COL4A5, causative for XLAS in our colony of mixed breed dogs, 5) development of a genetic test for identification of affected and carrier dogs in the colony and 6) assessment of gene expression in the kidneys of normal and XLAS-dogs. This assessment was performed using a canine-specific oligonucleotide microarray. XLAS dogs demonstrated up-regulation of many genes involved in extracellular matrix reorganization, cell structure, and immune response, as expected in a glomerulopathy with tubulointerstitial nephritis. Trends were verified by quantitative RT-PCR. A review of the current status of canine genetics research, and current understanding of hereditary diseases in the dog, concludes this dissertation. Advisors/Committee Members: Murphy, Keith E. (advisor), Womack, James E. (committee member), Lees, George E. (committee member), Derr, James E. (committee member).

Subjects/Keywords: canine; dog; kidney; renal; collagen; glomerular basement membrane; genomics

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Cox, M. L. (2004). Identification of a mutation in COL4A5 causative for X-linked Alport syndrome in the domestic dog and analysis of gene expression in the kidneys of affected and nonaffected siblings. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/244

Chicago Manual of Style (16^th Edition):

Cox, Melissa Luanne. “Identification of a mutation in COL4A5 causative for X-linked Alport syndrome in the domestic dog and analysis of gene expression in the kidneys of affected and nonaffected siblings.” 2004. Doctoral Dissertation, Texas A&M University. Accessed February 28, 2021. http://hdl.handle.net/1969.1/244.

MLA Handbook (7^th Edition):

Cox, Melissa Luanne. “Identification of a mutation in COL4A5 causative for X-linked Alport syndrome in the domestic dog and analysis of gene expression in the kidneys of affected and nonaffected siblings.” 2004. Web. 28 Feb 2021.

Vancouver:

Cox ML. Identification of a mutation in COL4A5 causative for X-linked Alport syndrome in the domestic dog and analysis of gene expression in the kidneys of affected and nonaffected siblings. [Internet] [Doctoral dissertation]. Texas A&M University; 2004. [cited 2021 Feb 28]. Available from: http://hdl.handle.net/1969.1/244.

Council of Science Editors:

Cox ML. Identification of a mutation in COL4A5 causative for X-linked Alport syndrome in the domestic dog and analysis of gene expression in the kidneys of affected and nonaffected siblings. [Doctoral Dissertation]. Texas A&M University; 2004. Available from: http://hdl.handle.net/1969.1/244

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