Matching Items (15)
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Description
The health situation of indigenous peoples is comparable to that of the world's poorest populations, but with the additional burdens of social and cultural marginalization, geographic and cultural barriers to accessing health services, and, in some areas, appropriation of land and natural resources. Cultural transmission (the transfer of beliefs, ideas,

The health situation of indigenous peoples is comparable to that of the world's poorest populations, but with the additional burdens of social and cultural marginalization, geographic and cultural barriers to accessing health services, and, in some areas, appropriation of land and natural resources. Cultural transmission (the transfer of beliefs, ideas, and behaviors from one culture to another) from outsider health institutions should presumably aid in closing this health gap by transferring knowledge, practices, and infrastructure to prevent and treat disease. This study examines the biosocial construction of the disease ecology of tuberculosis (TB) in indigenous communities of the Paraguayan Chaco with varying degrees of cultural transmission from outside institutions (government, religious, and NGOs), to determine the influence of cultural transmission on local disease ecologies. Using a biocultural epidemiological framework for the analysis of human infectious disease ecology, this study employed an interdisciplinary, mixed methods approach to examine the interactions of host, pathogen, and the environment in the Paraguayan Chaco. Three case studies examining aspects of TB disease ecology in indigenous communities are presented: (1) The effective cultural transmission of biomedical knowledge to isolated communities, (2) Public health infrastructure, hygiene, and the prevalence of intestinal parasites: co-morbidities that promote the progression to active TB disease, and (3) Community-level risk factors for TB and indigenous TB burden. Findings from the case studies suggest that greater influence from outside institutions was not associated with greater adoption of biomedical knowledge of TB. The prevalence of helminthiasis was unexpectedly low, but infection with giardia was common, even in a community with cleaner water sources. Communities with a health post were more likely to report active adult TB, while communities with more education were less likely to report active pediatric TB, suggesting that healthcare access is the major determinant of TB detection. More research is needed on the role of non-indigenous community residents and other measures of acculturation or integration in TB outcomes, especially at the household level. Indigenous TB burden in the Chaco is disproportionately high, and better understanding of the mechanisms that produce higher incidence and prevalence of the disease is needed.
ContributorsVansteelandt, Amanda (Author) / Hurtado, Ana Magdalena (Thesis advisor) / Stone, Anne (Thesis advisor) / Hruschka, Daniel (Committee member) / Rojas de Arias, Antonieta (Committee member) / Arizona State University (Publisher)
Created2014
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Description
This project studies two single nucleotide polymorphisms (SNPs) within the HBS1L-MYB loci. Both SNPs are associated with a heightened expression of fetal hemoglobin. DNA samples of NCAA athletes who have sickle cell trait were genotyped to find the allele frequency of each SNP. When comparing all populations using information provided

This project studies two single nucleotide polymorphisms (SNPs) within the HBS1L-MYB loci. Both SNPs are associated with a heightened expression of fetal hemoglobin. DNA samples of NCAA athletes who have sickle cell trait were genotyped to find the allele frequency of each SNP. When comparing all populations using information provided from the Human Genome Project on Ensembl, the minor A allele has a frequency of 22% and the major, G, allele has a frequency of 78%. The frequency distribution of the minor allele in the population data was higher than the frequency obtained from the sampled data by 15%. This means that the samples, which are heterozygous for sickle cell, display a lower frequency for the mutation than the global population.
ContributorsCiambella, Michelle Lynn (Author) / Stone, Anne (Thesis director) / Foy, Joseph (Committee member) / Madrigal, Lorena (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2014-05
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Description
Dire wolves have recently risen to fame as a result of the popular television program Game of Thrones, and thus many viewers know dire wolves as the sigil and loyal companions of the Stark house. Far fewer recognize dire wolves by their scientific name, Canis dirus, or understand the population

Dire wolves have recently risen to fame as a result of the popular television program Game of Thrones, and thus many viewers know dire wolves as the sigil and loyal companions of the Stark house. Far fewer recognize dire wolves by their scientific name, Canis dirus, or understand the population history of this ‘fearsome wolf’ species that roamed the Americas until the megafaunal mass extinction event of the Late Pleistocene. Although numerous studies have examined the species using morphological and geographical methods, thus far their results have been either inconclusive or contradictory. Remaining questions include the relationships dire wolves share with other members of the Canis genus and the internal structure of their populations. Advancements in ancient DNA recovery methods may make it possible to study dire wolf specimens at the molecular level for the first time and may therefore prove useful in clarifying the answers to these questions. Eighteen dire wolf specimens were collected from across the United States and subjected to ancient DNA extraction, library preparation, amplification and purification, bait preparation and capture, and next-generation sequencing. There was an average of 76.9 unique reads and 5.73% coverage when mapped to the Canis familiaris reference genome in ultraconserved regions of the mitochondrial genome. The results indicate that endogenous ancient DNA was not successfully recovered and perhaps ancient DNA recovery methods have not advanced to the point of retrieving informative amounts of DNA from particularly old, thermally degraded specimens. Nevertheless, the ever-changing nature of ancient DNA research makes it vital to continually test the limitations of the field and suggests that ancient DNA recovery methods will prove useful in illuminating dire wolf population history at some point in the future.
ContributorsSkerry, Katherine Marie (Author) / Stone, Anne (Thesis director) / Amdam, Gro (Committee member) / Larson, Greger (Committee member) / School of Human Evolution and Social Change (Contributor) / School of Nutrition and Health Promotion (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
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Description
Unlike the autosomes, recombination on the sex chromosomes is limited to the pseudoautosomal regions (PARs) at each end of the chromosome. PAR1 spans approximately 2.7 Mb from the tip of the proximal arm of each sex chromosome, and a pseudoautosomal boundary between the PAR1 and non-PAR region is thought to

Unlike the autosomes, recombination on the sex chromosomes is limited to the pseudoautosomal regions (PARs) at each end of the chromosome. PAR1 spans approximately 2.7 Mb from the tip of the proximal arm of each sex chromosome, and a pseudoautosomal boundary between the PAR1 and non-PAR region is thought to have evolved from a Y-specific inversion that suppressed recombination across the boundary. In addition to the two PARs, there is also a human-specific X-transposed region (XTR) that was duplicated from the X to the Y chromosome. Genetic diversity is expected to be higher in recombining than nonrecombining regions, particularly because recombination reduces the effects of linked selection, allowing neutral variation to accumulate. We previously showed that diversity decreases linearly across the previously defined pseudoautosomal boundary (rather than drop suddenly at the boundary), suggesting that the pseudoautosomal boundary may not be as strict as previously thought. In this study, we analyzed data from 1271 genetic females to explore the extent to which the pseudoautosomal boundary varies among human populations (broadly, African, European, South Asian, East Asian, and the Americas). We found that, in all populations, genetic diversity was significantly higher in the PAR1 and XTR than in the non-PAR regions, and that diversity decreased linearly from the PAR1 to finally reach a non-PAR value well past the pseudoautosomal boundary in all populations. However, we also found that the location at which diversity changes from reflecting the higher PAR1 diversity to the lower nonPAR diversity varied by as much as 500 kb among populations. The lack of genetic evidence for a strict pseudoautosomal boundary and the variability in patterns of diversity across the pseudoautosomal boundary are consistent with two potential explanations: (1) the boundary itself may vary across populations, or (2) that population-specific demographic histories have shaped diversity across the pseudoautosomal boundary.
ContributorsCotter, Daniel Juetten (Author) / Wilson Sayres, Melissa (Thesis director) / Stone, Anne (Committee member) / Webster, Timothy (Committee member) / School of Life Sciences (Contributor) / School of International Letters and Cultures (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
Within the primate lineage, skeletal traits that contribute to inter-specific anatomical variation and enable varied niche occupations and forms of locomotion are often described as the result of environmental adaptations. However, skeletal phenotypes are more accurately defined as complex traits, and environmental, genetic, and epigenetic mechanisms, such as DNA methylation

Within the primate lineage, skeletal traits that contribute to inter-specific anatomical variation and enable varied niche occupations and forms of locomotion are often described as the result of environmental adaptations. However, skeletal phenotypes are more accurately defined as complex traits, and environmental, genetic, and epigenetic mechanisms, such as DNA methylation which regulates gene expression, all contribute to these phenotypes. Nevertheless, skeletal complexity in relation to epigenetic variation has not been assessed across the primate order. In order to gain a complete understanding of the evolution of skeletal phenotypes across primates, it is necessary to study skeletal epigenetics in primates. This study attempts to fill this gap by identifying intra- and inter-specific variation in primate skeletal tissue methylation in order to test whether specific features of skeletal form are related to specific variations in methylation. Specifically, methylation arrays and gene-specific methylation sequencing are used to identify DNA methylation patterns in femoral trabecular bone and cartilage of several nonhuman primate species. Samples include baboons (Papio spp.), macaques (Macaca mulatta), vervets (Chlorocebus aethiops), chimpanzees (Pan troglodytes), and marmosets (Callithrix jacchus), and the efficiencies of these methods are validated in each taxon. Within one nonhuman primate species (baboons), intra-specific variations in methylation patterns are identified across a range of comparative levels, including skeletal tissue differences (bone vs. cartilage), age cohort differences (adults vs. juveniles), and skeletal disease state differences (osteoarthritic vs. healthy), and some of the identified patterns are evolutionarily conserved with those known in humans. Additionally, in all nonhuman primate species, intra-specific methylation variation in association with nonpathological femur morphologies is assessed. Lastly, inter-specific changes in methylation are evaluated among all nonhuman primate taxa and used to provide a phylogenetic framework for methylation changes previously identified in the hominin lineage. Overall, findings from this work reveal how skeletal DNA methylation patterns vary within and among primate species and relate to skeletal phenotypes, and together they inform our understanding of epigenetic regulation and complex skeletal trait evolution in primates.
ContributorsHousman, Genevieve (Author) / Stone, Anne (Thesis advisor) / Quillen, Ellen (Committee member) / Kusumi, Kenro (Committee member) / Stojanowski, Christopher (Committee member) / Arizona State University (Publisher)
Created2017
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Description

Bermuda Land Snails make up a genus called Poecilozonites that is endemic to Bermuda and is extensively present in its fossil record. These snails were also integral to the creation of the theory of punctuated equilibrium. The DNA of mollusks is difficult to sequence because of a class of proteins

Bermuda Land Snails make up a genus called Poecilozonites that is endemic to Bermuda and is extensively present in its fossil record. These snails were also integral to the creation of the theory of punctuated equilibrium. The DNA of mollusks is difficult to sequence because of a class of proteins called mucopolysaccharides that are present in high concentrations in mollusk tissue, and are not removed with standard DNA extraction methods. They inhibit Polymerase Chain Reactions (PCRs) and interfere with Next Generation Sequencing methods. This paper will discuss the DNA extraction methods that were designed to remove the inhibitory proteins that were tested on another gastropod species (Pomacea canaliculata). These were chosen because they are invasive and while they are not pulmonates, they are similar enough to Bermuda Land Snails to reliably test extraction methods. The methods that were tested included two commercially available kits: the Qiagen Blood and Tissue Kit and the Omega Biotek Mollusc Extraction Kit, and one Hexadecyltrimethylammonium Bromide (CTAB) Extraction method that was modified for use on mollusk tissue. The Blood and Tissue kit produced some DNA, the mollusk kit produced almost none, and the CTAB Extraction Method produced the highest concentrations on average, and may prove to be the most viable option for future extractions. PCRs attempted with the extracted DNA have all failed, though it is likely due to an issue with reagents. Further spectrographic analysis of the DNA from the test extractions has shown that they were successful at removing mucopolysaccharides. When the protocol is optimized, it will be used to extract DNA from the tissue from six individuals from each of the two extant species of Bermuda Land Snails. This DNA will be used in several experiments involving Next Generation Sequencing, with the goal of assembling a variety of genome data. These data will then be used to a construct reference genome for Bermuda Land Snails. The genomes generated by this project will be used in population genetic analyses between individuals of the same species, and between individuals of different species. These analyses will then be used to aid in conservation efforts for the species.

ContributorsClark, Patrick Louis (Author) / Stone, Anne (Thesis director) / Winingear, Stevie (Committee member) / School of Life Sciences (Contributor, Contributor) / School of Human Evolution & Social Change (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description

In biology and medicine today, Next Generation Sequencing (NGS) is used to quantify entire genomes and has changed genomics research by providing a low cost, streamlined approach to producing large amounts of genetic data. One of the main steps of NGS is library preparation and these libraries can be double

In biology and medicine today, Next Generation Sequencing (NGS) is used to quantify entire genomes and has changed genomics research by providing a low cost, streamlined approach to producing large amounts of genetic data. One of the main steps of NGS is library preparation and these libraries can be double or single stranded. When DNA is degraded or damaged, it can be difficult to create into double stranded libraries and analyze. In this case, single stranded libraries can be prepared when DNA input is low. However, most research on comparing single and double stranded libraries for degraded DNA is limited to ancient DNA. Here we compare SRSLY single stranded DNA libraries with Illumina double stranded DNA libraries using modern degraded DNA samples from deceased unidentified individuals. Our results potentially show that single stranded libraries had a greater concentration of degraded DNA. However, further research must be conducted using qPCR to definitively state that single stranded library preparation was more effective in capturing the modern degraded DNA.

ContributorsMehta, Rishika (Author) / Stone, Anne (Thesis director) / Parker, Cody (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / School of Human Evolution & Social Change (Contributor)
Created2023-05
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Description
Mycobacterium leprae, the causative agent of Hansen’s disease (leprosy), has plagued humans and other animal species for millennia and remains of concern to public health throughout the world today. Recent research into the expanded use of medical tissues preserved as formalin-fixed, paraffin-embedded samples (FFPE), opened the door for the study

Mycobacterium leprae, the causative agent of Hansen’s disease (leprosy), has plagued humans and other animal species for millennia and remains of concern to public health throughout the world today. Recent research into the expanded use of medical tissues preserved as formalin-fixed, paraffin-embedded samples (FFPE), opened the door for the study of M. leprae DNA from preserved skin samples. However, problems persist with damage to the DNA including fragmentation and cross linkage. This study evaluated two methods commonly used for the recovery of host DNA from FFPE samples for their efficacy in extracting pathogen DNA (hot alkaline lysis protocol and QIAGEN QIAamp FFPE DNA kit). Twenty FFPE skin samples collected from 1995-2015 from human subjects in the Pacific Islands suffering from M. leprae infection, each exhibiting a range of bacillary loads, were analyzed to determine which extraction method was most successful in terms of ability to consistently yield reliable, robust traces of M. leprae infection. This study further examined these samples to understand the phylogeny of leprosy in the region, where gaps in the evolutionary history of M. leprae persist. DNA recovery from paired samples was similar using either method. However, by extending the incubation time of post-paraffin removal sample lysis, both protocols were more likely to yield positive traces of M. leprae, with this enhancement being especially evident in paucibacillary samples with low bacterial presence. The qPCR assay findings suggest that the hot alkaline procedure is most likely to yield positive identification of infection in these traditionally challenging samples.
ContributorsKing, Felicia Clarice (Author) / Stone, Anne (Thesis advisor) / Wilson, Melissa (Committee member) / Buetow, Ken (Committee member) / Arizona State University (Publisher)
Created2023
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Description
Callithrix penicillata, also known as the Black-tufted marmoset primarily lives in the Brazilian highlands and has had little research conducted on it. For this project I performed a genome curation on the newly assembled genome of this species. The scaffolds obtained by the Dovetail Genomics reads were organized and labeled

Callithrix penicillata, also known as the Black-tufted marmoset primarily lives in the Brazilian highlands and has had little research conducted on it. For this project I performed a genome curation on the newly assembled genome of this species. The scaffolds obtained by the Dovetail Genomics reads were organized and labeled into chromosomes using the 2014 Callithrix jacchus genome as a reference. Then, using that same genome as a reference, 13 of the chromosomes were reverse complimented to be continuous with the 2014 Callithrix jacchus genome. The N50 statistics of the assembly were calculated and found to be 124 Mb. Quality scores were run for the final genome using referee and visualized with a bar plot, with 99% of sites scoring above 0. Heterozygosity was also calculated and found to be 0.3%. Finally, the final version of the genome was visually compared to the 2017 Callithrix jacchus genome and the GRCh38 human genome. This genome was submitted to the NCBIs database to await further approval.
ContributorsJohnson, Joelle Genevieve (Author) / Cartwright, Reed (Thesis director) / Stone, Anne (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-12
Description
Zoonotic pathogens that cause leprosy (Mycobacterium leprae) and tuberculosis (Mycobacterium tuberculosis complex, MTBC) continue to impact modern human populations. Therefore, methods able to survey mycobacterial infection in potential animal hosts are necessary for proper evaluation of human exposure threats. Here we tested for mycobacterial-specific single- and multi-copy loci using qPCR.

Zoonotic pathogens that cause leprosy (Mycobacterium leprae) and tuberculosis (Mycobacterium tuberculosis complex, MTBC) continue to impact modern human populations. Therefore, methods able to survey mycobacterial infection in potential animal hosts are necessary for proper evaluation of human exposure threats. Here we tested for mycobacterial-specific single- and multi-copy loci using qPCR. In a trial study in which armadillos were artificially infected with M. leprae, these techniques were specific and sensitive to pathogen detection, while more traditional ELISAs were only specific. These assays were then employed in a case study to detect M. leprae as well as MTBC in wild marmosets. All marmosets were negative for M. leprae DNA, but 14 were positive for the mycobacterial rpoB gene assay. Targeted capture and sequencing of rpoB and other MTBC genes validated the presence of mycobacterial DNA in these samples and revealed that qPCR is useful for identifying mycobacterial-infected animal hosts.
Created2015-11-16