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- All Subjects: Genetics
Description
Rhesus (Macaca mulatta) and cynomolgus (M. fascicularis) macaques are the most commonly used nonhuman primate models in biomedical research. It is therefore critical to correctly infer each study animal's ABO blood group phenotype to prevent fatal transfusion- and transplantation-induced immune responses. While most macaques can be efficiently and accurately phenotyped using a DNA-based assay, we have identified some animals that are unable to be classified as type A, B, or AB and therefore exhibit an indeterminate phenotype. The purpose of this study was to develop a protocol for resolving indeterminate blood group phenotypes and consequently determine if these animals do indeed belong to an O blood phenotype. We attempted both direct and cloning-based sequencing of 21 animals phenotyped as A, B, AB, or indeterminate in order to assess variation at the functional mutation site in exon 7 of the macaque ABO gene. Although direct-from-PCR Sanger sequencing was unable to generate reliable sequence results, our cloned plasmid protocol yielded high quality sequences consistent with known blood group-specific alleles and as such can be used to identify informative polymorphisms at this locus.
ContributorsVizor, Choice Popsira (Author) / Kanthaswamy, Sreetharan (Thesis director) / Oldt, Robert (Committee member) / Department of Information Systems (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Porbeagles (Lamna nasus) are a highly commercially important shark species that is threatened with extinction due to overfishing. Mitochondrial DNA (mtDNA) displacement loop (D-loop) sequence data from 18 Northwest (NW) Atlantic and 30 Southwest (SW) Pacific porbeagles reveal that these regional populations have been genetically separated between 1.39 and 1.25 million years ago (MYA), a time frame which correlates with the end of the earth’s last cooling period. There is far greater genetic differentiation (FST = 0.835) between the NW and SW populations than among sharks within each population supporting a very high level of divergence. A lack of gene flow probably stemming from their limited distribution to cold water temperatures (-1oC to 15oC) has led to their genetic divergence. The NW Atlantic population exhibited fewer haplotypes than the SW Pacific population (2 vs 4). The mean nucleotide diversity value of the NW Atlantic population was also 50% lower (0.00143 vs. 0.00228). Male and female NW Atlantic individuals reflected virtually identical mean population diversity values (0.00393 vs 0.00399); however, females were prevalent near shorelines while the males were more often found in open waters. Of the three age groups within the NW Atlantic population, the immature individuals exhibited the greatest mean nucleotide diversity (0.00452), followed by the sub-adult group (0.00293) and the mature group (0.00288), suggesting that dispersion starts earlier in their life cycle and reduces as they get older. The porbeagle population biology, as revealed by D-loop sequence information, may have significant implications for the conservation efforts of this species. As differences in age-based and sex-based dispersion exist, it is important to understand the relative contributions of gene flow by adults of both sexes in order to implement more effective conservation strategies.
ContributorsHickey, Kaitlyn (Author) / Kanthaswamy, Sreetharan (Thesis advisor) / Sulikowski, James (Committee member) / Zhao, Yunpeng (Committee member) / Arizona State University (Publisher)
Created2022
Description
Recovering high-quality DNA from thermally altered human remains poses a significant challenge for research and law enforcement agencies due to high levels of DNA degradation resulting from exposure to extremely high temperatures (e.g., fire). The current standard practice for the DNA identification of badly burned skeletal remains is to extract DNA from dense cortical bone collected from recovered skeletal elements. Some of the problems associated with this method are that it requires specialized equipment and training, is highly invasive (involving the physical destruction of sample material), time-consuming, and does not reliably guarantee the successful identification of the remains in question. At low-medium levels of thermal exposure, charred tissue is often adhered to these skeletal remains and typically discarded. In cases where burned/charred tissue is recoverable, it has the potential to be a more efficient alternative to the sampling of cortical bone. However, little has been done to test the viability of thermally altered soft tissue in terms of DNA identification to date. Burned/charred tissue was collected from skeletal samples provided by the University of Tennessee Forensic Anthropology Center, as a part of a controlled burn from donor individuals, for downstream laboratory processing and DNA analysis as part of the Stone Lab (Arizona State University, School of Human Evolution and Social Change). DNA from this charred tissue was extracted using the Qiagen DNeasy Blood and Tissue Kit, and resulting yields were quantified via fluorometry using the Qubit Fluorometer 2.0 and Agilent TapeStation 4200 High-Sensitivity D5000 assay. It was found that between the temperatures of ~200-300 ℃ (burn category 2) and ~300-350 ℃ (burn category 3), tissue was the most efficient extraction type, especially from tissue taken from the surface of the ilium and the rib. As for bone, both the Dabney and the Loreille protocol performed similarly, so choice in extraction type comes down to personal preference, type of equipment on hand, and training. Although, for samples with low input material, the Dabney protocol is optimal.
ContributorsCoffman, Amber (Author) / Stone, Anne C (Thesis advisor) / Parker, Cody (Committee member) / Kanthaswamy, Sreetharan (Committee member) / Arizona State University (Publisher)
Created2023
Description
The study of macaque monkeys harbors advancements in the field of biomedical research. It is imperative to understand the genetic composition of different species of macaques to assess their accuracy as non-human primate (NHP) models for disease detection and treatment assessments. We sought to characterize the hybridization and admixture of the Southeast Asian macaques using single nucleotide polymorphism markers and analyzing the populations on the mainland and the island. Using AMOVA tests and STRUCTURE analysis, we determined that there are three distinct populations: Macaca mulatta, M. fascicularis fascicularis, and M. f. aurea. Furthermore, the island species holds an isolated population of M. f. aurea that demonstrate high inbreeding and genetic uniqueness compared to the mainland species. Findings from this study confirm that NHP models may need to be modified or updated according to changing allelic frequencies and genetic drift.
ContributorsFalak, Asiya (Author) / Kanthaswamy, Sreetharan (Thesis director) / Oldt, Robert (Committee member) / Barrett, The Honors College (Contributor) / Computer Science and Engineering Program (Contributor) / School of Life Sciences (Contributor)
Created2022-05