Browsing by Subject "Genotype"
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Item The functional network in predictive biology : predicting phenotype from genotype and predicting human disease from fungal phenotype(2008-12) McGary, Kriston Lyle; Marcotte, Edward M.The ability to predict is one of the hallmarks of successful theories. Historically, the predictive power of biology has lagged behind disciplines like physics because the biological world is complex, challenging to quantify, and full of exceptions. However, in recent years the amount of available data has expanded exponentially and biological predictions based on this data become a possibility. The functional gene network is a quantitative way to integrate this data and a useful framework for making biological predictions. This study demonstrates that functional networks capture real biological insight and uses the network to predict both subcellular protein localization and the phenotypic outcome of gene knockouts. Furthermore, I use the functional network to evaluate genetic modules shared between diverse organisms that lead to orthologous phenotypes, many that are non-obvious. I show that the successful predictions of the functional network have broad applicability and implications that range from the design of large-scale biological experiments to the discovery of genes with potential roles in human disease.Item Interactions among Silvicultural Intensity, Genotype, and Environment and Their Effects on the Growth and Mortality of Loblolly Pine and Slash Pine Families(2013-08-13) Zhai, LuManaged pine forests are central to the economic vitality of the southeastern US. Over the past fifty years, the productivity of managed pine forests of this region have increased significantly with the development of new silvicultural technologies and the use of improved tree genetic material. Of the pine species present in the southeastern US, loblolly pine has arguably been the most intensively studied and widely planted by forest managers. Efficient operational deployment of improved genetic materials requires an understanding of how possible site conditions and silvicultural treatment may interact to affect maximum yield. There are a wide range of site conditions in the south as the result of regional climate gradients, soil type and soil drainage patterns. On the western edge of loblolly pine?s natural extent, Texas has a drier climate than areas to the east, and in Louisiana, there are also poorly drained Ultisols that are found in areas with little relief and are prone to flooding. However, on the basis of 10-year forest inventory data of pure-family plots from three different sites and under two levels of cultural regime intensity, my study found that superior genotype, Lob 5 from South Carolina, still showed best performance in the Western Gulf area, and high intensive treatment could improve stand growth and resistance to wind damage significantly. Further, my study compared the stand production and dynamics between pure- and mixed-family plots. I found that Lob 5 and Lob 4 showed the growth traits of competitive ideotype, and low intensive treatment increased the deployment effect significantly for competitive ideotype. Finally, my study examined leaf area index (LAI) and foliar nitrogen concentration (foliar N). The result showed that fast growing genotype had lower LAI and foliar N than slow growing one. It indicated that fast growing genotype had high resource use efficiency and nutrient requirement. This research provided critical information to guide industrial forest management in the WG (Western Gulf) area. First, introduced superior genotype continued to show good performance in this area. Second, combination of good genotype and high intensive treatment would increase plantation production significantly. Third, identification of ideotype would increase the accuracy of growth potential estimation in progeny test.Item Methods of genotype imputation for genome-wide association studies(2016-08) Qiu, Lin, M.S. in Statistiscs; Daniels, Michael Joseph; Lin, LizhenIn genetic epidemiological studies, missing data problems arise when genotypes of particular markers are unavailable for reasons of data quality, cost efficiency or technical design. Genotype imputation is a well-established statistical technique for estimating unobserved genotypes in association studies. Imputation methods are implemented by copying haplotype segments from a densely genotyped reference panel into individuals typed at a subset of the reference variants. By this way, genotypes can be estimated and tested for association at variants that were not assayed in a study. This report first summarizes the missing data mechanisms. Then an overview of the different methods that have been proposed for genotype imputation is provided and some thoughts for future directions are given.Item Variation in the neural mechanisms of monogamy(2014-08) Dehghani, Zahra; Phelps, Steven Michael, 1970-Male monogamous prairie voles vary in the way they use space, with some males intruding extensively on the territories of others, while others do not. We hypothesize that individual differences in the way males set up their territories is due to individual differences in their cognition and neural peptide receptor expression. Indeed, our lab has identified individual differences in vasopressin receptor expression in the retrosplenial cortex that are associated with differences in space use in the wild; this brain variation is predicted in part by sequence variants in the avpr1a gene. To test this hypothesis we first tested different behavioral paradigms that could be used to assess social cognition in the monogamous prairie vole. We tested the voles in a test of scent mark memory. We tried to establish conditioned place preference for male urine or postpartum estrus urine. Lastly, we developed a novel Barnes maze paradigm for looking at vi socio-spatial memory associated with escape. Male voles improved their performance in the Barnes maze over the course of 4 days, but did not respond to the overmark task or the conditioned place preference test. Next we used the Barnes maze to assess whether males of HI and LO RSC-V1aR genotypes perform differently in the task. Males of different genotypes did not perform differently in the Barnes maze. We also looked at V1aR expression levels in the brains of the animals that were tested in the Barnes maze. V1aR expression in the RSC did not correlate to Barnes maze performance. In addition to genetic influences, RSC-V1aR is known to be affected by neonatal exposure to oxytocin antagonist. Here we show preliminary results indicating that the RSC V1aR expression is reduced in LO animals, but not in HI animals. In addition, V1aR expression the anterior medial BNST was affected by neonatal exposure to OTA. The posterior lateral and ventral BNST, medial and lateral DT, and LS were not affected by neonatal exposure to OTA.