Bioinformatics Commons^™

The Evolution And Mechanics Of Translational Control In Plants, Justin N. Vaughn

Doctoral Dissertations

The expression of numerous plant mRNAs is attenuated by RNA sequence elements located in the 5' and 3' untranslated regions (UTRs). For example, in plants and many higher eukaryotes, roughly 35% of genes encode mRNAs that contain one or more upstream open reading frames (uORFs) in the 5' UTR. For this dissertation I have analyzed the pattern of conservation of such mRNA sequence elements. In the first set of studies, I have taken a comparative transcriptomics approach to address which RNA sequence elements are conserved between various families of angiosperm plants. Such conservation indicates an element's fundamental importance to plant …

Gata-Family Transcription Factors In Magnaporthe Oryzae, Cristian F. Quispe

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

The filamentous fungus, Magnaporthe oryzae, responsible for blast rice disease, destroys around 10-30% of the rice crop annually. Infection begins when the specialized infection structure, the appressorium, generates enormous internal turgor pressure through the accumulation of glycerol. This turgor acts on a penetration peg emerging at the base of the cell, causing it to breach the leaf surface allowing its infection.

The enzyme trehalose-6- phosphate synthase (Tps1) is a central regulator of the transition from appressorium development to infectious hyphal growth. In the first chapter we show that initiation of rice blast disease requires a regulatory mechanism involving an …

The Use Of Imputed Values In The Meta-Analysis Of Genome-Wide Association Studies., Shuo Jiao, Li Hsu, Carolyn Hutter, Ulrike Peters

Shuo Jiao

In genome-wide association studies (GWAS), it is a common practice to impute the genotypes of untyped single nucleotide polymorphism (SNP) by exploiting the linkage disequilibrium structure among SNPs. The use of imputed genotypes improves genome coverage and makes it possible to perform meta-analysis combining results from studies genotyped on different platforms. A popular way of using imputed data is the "expectation-substitution" method, which treats the imputed dosage as if it were the true genotype. In current practice, the estimates given by the expectation-substitution method are usually combined using inverse variance weighting (IVM) scheme in meta-analysis. However, the IVM is not …

Evolving Hard Problems: Generating Human Genetics Datasets With A Complex Etiology, Daniel S Himmelstein, Casey S Greene, Jason H Moore

Dartmouth Scholarship

BackgroundA goal of human genetics is to discover genetic factors that influence individuals' susceptibility to common diseases. Most common diseases are thought to result from the joint failure of two or more interacting components instead of single component failures. This greatly complicates both the task of selecting informative genetic variants and the task of modeling interactions between them. We and others have previously developed algorithms to detect and model the relationships between these genetic factors and disease. Previously these methods have been evaluated with datasets simulated according to pre-defined genetic models.

Linear Methods For Analysis And Quality Control Of Relative Expression Ratios From Quantitative Real-Time Polymerase Chain Reaction Experiments, Robert B. Page, Arnold J. Stromberg

Biology Faculty Publications

Relative expression quantitative real-time polymerase chain reaction (RT-qPCR) experiments are a common means of estimating transcript abundances across biological groups and experimental treatments. One of the most frequently used expression measures that results from such experiments is the relative expression ratio (R_E), which describes expression in experimental samples (i.e., RNA isolated from organisms, tissues, and/or cells that were exposed to one or more experimental or nonbaseline condition) in terms of fold change relative to calibrator samples (i.e., RNA isolated from organisms, tissues, and/or cells that were exposed to a control or baseline condition). Over the past decade, several …

Clustering With Exclusion Zones: Genomic Applications, Mark Segal, Yuanyuan Xiao, Fred Huffer

Mark R Segal

Methods for formally evaluating the clustering of events in space or time, notably the scan statistic, have been richly developed and widely applied. In order to utilize the scan statistic and related approaches, it is necessary to know the extent of the spatial or temporal domains wherein the events arise. Implicit in their usage is that these domains have no “holes”—hereafter “exclusion zones”—regions in which events a priori cannot occur. However, in many contexts, this requirement is not met. When the exclusion zones are known, it is straightforward to correct the scan statistic for their occurrence by simply adjusting the …