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

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 27, 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. 27 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 27]. 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 · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

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 27, 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. 27 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 27]. 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 27, 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. 27 Feb 2021.

Vancouver:

Dobson LK. Sequencing the Genome of the North American Bison. [Internet] [Doctoral dissertation]. Texas A&M University; 2015. [cited 2021 Feb 27]. 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 27, 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. 27 Feb 2021.

Vancouver:

Chen J. Bovine Nk-Lysins: Genomic Expansion and Functional Diversification. [Internet] [Doctoral dissertation]. Texas A&M University; 2016. [cited 2021 Feb 27]. 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 27, 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. 27 Feb 2021.

Vancouver:

Dobson LK. Sequencing the Genome of the North American Bison. [Internet] [Doctoral dissertation]. Texas A&M University; 2015. [cited 2021 Feb 27]. 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. 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 27, 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. 27 Feb 2021.

Vancouver:

Downey-Slinker ED. Studies of Immunogenetic Variation in Cattle. [Internet] [Doctoral dissertation]. Texas A&M University; 2016. [cited 2021 Feb 27]. 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

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

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 27, 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. 27 Feb 2021.

Vancouver:

Fagundes De Avila F. Comparative Mapping of the Alpaca Genome. [Internet] [Doctoral dissertation]. Texas A&M University; 2014. [cited 2021 Feb 27]. 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

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

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 27, 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. 27 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 27]. 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

9. 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 27, 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. 27 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 27]. 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

10. 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 27, 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. 27 Feb 2021.

Vancouver:

Flores EG. Characterization of the Bovine Cathelicidin Gene Family. [Internet] [Doctoral dissertation]. Texas A&M University; 2012. [cited 2021 Feb 27]. 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

11. 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 27, 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. 27 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 27]. 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

12. 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 27, 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. 27 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 27]. 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

13. 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 27, 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. 27 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 27]. 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

14. 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 27, 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. 27 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 27]. 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

15. 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 27, 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. 27 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 27]. 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

16. 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 27, 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. 27 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 27]. 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

17. 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 27, 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. 27 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 27]. 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

18. 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 (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 27, 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. 27 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 27]. 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

19. 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 (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 27, 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. 27 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 27]. 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

20. 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 (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 27, 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. 27 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 27]. 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

21. 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 27, 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. 27 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 27]. 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

Texas A&M University

22. Petrescu, Anca Daniela. Ligand binding proteins: roles in ligand transfer and activation of nuclear receptors.

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

URL: http://hdl.handle.net/1969.1/290

► Cholesterol and fatty acyl-coenzymeA thioesters are signalling molecules with role in regulation of genes involved in lipid and glucose transport and metabolism. The studies described… (more)

▼ Cholesterol and fatty acyl-coenzymeA thioesters are signalling molecules with role in regulation of genes involved in lipid and glucose transport and metabolism. The studies described herein focused on three proteins that bind lipids and have different cellular functions: steroidogenic acute regulatory protein (StAR), hepatocyte nuclear factor-4a (HNF-4a) and acyl-CoA binding protein (ACBP). First, StAR mediates delivery of cholesterol to inner mitochondrial membrane in steroidogenesis by a poorly understood mechanism. In our studies, fluorescent NBD-cholesterol binding assays demonstrate that StAR binds cholesterol at two binding sites with 32 nM Kds and circular dichroism spectra show that cholesterol binding results in changes of StAR secondary structure. Fluorescent sterol exchange assays between donor and acceptor mitochondrial membranes indicate that StAR significantly increased the formation of rapidly transferable cholesterol domains. Second, HNF-4a, a nuclear receptor, had been shown to bind fatty acyl-CoAs as natural ligands with apparent low affinities obtained with radiolabeled ligand binding assays. Our fluorescence spectroscopy studies demonstrate that HNF-4a ligand binding domain (HNF-4aLBD) binds acyl-CoAs at a single binding site with Kds of 1.6-4 nM. Fluorescence resonance energy transfer (FRET) between HNF-4aLBD tryptophan residues and cis-parinaroyl-CoA yielded an intermolecular distance of 42 Â thus pointing to direct molecular interaction. Third, although ACBP has been detected in the nucleus, it is not known whether ACBP may directly and/or functionally interact with a nuclear acyl-CoA binding protein such as HNF-4a to regulate transcription. Our present studies in vitro and in intact cultured cells, including circular dichroism of HNF-4a in the presence of ACBP, coimmunoprecipitation of HNF-4a/ACBP complexes, ACBP and HNF-4a colocalization in nuclei of cells by confocal microscopy demonstrate a physical association of ACBP and HNF-4a. FRET microscopy data indicated an intermolecular distance of 53 Â between ACBP and HNF-4a in rat hepatoma cells. Functional assays (transactivation of an HNF4a-dependent reporter gene) showed significant increase in the presence of ACBP in two different cell lines. Expression of ACBP anti-sense RNA decreased HNF-4a-mediated transactivation, pointing to a role of ACBP in co-regulating HNF-4a-dependent transcription. Advisors/Committee Members: Schroeder, Friedhelm (advisor), Womack, James E. (committee member), Phillips, Timothy D. (committee member), Chapkin, Robert S. (committee member).

Subjects/Keywords: cholesterol; fatty acid; fatty acyl-CoA; HNF-4alpha; StAR; ACBP

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

APA (6^th Edition):

Petrescu, A. D. (2004). Ligand binding proteins: roles in ligand transfer and activation of nuclear receptors. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/290

Chicago Manual of Style (16^th Edition):

Petrescu, Anca Daniela. “Ligand binding proteins: roles in ligand transfer and activation of nuclear receptors.” 2004. Doctoral Dissertation, Texas A&M University. Accessed February 27, 2021. http://hdl.handle.net/1969.1/290.

MLA Handbook (7^th Edition):

Petrescu, Anca Daniela. “Ligand binding proteins: roles in ligand transfer and activation of nuclear receptors.” 2004. Web. 27 Feb 2021.

Vancouver:

Petrescu AD. Ligand binding proteins: roles in ligand transfer and activation of nuclear receptors. [Internet] [Doctoral dissertation]. Texas A&M University; 2004. [cited 2021 Feb 27]. Available from: http://hdl.handle.net/1969.1/290.

Council of Science Editors:

Petrescu AD. Ligand binding proteins: roles in ligand transfer and activation of nuclear receptors. [Doctoral Dissertation]. Texas A&M University; 2004. Available from: http://hdl.handle.net/1969.1/290

Texas A&M University

23. Camacho, Zenaido. Characterization of candidate genes in English cocker spaniel hereditary nephritis.

Degree: PhD, Veterinary Microbiology, 2005, Texas A&M University

URL: http://hdl.handle.net/1969.1/1600

► Six different isoforms of Type IV collagen (colIVα1-6) have been identified. The individual isoforms of colIV are termed alpha chains and are translated from six… (more)

▼ Six different isoforms of Type IV collagen (colIVα1-6) have been identified. The individual isoforms of colIV are termed alpha chains and are translated from six different COLIV genes (COLIVA1-A6). Collagen Type IV gene products compose the structural framework of basement membranes. The glomerular basement membrane (GBM) is a specialized basement membrane involved in the ultrafiltration processes of the kidney. The colIVα1-α5 chains are expressed in the human GBM while the colIV α1-α6 chains are expressed in the canine GBM. Many inherited diseases of the kidney have been reported and mutations in genes regulating kidney function have been identified. Alport syndrome (AS) is the most common form of human hereditary nephritis (HN). AS is defined as an inherited progressive kidney disorder associated with sensoneural deafness and is characterized by extensive thickening and multilamminar splitting of the GBM when examined by electron microscopy. AS has both X-linked (XLAS) and autosomal (ARAS) modes of inheritance. Mutations in the COLIVA5 gene are responsible for XLAS. A form of HN with characteristic splitting of the GBM with X-linked inheritance has been described in Samoyed dogs. A specific mutation in the COLIVA5 gene has been identified in Samoyed dogs affected with HN. Mutations in the COLIVA3 and COLIVA4 genes are responsible for ARAS. A form of HN has been identified in English cocker spaniel dogs (ECS) that has been described as autosomal in inheritance and includes GBM abnormalities including extensive lammination characteristic of ARAS. Both ARAS and ECS-HN show loss of the colIVA3 and colIVA4 chains in the GBM when examined with monoclonal anitibodies. ECS-HN has been hypothesized to have the same molecular basis of disease as ARAS. As such, we have isolated and characterized canine COLIVA3 and COLIVA4 sequences from normal dogs and ECS dogs affected with HN and compared the coding regions of these candidate genes. Advisors/Committee Members: Templeton, Joe (advisor), Busbee, David (committee member), Lees, George E. (committee member), Womack, James E. (committee member).

Subjects/Keywords: kidney disease; english cocker spaniel; collagen gene

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APA (6^th Edition):

Camacho, Z. (2005). Characterization of candidate genes in English cocker spaniel hereditary nephritis. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/1600

Chicago Manual of Style (16^th Edition):

Camacho, Zenaido. “Characterization of candidate genes in English cocker spaniel hereditary nephritis.” 2005. Doctoral Dissertation, Texas A&M University. Accessed February 27, 2021. http://hdl.handle.net/1969.1/1600.

MLA Handbook (7^th Edition):

Camacho, Zenaido. “Characterization of candidate genes in English cocker spaniel hereditary nephritis.” 2005. Web. 27 Feb 2021.

Vancouver:

Camacho Z. Characterization of candidate genes in English cocker spaniel hereditary nephritis. [Internet] [Doctoral dissertation]. Texas A&M University; 2005. [cited 2021 Feb 27]. Available from: http://hdl.handle.net/1969.1/1600.

Council of Science Editors:

Camacho Z. Characterization of candidate genes in English cocker spaniel hereditary nephritis. [Doctoral Dissertation]. Texas A&M University; 2005. Available from: http://hdl.handle.net/1969.1/1600

Texas A&M University

24. Gao, Wenxiang. Wide-cross whole-genome radiation hybrid (WWRH) mapping and identification of cold-responsive genes using oligo-gene microarray analysis in cotton.

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

URL: http://hdl.handle.net/1969.1/1601

► The first part of this research focused on wide-cross whole-genome radiation hybrid (WWRH) mapping of the cotton (Gossypium) genome. Radiation hybrid mapping has been used… (more)

▼ The first part of this research focused on wide-cross whole-genome radiation hybrid (WWRH) mapping of the cotton (Gossypium) genome. Radiation hybrid mapping has been used extensively to map the genomes of human and certain animal species, but not plant species. In lieu of in vitro hybrid cell line technologies for plants, we developed a novel approach for radiation hybrid mapping based on wide-cross in vivo hybridization. Flowers from one species of cotton, either G. hirsutum or G. barbadense, were -irradiated and then used to pollinate the other species. The resulting hybrid plants were assessed as a mapping tool. Two WWRH mapping panels were constructed from 5- and 8-krad -irradiation treatments. Both panels demonstrated that the WWRH mapping method can be used to map the cotton genome, and that this method complements traditional linkage mapping approaches. The second part of this research focused on the identification of cold-responsive genes using spotted oligo-gene microarray analysis. Increased cold-tolerance in cotton would promote early and uniform seedling establishment, expand the growing season, decrease susceptibility to fungal infections and certain diseases, and increase fiber yield and quality. BLAST searches of the cotton database using amino acid sequences of 93 drought/cold-related genes from Arabidopsis and several other plant species led to 806 cotton orthologous cDNAs and expressed sequence tags (ESTs). Eight hundred and six cotton 70-mer oligos were designed and included in an oligo-gene microarray containing 1,536 70-mer oligos, each representing a cDNA or EST from cotton, or one of 121 chloroplast genes or 66 mitochondrial genes from Arabidopsis. Thirty-eight cotton cDNAs and ESTs were identified as cold-responsive genes based on experimental treatment and oligo-gene microarray analysis. Expression was up-regulated for 36 genes and down-regulated for two genes by cold treatment. Results from microarray analysis were tested and confirmed by northern blot analysis for 16 genes. Our data suggest that Arabidopsis orthologous genes can be used to identify homologous cotton genes. The oligo-gene microarray is a valid approach to study transcriptional changes in cotton. Advisors/Committee Members: Stelly, David M. (advisor), Chen, Z. Jeffrey (advisor), Smith, C. Wayne (committee member), Womack, James E. (committee member).

Subjects/Keywords: Gossypium; cotton; genome mapping; radiation hybrid; wide-cross; cold stress; microarray

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APA (6^th Edition):

Gao, W. (2005). Wide-cross whole-genome radiation hybrid (WWRH) mapping and identification of cold-responsive genes using oligo-gene microarray analysis in cotton. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/1601

Chicago Manual of Style (16^th Edition):

Gao, Wenxiang. “Wide-cross whole-genome radiation hybrid (WWRH) mapping and identification of cold-responsive genes using oligo-gene microarray analysis in cotton.” 2005. Doctoral Dissertation, Texas A&M University. Accessed February 27, 2021. http://hdl.handle.net/1969.1/1601.

MLA Handbook (7^th Edition):

Gao, Wenxiang. “Wide-cross whole-genome radiation hybrid (WWRH) mapping and identification of cold-responsive genes using oligo-gene microarray analysis in cotton.” 2005. Web. 27 Feb 2021.

Vancouver:

Gao W. Wide-cross whole-genome radiation hybrid (WWRH) mapping and identification of cold-responsive genes using oligo-gene microarray analysis in cotton. [Internet] [Doctoral dissertation]. Texas A&M University; 2005. [cited 2021 Feb 27]. Available from: http://hdl.handle.net/1969.1/1601.

Council of Science Editors:

Gao W. Wide-cross whole-genome radiation hybrid (WWRH) mapping and identification of cold-responsive genes using oligo-gene microarray analysis in cotton. [Doctoral Dissertation]. Texas A&M University; 2005. Available from: http://hdl.handle.net/1969.1/1601

Texas A&M University

25. Cargill, Edward James. Development of a multiplexing strategy for whole genome scans of the domestic dog and analysis of hereditary deafness in the Dalmatian.

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

URL: http://hdl.handle.net/1969.1/2232

► The Dalmatian is affected by deafness more than any other breed of domestic dog, with 30% of the United States population suffering from unilateral or… (more)

▼ The Dalmatian is affected by deafness more than any other breed of domestic dog, with 30% of the United States population suffering from unilateral or bilateral deafness. The genetic origin of deafness in the Dalmatian is unknown. The objective of this work was to identify, using linkage analysis, any chromosomal region(s) in which the gene(s) responsible for deafness in the Dalmatian may be located. To achieve this objective it was necessary to 1) develop multiplexed microsatellite markers for an efficient whole genome scan, 2) assemble a multigenerational Dalmatian kindred segregating deafness, 3) estimate the heritability of deafness and perform complex segregation analysis, and 4) perform linkage analysis of deafness, and other phenotypic traits, in the Dalmatian kindred. A set of 172 microsatellite markers, termed Minimal Screening Set 1 (MSS1), was characterized, prior to this work, for whole genome scans of the domestic dog. 155 of the MSS1 markers were multiplexed into 48 multiplex sets. Amplification of the multiplex sets was achieved using a single thermal cycling program. The markers were labeled with fluorescent dyes and optimized for resolution on an ABI 310 Genetic Analyzer or ABI 377 Sequencer. A kindred of 266 Dalmatians was assembled, of which 199 had been diagnosed using the brainstem auditory evoked response to determine auditory status. Of these, 74.4% (N = 148) had normal hearing, 18.1% (N = 36) were unilaterally deaf, and 7.5% (N = 15) were bilaterally deaf. A heritability of 0.73 was estimated considering deafness a dichotomous trait and 0.75 as a trichotomous trait. Although deafness in the Dalmatian is clearly heritable, the evidence for the presence of a major gene affecting the disorder was not persuasive. Dalmatians (N = 117) from the assembled kindred were genotyped for the MSS1 markers (149 were polymorphic). Linkage analysis was performed for deafness, eye color, and spot color. The maximum LOD scores for deafness were found with markers Cos15 on CFA17 (LOD = 1.69) and FH2585 on CFA28 (LOD = 1.34). No significant linkage was found with eye color. Significant linkage for spot color was found with marker FH2319 (LOD = 9.7) on CFA11. Advisors/Committee Members: Murphy, Keith E. (advisor), Womack, James E. (committee member), Derr, James N. (committee member), Westhusin, Mark E. (committee member).

Subjects/Keywords: canine; deafness; heritability; multiplexing; linkage analysis

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APA (6^th Edition):

Cargill, E. J. (2005). Development of a multiplexing strategy for whole genome scans of the domestic dog and analysis of hereditary deafness in the Dalmatian. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/2232

Chicago Manual of Style (16^th Edition):

Cargill, Edward James. “Development of a multiplexing strategy for whole genome scans of the domestic dog and analysis of hereditary deafness in the Dalmatian.” 2005. Doctoral Dissertation, Texas A&M University. Accessed February 27, 2021. http://hdl.handle.net/1969.1/2232.

MLA Handbook (7^th Edition):

Cargill, Edward James. “Development of a multiplexing strategy for whole genome scans of the domestic dog and analysis of hereditary deafness in the Dalmatian.” 2005. Web. 27 Feb 2021.

Vancouver:

Cargill EJ. Development of a multiplexing strategy for whole genome scans of the domestic dog and analysis of hereditary deafness in the Dalmatian. [Internet] [Doctoral dissertation]. Texas A&M University; 2005. [cited 2021 Feb 27]. Available from: http://hdl.handle.net/1969.1/2232.

Council of Science Editors:

Cargill EJ. Development of a multiplexing strategy for whole genome scans of the domestic dog and analysis of hereditary deafness in the Dalmatian. [Doctoral Dissertation]. Texas A&M University; 2005. Available from: http://hdl.handle.net/1969.1/2232

Texas A&M University

26. Seabury, Ashley Gustafson. Physical mapping and characterization of the equine lymphocyte antigen (ELA) complex.

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

URL: http://hdl.handle.net/1969.1/2345

► The major histocompatibility complex (MHC) is a genomic region comprised of a linked cluster of genes and gene families that play an important role in… (more)

▼ The major histocompatibility complex (MHC) is a genomic region comprised of a linked cluster of genes and gene families that play an important role in both the adaptive and innate immune responses. Genes within the MHC have also been associated with susceptibility and/or resistance to certain diseases, such as haemochromatosis, insulindependent diabetes, and psoriasis. As a result of these associations the MHC is one the most extensively studied regions of the mammalian genome. The MHCs of a wide variety of species, such as human (HLA), mouse (H-2), pig (SLA), and cow (BoLA), have been characterized with respect to gene content, genomic organization of class I, class II, and class III regions, and comparative organization. Comparative analyses have been useful in delineating the evolutionary development of the MHC. While the MHC of many mammalian species has been investigated, little research has been performed on the equine (Equus caballus) MHC. The equine MHC is referred to as the equine lymphocyte antigen (ELA) complex and is located on chromosome ECA20q. The research that has been done on ELA focused on identifying gene copy number and genetic polymorphisms in the classical class I and class II genes. To better characterize the gene content and organization of ELA, we isolated 103 bacterial artificial chromosome (BAC) clones from a horse BAC library containing well conserved genes found within mammalian MHCs. These BAC clones were assembled into two sequence-ready ordered contigs that span the ELA complex. The first contig which has a minimum tiling path of nine BAC clones contains the ELA class II region and spans 800 kb. The class I and III regions are contained within the second contig which has a 14 BAC clone minimum tiling path and spans 1.6 Mb. This study will report on the construction of the two BAC contigs which span the ELA complex, and characterization of the gene content and organization of the ELA complex. Advisors/Committee Members: Skow, Loren C. (advisor), Chowdhary, Bhanu P. (committee member), Tizard, Ian R. (committee member), Womack, James E. (committee member).

Subjects/Keywords: MHC; horse

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APA (6^th Edition):

Seabury, A. G. (2005). Physical mapping and characterization of the equine lymphocyte antigen (ELA) complex. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/2345

Chicago Manual of Style (16^th Edition):

Seabury, Ashley Gustafson. “Physical mapping and characterization of the equine lymphocyte antigen (ELA) complex.” 2005. Doctoral Dissertation, Texas A&M University. Accessed February 27, 2021. http://hdl.handle.net/1969.1/2345.

MLA Handbook (7^th Edition):

Seabury, Ashley Gustafson. “Physical mapping and characterization of the equine lymphocyte antigen (ELA) complex.” 2005. Web. 27 Feb 2021.

Vancouver:

Seabury AG. Physical mapping and characterization of the equine lymphocyte antigen (ELA) complex. [Internet] [Doctoral dissertation]. Texas A&M University; 2005. [cited 2021 Feb 27]. Available from: http://hdl.handle.net/1969.1/2345.

Council of Science Editors:

Seabury AG. Physical mapping and characterization of the equine lymphocyte antigen (ELA) complex. [Doctoral Dissertation]. Texas A&M University; 2005. Available from: http://hdl.handle.net/1969.1/2345

Texas A&M University

27. Seabury, Christopher Mark. Genetic evaluation of the ovine and bovine prion protein genes (PRNP).

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

URL: http://hdl.handle.net/1969.1/3333

► Transmissible spongiform encephalopathies (TSEs), or prion diseases, are a group of inevitably fatal neurodegenerative diseases that occur in mammalian species. Ovine susceptibility to scrapie, the… (more)

▼ Transmissible spongiform encephalopathies (TSEs), or prion diseases, are a group of inevitably fatal neurodegenerative diseases that occur in mammalian species. Ovine susceptibility to scrapie, the prototypical TSE, is predominantly modulated by nonsynonymous polymorphisms within exon 3 of the ovine prion protein gene (PRNP). Investigation of PRNP exon 3 for two hair-sheep breeds revealed a novel predicted amino acid substitution (P116) associated with the ovine ARQ allele (P116A136R154Q171). Additionally, two novel ovine PRNP genotypes (PARQ/ARR; PARQ/ARQ) also were detected, and most of the hair sheep sampled possessed PRNP exon 3 genotypes associated with some degree of resistance to scrapie and/or experimental BSE (bovine spongiform encephalopathy). Unlike sheep, expression of bovine spongiform encephalopathy (BSE) in cattle and other bovids has not been associated with nucleotide variation within bovine PRNP exon 3. However, BSE susceptibility has been tentatively associated with specific insertion-deletion (indel) polymorphisms within the putative bovine PRNP promoter, and to a lesser extent intron 1, for a few German cattle breeds. Evaluation of the patterns of nucleotide variation associated with bovine PRNP exon 3 provided evidence that strong purifying selection has intensely constrained bovine exon 3 over the long-term evolutionary history of the subfamily Bovinae, as well as evidence for significant purifying selection in regions of bovine PRNP exon 3 that are considered to be of functional, structural, and pathogenic importance in other mammalian species. Evaluation of the frequencies of known indel polymorphisms within the putative bovine PRNP promoter for a panel of U. S. cattle sires revealed no significant differences in the distribution of promoter alleles and/or genotypes between U. S. cattle sires and BSEaffected German cattle. Notably, a nonsynonymous PRNP exon 3 polymorphism (T50C) identified in American bison (Bison bison) was tentatively associated with Brucella spp. seropositivity. Specifically, a significant overabundance (P = 0.021) of Yellowstone National Park bison possessing the CC genotype were Brucella spp. seropositive. Furthermore, the T-allele and TT genotype were observed at significantly higher frequencies in three bison populations that were either founded from Brucella spp. seronegative stock or previously subjected to test-and-slaughter management to eradicate brucellosis. Advisors/Committee Members: Derr, James N. (advisor), Womack, James E. (committee member), Templeton, Joe W. (committee member), Honeycutt, Rodney L. (committee member).

Subjects/Keywords: PRNP; BSE; prion; evolution

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APA (6^th Edition):

Seabury, C. M. (2006). Genetic evaluation of the ovine and bovine prion protein genes (PRNP). (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/3333

Chicago Manual of Style (16^th Edition):

Seabury, Christopher Mark. “Genetic evaluation of the ovine and bovine prion protein genes (PRNP).” 2006. Doctoral Dissertation, Texas A&M University. Accessed February 27, 2021. http://hdl.handle.net/1969.1/3333.

MLA Handbook (7^th Edition):

Seabury, Christopher Mark. “Genetic evaluation of the ovine and bovine prion protein genes (PRNP).” 2006. Web. 27 Feb 2021.

Vancouver:

Seabury CM. Genetic evaluation of the ovine and bovine prion protein genes (PRNP). [Internet] [Doctoral dissertation]. Texas A&M University; 2006. [cited 2021 Feb 27]. Available from: http://hdl.handle.net/1969.1/3333.

Council of Science Editors:

Seabury CM. Genetic evaluation of the ovine and bovine prion protein genes (PRNP). [Doctoral Dissertation]. Texas A&M University; 2006. Available from: http://hdl.handle.net/1969.1/3333

Texas A&M University

28. Goh, Glenda Lay Bee. High resolution physical and comparative maps of horse chromosomes 14 (ECA14) and 21 (ECA21).

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

URL: http://hdl.handle.net/1969.1/3750

► In order to identify genes or markers responsible for economically important traits in the horse, the development of high resolution gene maps of individual equine… (more)

▼ In order to identify genes or markers responsible for economically important traits in the horse, the development of high resolution gene maps of individual equine chromosomes is essential. We herein report the construction of high resolution physically ordered radiation hybrid (RH) and comparative maps for horse chromosomes 14 and 21 (ECA14 and ECA21). These chromosomes predominantly share correspondence with human chromosome 5 (HSA5), though a small region on the proximal part of ECA21 corresponds to a ~5Mb region from the short arm of HSA19. The map for ECA14 consists of 128 markers (83 Type I and 45 Type II) and spans a total of 1828cR.Compared to this, the map of ECA21 is made up of 90 markers (64 Type I and 26 Type II), that segregate into two linkage groups spanning 278 and 760cR each. A total of 218 markers provide on average one marker every 0.9Mb along the length of the two equine chromosomes. This represents a 5-fold improvement over the previous maps. Of greater significance is the ~8-fold increase in the density of Type I loci that provide a comprehensive and finely aligned map for the two chromosomes in relation to homologues in a range of evolutionarily distantly related species, viz., human, chimpanzee, mouse, rat, dog, cattle, pig, cat and chicken. The orientation and alignment of the linkage groups was strengthened by 28 new FISH localizations, of which 27 are gene-specific (22 from HSA5 and 5 from HSA19). Comparative analysis between the horse and human reveals that the order of genes on HSA5 is remarkably well conserved in the horse, with an evolutionary break/fusion point that could be correlated to a ~2Mb region between 68.5 Â 70.9Mb positions on HSA5. Among the species analyzed to date, the HSA5 and 19p neighboring segment combination is unique to Perissodactyls and Cetartiodactyls, but, in the Perissodactyls, the portion of HSA5 that corresponds to this combination is HSA5p Â q13, while in the Cetartiodactyls, it is HSA5q13 Â qter. This leads us to postulate that this neighboring segment combination arose as separate events during the divergence of Perissodactyls and Cetartiodactyls from a common ancestor. Advisors/Committee Members: Chowdhary, Bhanu P. (advisor), Derr, James N (committee member), Skow, Loren C (committee member), Womack, James E (committee member).

Subjects/Keywords: RH mapping; Horse

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APA (6^th Edition):

Goh, G. L. B. (2006). High resolution physical and comparative maps of horse chromosomes 14 (ECA14) and 21 (ECA21). (Masters Thesis). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/3750

Chicago Manual of Style (16^th Edition):

Goh, Glenda Lay Bee. “High resolution physical and comparative maps of horse chromosomes 14 (ECA14) and 21 (ECA21).” 2006. Masters Thesis, Texas A&M University. Accessed February 27, 2021. http://hdl.handle.net/1969.1/3750.

MLA Handbook (7^th Edition):

Goh, Glenda Lay Bee. “High resolution physical and comparative maps of horse chromosomes 14 (ECA14) and 21 (ECA21).” 2006. Web. 27 Feb 2021.

Vancouver:

Goh GLB. High resolution physical and comparative maps of horse chromosomes 14 (ECA14) and 21 (ECA21). [Internet] [Masters thesis]. Texas A&M University; 2006. [cited 2021 Feb 27]. Available from: http://hdl.handle.net/1969.1/3750.

Council of Science Editors:

Goh GLB. High resolution physical and comparative maps of horse chromosomes 14 (ECA14) and 21 (ECA21). [Masters Thesis]. Texas A&M University; 2006. Available from: http://hdl.handle.net/1969.1/3750

Texas A&M University

29. Dere, Ruhee J. The molecular mechanisms involved in the genetic instability of the CCTG. CAGG repeats associated with myotonic dystrophy type 2.

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

URL: http://hdl.handle.net/1969.1/3783

► Myotonic dystrophy type 2 (DM2) is caused by the extreme expansion (from < 30 repeats in normal individuals to ~ 11,000 for the full mutation… (more)

▼ Myotonic dystrophy type 2 (DM2) is caused by the extreme expansion (from < 30 repeats in normal individuals to ~ 11,000 for the full mutation in certain patients) of the repeating tetranucleotide CCTGÂCAGG sequence in the intron of the zinc finger protein 9 (ZNF9) gene. The genetic instabilities of the CCTGÂCAGG repeats were investigated to evaluate the molecular mechanisms responsible for these massive expansions. The effects of replication, recombination, repair and transcription on the genetic instabilities have been investigated in COS-7 cells and E. coli model systems. A replication assay was established in COS-7 cells wherein the CCTGÂCAGG repeats cloned proximal to the SV40 origin of replication resulted in expansions and deletions in a length and orientation-specific manner, whereas the repeats cloned distal to the same origin were comparatively stable. These results fit with our data obtained from biochemical studies on synthetic oligonucleotides since these biochemical studies revealed that the d(CAGG)26 oligomer had a marked propensity to adopt a hairpin structure as opposed to its complementary d(CCTG)26 that lacked this capacity. Furthermore, a genetic assay in E. coli was used to monitor the intramolecular frequency of recombination. This assay revealed that the tetranucleotide repeats were indeed hot spots for recombination. Moreover, studies conducted in SOS-repair mutants showed that recombination frequencies were much lower in a SOSÂ¯ strain as compared to a SOS+ strain. However, experiments conducted to ascertain the level of induction of the SOS response revealed that the SOS pathway was not stimulated in our studies. These results revealed that although breaks may occur within the repeats, the damage is most likely repaired without induction of the SOS response contrary to previous beliefs. Thus, a complex interplay of replication, recombination, and repair is likely responsible for the expansions observed in DM2. Advisors/Committee Members: Wells, Robert D. (advisor), Finnell, Richard H. (committee member), Sinden, Richard R. (committee member), Womack, James E. (committee member).

Subjects/Keywords: DM2; Genetic instability; molecular mechanisms

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APA (6^th Edition):

Dere, R. J. (2006). The molecular mechanisms involved in the genetic instability of the CCTG. CAGG repeats associated with myotonic dystrophy type 2. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/3783

Chicago Manual of Style (16^th Edition):

Dere, Ruhee J. “The molecular mechanisms involved in the genetic instability of the CCTG. CAGG repeats associated with myotonic dystrophy type 2.” 2006. Doctoral Dissertation, Texas A&M University. Accessed February 27, 2021. http://hdl.handle.net/1969.1/3783.

MLA Handbook (7^th Edition):

Dere, Ruhee J. “The molecular mechanisms involved in the genetic instability of the CCTG. CAGG repeats associated with myotonic dystrophy type 2.” 2006. Web. 27 Feb 2021.

Vancouver:

Dere RJ. The molecular mechanisms involved in the genetic instability of the CCTG. CAGG repeats associated with myotonic dystrophy type 2. [Internet] [Doctoral dissertation]. Texas A&M University; 2006. [cited 2021 Feb 27]. Available from: http://hdl.handle.net/1969.1/3783.

Council of Science Editors:

Dere RJ. The molecular mechanisms involved in the genetic instability of the CCTG. CAGG repeats associated with myotonic dystrophy type 2. [Doctoral Dissertation]. Texas A&M University; 2006. Available from: http://hdl.handle.net/1969.1/3783

Texas A&M University

30. Childers, Christopher P. Sequence assembly and annotation of the bovine major histocompatibility complex (BoLA) class IIb region, and in silico detection of sequence polymorphisms in BoLA IIb.

Degree: PhD, Genetics, 2007, Texas A&M University

URL: http://hdl.handle.net/1969.1/4821

► Cattle are vitally important to American agriculture industry, generating over 24.6 billion pounds of beef (by carcass weight), and 79.5 billion dollars in 2005, and… (more)

▼ Cattle are vitally important to American agriculture industry, generating over 24.6 billion pounds of beef (by carcass weight), and 79.5 billion dollars in 2005, and over 27 billion dollars in milk sales in 2004. As of July 2006, the U.S. beef and dairy industry is comprised of 104.5 million head of cattle, 32.4 million of which were processed in 2005. The health of the animals has always been an important concern for breeders, as healthy animals grow faster and are more likely to reach market weight. Animals that exhibit natural resistance to disease do not require chemicals to stimulate normal weight gain, and are less prone to disease related wasting. The major histocompatibility complex (MHC) is a collection of genes, many of which function in antigen processing and presentation. The bovine MHC (BoLA) differs from typical mammalian MHCs in that the class II region was disrupted by a chromosomal inversion into two subregions, designated BoLA IIa and BoLA IIb. BoLA IIb was transposed to a position near the centromere on bovine chromosome 23,while BoLA IIa retains its position in BoLA. Comparative sequence analysis of BoLA IIb with the human MHC revealed the location of the region containing the proximal inversion breakpoint. Gene content, order and orientation of BoLA IIb are consistent with the single inversion hypothesis when compared to the corresponding region of the human class II MHC (HLA class II). BoLA IIb spans approximately 450 kb. The genomic sequence of BoLA IIb was used to detect sequence variation through comparison to other bovine sequences, including data from the bovine genome project, and two regions in the BAC scaffold used to develop the BoLA IIb sequence. Analysis of the bovine genome project sequence revealed a total of 10,408 mismatching bases, 30 out of 231 polymorphic microsatellites, and 15 sequences corresponding to the validated SNP panel generated by the bovine genome sequencing project. The two overlapping regions in the BoLA IIb BAC scaffold were found to have 888 polymorphisms, including a total of 6 out of 42 polymorphic microsatellites indicating that each BAC derived from a different chromosome. Advisors/Committee Members: Skow, Loren C. (advisor), Adelson, David L. (committee member), Chowdhary, Bhanu P. (committee member), Womack, James E. (committee member).

Subjects/Keywords: Genetics; MHC; BoLA IIb; BoLA; Genomic Sequence; Major Histocompatibility Complex; Cow

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

APA (6^th Edition):

Childers, C. P. (2007). Sequence assembly and annotation of the bovine major histocompatibility complex (BoLA) class IIb region, and in silico detection of sequence polymorphisms in BoLA IIb. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/4821

Chicago Manual of Style (16^th Edition):

Childers, Christopher P. “Sequence assembly and annotation of the bovine major histocompatibility complex (BoLA) class IIb region, and in silico detection of sequence polymorphisms in BoLA IIb.” 2007. Doctoral Dissertation, Texas A&M University. Accessed February 27, 2021. http://hdl.handle.net/1969.1/4821.

MLA Handbook (7^th Edition):

Childers, Christopher P. “Sequence assembly and annotation of the bovine major histocompatibility complex (BoLA) class IIb region, and in silico detection of sequence polymorphisms in BoLA IIb.” 2007. Web. 27 Feb 2021.

Vancouver:

Childers CP. Sequence assembly and annotation of the bovine major histocompatibility complex (BoLA) class IIb region, and in silico detection of sequence polymorphisms in BoLA IIb. [Internet] [Doctoral dissertation]. Texas A&M University; 2007. [cited 2021 Feb 27]. Available from: http://hdl.handle.net/1969.1/4821.

Council of Science Editors:

Childers CP. Sequence assembly and annotation of the bovine major histocompatibility complex (BoLA) class IIb region, and in silico detection of sequence polymorphisms in BoLA IIb. [Doctoral Dissertation]. Texas A&M University; 2007. Available from: http://hdl.handle.net/1969.1/4821

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