The power of microsatellite markers lies in their ability to identify. Whether it is the identification of genes and associating them with known phenotypes or identifying and discerning individuals from one another, the role they play in the genetic field has been immense. Parentage testing of horses today is done via molecular means as opposed to serology. Microsatellite marker panels are decided upon by bodies such as the International Society for Animal Genetics (ISAG) in order to uphold international genotyping standards. The current horse microsatellite marker panel is not fully characterized and many markers are amplified by primers originally designed for linkage studies and were never intended for multiplex PCR analysis. The aim of this study was to refine and validate the current marker panel used for horses through sequencing of the repeat elements and flanking regions as well as the design of new primers for the setup of a marker panel incorporating more microsatellites and better primers. Sequencing of microsatellite flanking regions revealed that much variation lies within the regions flanking a microsatellite repeat element. Sequencing of the repeat element showed that not all markers are simple repeats, as was previously thought. The primers used to amplify microsatellite markers for horses were re-designed in the course of this study, utilizing knowledge gained from flanking region variation and repeat element length. New primers and known allele sizes allowed for the implementation of a nomenclature system in horses based on repeat element length as opposed to alphabet letters. By incorporating more markers into the panel it was hoped that a greater discriminatory power would be achieved. Measures of genetic diversity such as Observed Heterozygosity and Polymorphism Information Content showed negligible differences between the two panels however genotyping data from the old ISAG panel of nine markers showed that the probability of excluding an individual in a parentage test was better when using more markers. / Dissertation (MSc)--University of Pretoria, 2010. / Production Animal Studies / unrestricted

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第18122号 / 理博第4000号 / 新制||理||1577(附属図書館) / 30980 / 京都大学大学院理学研究科生物科学専攻 / (主査)教授 村山 美穂, 教授 幸島 司郎, 教授 伊谷 原一 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DFAM

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第20428号 / 農博第2213号 / 新制||農||1048(附属図書館) / 学位論文||H29||N5049(農学部図書室) / 京都大学大学院農学研究科森林科学専攻 / (主査)教授 井鷺 裕司, 教授 柴田 昌三, 教授 神﨑 護 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

Glioblastoma multiforme (GBM) is an extremely aggressive and almost always fatal brain tumor. GBM literature indicates defective mismatch repair (MMR) mechanisms are not involved in GBM tumorigenesis as in other tumors, and instigating mechanisms of GBM tumorigenesis remain unclear. GBM and neural progenitor (NPR) cells were exposed to three concentrations of H2O2 (0, 0.5, and 1.0 μM), cultured, and then harvested 0, 2, 4, and 6 days post-exposure; DNA from cells was amplified with microsatellite primers, investigating whether or not H2O2 exposure affected microsatellite instability (MSI) in target sequences. Three out of six markers showed significant MSI in the H2O2-exposed NPR cells. Our results suggest H2O2, which generates reactive oxygen species (ROS), correlated with MSI accumulation that occurred in NPR cells in specific DNA regions. Thus, gene expression analysis to assess normal and abnormal gene expression of GBM and NPR cellss is warranted.

Cañahua (Chenopodium pallidicaule Aellen) is a poorly studied, annual subsistence crop of the high Andes of South America. Its nutritionally value (high in protein and mineral content) and ability to thrive in harsh climates (drought, extreme elevations, etc.) make it an important regional food crop throughout the Andean region. The objectives of this study were to develop genetic markers and to quantify genetic diversity within cañahua. A set of 43 wild and cultivated cañahua genotypes and two related species (C. quinoa and C. petiolare) were evaluated for polymorphism using 192 microsatellite markers derived from random genomic sequences produced by 454 pyro-sequencing of cañahua genomic DNA. In addition, another and 424 C. quinoa based microsatellite markers were evaluate as potential cross-species marker loci. A total of 48 polymorphic microsatellite marker loci were identified which detected a total of 168 alleles with an average of 3.5 alleles per marker locus and an average heterozygosity value of 0.47. A cluster analysis, based on Nei genetic distance, grouped the cultivated cañahua into a single dominant branch clearly separated from wild cañahua genotypes and the outgroup species. Within the cultivated genotypes, two dominant subclades were present that were further partitioned by AMOVA analysis into five model-based clusters. Significant correlations were found between genetic distance and morphological traits. The isolation by distance test displayed no significant correlation between geographic collection origin and genotypic data, suggesting that cañahua populations have moved extensively, presumably via ancient food exchange strategies among native peoples of the Andean region. The molecular markers reported here are a significant resource for ongoing efforts to characterize the extensive Bolivian and Peruvian cañahua germplasm banks, including the development of core germplasm collections needed to support emerging breeding programs.

Behavioral studies in the green turtle (Chelonia mydas) have indicated that promiscuous mating is commonplace. Though it has been shown that there is much variation in the rate of polyandry (females mating with multiple males), the drivers behind polyandry in this species are unknown. It has been speculated, but never demonstrated, that indirect benefits (fitness benefits resulting from offspring genetic diversity) play a role. However, previous tests of this hypothesis have limited scope of inference due to lack of environmental control. In this thesis, I attempted to study the indirect benefits of polyandry in Archie Carr National Wildlife Refuge (ACNWR) green turtles, limiting environmental variation by selecting nests over two week periods in a small subset of the ACNWR. Through the use of highly polymorphic microsatellite markers, I show that 85.7% of ACNWR green turtle females mate with multiple males, the highest rate yet reported for green turtles. I was successful in limiting environmental variation; however, I was unable to make comparisons among nests with one or multiple fathers because of a limited sample size of single father nests. Regardless, my thesis provides preliminary evidence (number of males per nest) that the density of males off Florida’s beaches may be relatively high, which is expected to be a driver behind the evolution of polyandry and likely plays a large role both in this population and the prevalence of multiple paternity in green turtles as a whole

<p>Over the last two decades, mycoflorostic studies undertaken in Guyanese forests have uncovered hundreds of new fungal species and genera. One of the recovered fungal families was the Xylariaceae, although most were not identified to species. Members of this family play ecological roles as decomposers, endophytes, and pathogens of vascular plants and grass species. In addition, this group is increasingly recognized as a significant source of novel metabolic products with potential for applications in medicine, agriculture, and industrial biofuel. Given its potential, we took a more targeted approach to the documentation of this group. Our sampling efforts drawing on more than two decades of field collections yielded ca. 90 species in 12 genera, including a putative pathogen, <em>Xylaria karyophthora</em> of the seeds of <em>Chlorocardium</em> spp (Greenheart). Despite the significance of Greenheart to the Guyanese economy, little is known about the biology and ecology of this fungus. Due to the lack of available resources to study this fungus, our objectives were two-fold: first, to sequence and annotate the genome of <em>X. karyophthora</em> to provide a resource for genome-centric explorations, and to use this genome to infer the biology and ecology of this fungus. We focused on identifying and characterizing secretomes, viz. carbohydrate-active enzymes (CAZymes) and secondary metabolites biosynthetic gene clusters (SMBGCs) to infer the nutritional strategy of this fungus. Our results suggest that <em>X. karyophthora</em> has the capacity to act as both an endophyte and a pathogen. To make further inferences about the population, we used SSR markers to elucidate the genetic diversity and population structure of <em>X. karyophthora</em>. <em>X. karyophthora</em> populations have high genetic diversity, potentially exploiting both outcrossing and inbreeding reproductive strategies, and demonstrate a pattern consistent with human-mediated spread. This work will contribute information on new species and records of Xylariaceous fungi and their allies from Guyana with particular emphasis on unraveling the epidemiology, genetic diversity, and population structure of <em>X. karyophthora.</em></p>

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