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Targeted Mapping Of Oryza Sativa Chilling Tolerance Candidate Genes Using Multiple Stress-Relevant Quantitative Traits, Naoki Simon Shimoyama

Dissertations (1934 -)

Developing chilling tolerant accessions of domesticated Asian rice is a potential source of significant crop improvement to address the needs of a growing global population. The uniquely chilling sensitive nature of the tropically originating Oryza sativa make it the most important staple crop that could gain the maximum benefit from improved tolerance to low temperature stress. However, mechanisms underlying this complex trait are not fully understood. Oryza sativa has two major varietal groups with different levels of chilling tolerance, JAPONICA and INDICA, providing an ideal tool to investigate mechanistic differences in the chilling stress tolerance responses within this important crop …

Survival-Related Clustering Of Cancer Patients By Integrating Clinical And Biological Datasets, Xinming Wei

Master's Theses (2009 -)

Subtype-based treatments and drug therapies are essential aspects to be considered in cancer patients' clinical trials to provide appropriate personalized therapies. With the advancement of the next-generation sequencing technology, several computational models, integrating genomic and transcriptomic datasets (i.e., multi-omics) in the prediction of subtype-based classification in cancer patients, were emerged. However, integration of the prognostic features from the clinical data, related to survival risks with the multi-omics datasets in the prediction of different subtypes, is limited and an important research area to be explored. In this study, we proposed a data integration pipeline with the prognostic features from the clinical …

Causal Varian Discovery In Familial Congenital Heart Disease - An Integrative -Omic Approach, Wendy Demos

Master's Theses (2009 -)

Hypoplastic left heart syndrome (HLHS) is a congenital heart defect that leads to neonatal death or compromised quality of life for those affected and their families. This syndrome requires extensive medical intervention for the affected to survive. It is characterized by significant underdevelopment or non-existence of the components of the left heart and the aorta, including the left ventricular cavity and mass. There are many factors ranging from genetics to environmental relationships hypothesized to lead to the development of the syndrome, including recent studies suggesting a link between hearing impairment and congenital heart defects (CHD). Although broadly characterized those factors …

Database Methods For Copy Number Variant Analysis Of One Hundred Disease Associated Genes In Human Congenital Heart Disease, Maureen E. Tuffnell

Master's Theses (2009 -)

Human genetic variation occurs more commonly than was recognized after the completion of the Human Genome Sequencing Project in 2003. Submicroscopic human DNA analysis has revealed copy number variation (CNV) as the deletion or duplication of a genomic region potentially affecting gene dosage. Advanced genetic research now includes the study of CNVs in diseased subject groups compared to in house controls or online published datasets of control CNV data. Research labs choose from different bioinformatic algorithms to make the copy number calls. Solutions for further processing the copy number data into quantifiable form require collaboration with data analysts and include …

Bistro-Primer - Tool To Design And Validate Specific Pcr Primer Pairs For Phylogenetic Analysis, Praful Aggarwal

Master's Theses (2009 -)

Polymerase Chain Reaction is a widely used biological technique which helps in amplifying small quantities of DNA. These amplified DNA copies are then used in several other experiments like DNA sequencing, phylogenetic analysis, etc. PCR primers are short subsequences of nucleotides (basic unit of DNA) that help identify larger regions of the DNA sequence. They help in successfully amplifying the target DNA sequence by identifying complementary regions on the DNA template. Therefore, to successfully perform PCR it is imperative to design good quality primers.

PCR can be used for identifying the phylogenetic classification of an organism. For example, in an …