Genetics Commons^™

Poor Performance Of Bootstrap Confidence Intervals For The Location Of A Quantitative Trait Loucs, Ani Manichaikul, Josee Dupuis, Saunak Sen, Karl W. Broman

Johns Hopkins University, Dept. of Biostatistics Working Papers

The aim of many genetic studies is to locate the genomic regions (called quantitative trait loci, QTLs) that contribute to variation in a quantitative trait (such as body weight). Confidence intervals for the locations of QTLs are particularly important for the design of further experiments to identify the gene or genes responsible for the effect. Likelihood support intervals are the most widely used method to obtain confidence intervals for QTL location, but the non-parametric bootstrap has also been recommended. Through extensive computer simulation, we show that bootstrap confidence intervals are poorly behaved and so should not be used in this …

Multiple Tests Of Association With Biological Annotation Metadata, Sandrine Dudoit, Sunduz Keles, Mark J. Van Der Laan

U.C. Berkeley Division of Biostatistics Working Paper Series

We propose a general and formal statistical framework for the multiple tests of associations between known fixed features of a genome and unknown parameters of the distribution of variable features of this genome in a population of interest. The known fixed gene-annotation profiles, corresponding to the fixed features of the genome, may concern Gene Ontology (GO) annotation, pathway membership, regulation by particular transcription factors, nucleotide sequences, or protein sequences. The unknown gene-parameter profiles, corresponding to the variable features of the genome, may be, for example, regression coefficients relating genome-wide transcript levels or DNA copy numbers to possibly censored biological and …

The Scarlet Gene: Behavioral Genetics, Criminal Law, And Racial And Ethnic Stigma, Karen H. Rothenberg, Alice Wang

Faculty Scholarship

Imagine that a scientist from the state university asks you and your family to participate in a study on a particular gene variant associated with alcoholism. The project focuses on your ethnic group, the Tracy Islanders, who have a higher incidence of alcoholism, as well as a higher incidence of the gene variant, than the general population. You will not be informed whether you have the gene variant, but your participation in the study might help scientists develop drugs to help individuals control their addiction to alcohol. You have a family history of alcoholism, and you are concerned that your …

Conservation Of The Pho Regulon In Pseudomonas Fluorescens Pf0-1, Russell D. Monds, Peter D. Newell, Julia A. Schwartzman, George A. O'Toole

Dartmouth Scholarship

The Pho regulon integrates the sensing of environmental inorganic phosphate (Pi) availability with coregulation of gene expression, mediating an adaptive response to Pi limitation. Many aspects of the Pho regulon have been addressed in studies of Escherichia coli; however, it is unclear how transferable this knowledge is to other bacterial systems. Here, we report work to discern the conservation of the Pho regulon in Pseudomonas fluorescens Pf0-1. We demonstrate by mutational studies that PhoB/PhoR and the Pst system have conserved functions in the regulation of Pi-induced phosphatase activities, as well as expression of other Pi-regulated genes. A genetic screen was …

Gpnn: Power Studies And Applications Of A Neural Network Method For Detecting Gene-Gene Interactions In Studies Of Human Disease, Alison A. Motsinger, Stephen L. Lee, George Mellick, Marylyn D. Ritchie

Dartmouth Scholarship

The identification and characterization of genes that influence the risk of common, complex multifactorial disease primarily through interactions with other genes and environmental factors remains a statistical and computational challenge in genetic epidemiology. We have previously introduced a genetic programming optimized neural network (GPNN) as a method for optimizing the architecture of a neural network to improve the identification of gene combinations associated with disease risk. The goal of this study was to evaluate the power of GPNN for identifying high-order gene-gene interactions. We were also interested in applying GPNN to a real data analysis in Parkinson's disease.

Australian Temperate Strawberry Breeding Program (Western Australia) Selection Of New And Advanced Short Day Breeding Lines And Cultivars In Western Australia - 2005/2006, Michaela Antoine, Dennis Phillips

Horticulture research reports

Sixty-eight 'short day' selections from the Australian Temperate breeding program were compared in a trial planting on a commercial property at Wanneroo from a mid May planting. Thirty-three of the selections were derived from crosses made in 2003 (new Stage 4 selections) and twenty-nine were from crosses made between 1998 and 2002 (Intermediate Stages 5 and 6). In addition, three advanced selections were compared in large plots of 1,000-1 ,500 plants together with three commercial control cultivars, Gaviota, Camino Real and Kiewa. These selections were 'fast tracked' for future commercialisation by being selected for bulking up in September 2004.

Seven …

Taking A Bite Out Of Hypertrophic Cardiomyopathy: Soy Diet And Disease, Cathy J. Hatcher, Craig T. Basson

PCOM Scholarly Works

Some forms of hypertrophic cardiomyopathy (HCM) are caused by mutations in cardiac sarcomeric genes, but environmental factors are believed to influence the hypertrophic response. A highly variable but potentially significant environmental factor is diet. Since soy-rich diets have been speculated to confer protection against cardiovascular disease, Stauffer et al. have explored the influence of a soy diet on cardiac growth and function in a transgenic mouse model of HCM (see the related article beginning on page 209). They report that mice fed a soy diet exhibited significantly worse HCM than mice fed a soy-free (milk protein) diet. This study provides …

Eye Development At The Houston "Fly Meeting", Amit Singh

Biology Faculty Publications

Meeting report: The 47th Annual Drosophila Research Conference or "Fly Meeting" took place at Houston, Texas, USA from March 29th- April 2nd, 2006, under the aegis of the Genetics Society of America. The Fly Meeting provides an excellent opportunity for fly researchers to present their work and to get a snapshot of recent developments and upcoming trends in their research field. The fruit fly, Drosophila melanogaster, is a very versatile model to study growth, patterning, neural development, evolution, systemetics and various other facets of biomedical science. The topics presented in the meeting covered a very broad spectrum of fly research. …

Neural Induction And Differentiation Of Stem Cells Using The Developmental Gene Pax7, Vijesh G. Vaghjiani

Theses : Honours

Neurodegenerative disorders are conditions that mainly affect the brain and the central nervous system (CNS). Each disease type is characterised by loss of function which results from death of a particular region. Interestingly enough, most of the time disease pathology is due to loss of specific cell types in the CNS. These pathological conditions have both high economic costs and social implications for society. To treat such conditions, either the lost cells must be replaced or the cells surrounding the damaged tissue must be induced to undergo repair to replace the lost cells. The former looks more achievable whereas the …

The Functional Significance Of Multiple Pax7 Isoforms, Chantel L. Burchill

Theses : Honours

The Pax7 gene is critical for specification of both neurons in the mid-brain and skeletal muscle satellite cells. Several alternate transcripts are transcribed from the single gene. Previous studies have shown that the resultant alternate Pax7 isoforms differ in the structure of their paired domain (a DNA-binding domain that influences target gene selection), yet the functional significance of each isoform for specification of neurogenic and myogenic cell types remains unknown. Although previous studies have identified the presence of multiple alternate Pax7 transcripts in both neurogenic and myogenic cell lines, more research is necessary to understand the functional significance of the …

Chironomid Hemoglobin Genetic Diversity As An Indicator Of The New Jersey Hackensack Meadowlands Wetland Health, Lene Marie De Coursin Jacobs

Seton Hall University Dissertations and Theses (ETDs)

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