Genetics and Genomics Commons^™

The Acyl-Coa Thioesterase I (Acot1) Is Regulated By The Peroxisome Proliferator-Activated Receptor Alpha And Hepatocyte Nuclear Factor 4 Alpha Via A Distal Response Element In The Promotor., Bikesh Dongol, Yatrik Shah, Insook Kim, Frank J. Gonzalez, Mary Hunt

Articles

The cytosolic acyl-CoA thioesterase I (Acot1) is an enzyme that hydrolyzes longchain acyl-CoAs of C12-C20-CoA in chain-length, to the free fatty acid and coenzyme A. Acot1 was previously shown to be strongly upregulated at mRNA and protein level in rodents by fibrates. In this study, we show that Acot1 mRNA levels were increased 90-fold in liver by treatment with Wy-14,643 and that Acot1 mRNA is also increased 15-fold in the liver of hepatocyte nuclear factor 4 alpha (HNF4a) knockout animals. Our study identified a direct repeat 1 (DR1) located in the Acot1 gene promotor in mouse, which binds the peroxisome …

Search For A Knox Gene In Kalanchöe Pinnatum, Ryan Michael Gleason

Undergraduate Honors Thesis Collection

Knox genes have been found in nearly all eukaryotic organisms. These genes code for a protein that is able to bind DNA. By binding to DNA, it is capable of controlling the expression of other genes. The coded sequence of these genes has been determined in many different organisms, but has yet to be searched for in the air plant, Kalanchoe pinnatum. I did research over the past year in an attempt to find the coded sequence of Kalanchoe's Knox gene. I grew Kalanchoe in Butler's greenhouse to accumulate enough plant material to begin work. I then extracted the RNA …

Single-Stranded Dna-Binding Proteins Regulate The Abundance Of Lim Domain And Lim Domain-Binding Proteins, Zhixiong Xu, Xianzhang Meng, Ying Cai, Hong Liang, Lalitha Nagarajan, Stephen J Brandt

Faculty, Staff and Student Publications

The LIM domain-binding protein Ldb1 is an essential cofactor of LIM-homeodomain (LIM-HD) and LIM-only (LMO) proteins in development. The stoichiometry of Ldb1, LIM-HD, and LMO proteins is tightly controlled in the cell and is likely a critical determinant of their biological actions. Single-stranded DNA-binding proteins (SSBPs) were recently shown to interact with Ldb1 and are also important in developmental programs. We establish here that two mammalian SSBPs, SSBP2 and SSBP3, contribute to an erythroid DNA-binding complex that contains the transcription factors Tal1 and GATA-1, the LIM domain protein Lmo2, and Ldb1 and binds a bipartite E-box-GATA DNA sequence motif. In …

What Is The Best Reference Rna? And Other Questions Regarding The Design And Analysis Of Two-Color Microarray Experiments, Kathleen F. Kerr, Kyle A. Serikawa, Caimiao Wei, Mette A. Peters, Roger E. Bumgarner

UW Biostatistics Working Paper Series

The reference design is a practical and popular choice for microarray studies using two-color platforms. In the reference design, the reference RNA uses half of all array resources, leading investigators to ask: What is the best reference RNA? We propose a novel method for evaluating reference RNAs and present the results of an experiment that was specially designed to evaluate three common choices of reference RNA. We found no compelling evidence in favor of any particular reference. In particular, a commercial reference showed no advantage in our data. Our experimental design also enabled a new way to test the effectiveness …

Shark Bay Prawn And Scallop Fisheries. Draft Review Report, Department Of Fisheries Western Australia

Fisheries Management Papers

In recent times, the Department of Fisheries has received representations from both sectors about the ongoing interaction of the fisheries and their respective management settings. As a result, a decision was made to comprehensively review the fisheries, taking into account matters of fishery sustainability and gear interactions, together with industry economics and market considerations. The review has also addressed research requirements to ensure an appropriate scientific basis for decision-making into the future.

A 368-Base-Pair Cis-Acting Hwp1 Promoter Region, Hcr, Of Candida Albicans Confers Hypha-Specific Gene Regulation And Binds Architectural Transcription Factors Nhp6 And Gcf1p, Samin Kim, Michael J. Wolyniak, Janet F. Staab, Paula Sundstrom

Dartmouth Scholarship

To elucidate the molecular mechanisms controlling the expression of the hypha-specific adhesin gene HWP1 of Candida albicans, its promoter was dissected and analyzed using a green fluorescent protein reporter gene. A 368-bp region, the HWP1 control region (HCR), was critical for activation under hypha-inducing conditions and conferred developmental regulation to a heterologous ENO1 promoter. A more distal region of the promoter served to amplify the level of promoter activation. Using gel mobility shift assays, a 249-bp subregion of HCR, HCRa, was found to bind at least four proteins from crude extracts of yeasts and hyphae with differing binding patterns dependent …

A Molecular Evaluation Of The North American “Grassland” Sparrow Clade, John Klicka, Garth M. Spellman

Ornithology Program (HRC)

Because they share several morphological and ecological characters, the North American sparrow (Emberizidae) genera Ammodramus, Passerculus, and Xenospiza have historically been considered members of a well-defined “grassland” sparrow assemblage. Relationships among the 11 members of this group have been the subject of much taxonomic debate, yet no comprehensive molecular assessment of relationships has been done. We investigated these relationships using mitochondrial DNA sequence data that included complete cytochrome-b and ND2 genes. Phylogenetic reconstructions derived via parsimony, likelihood, and Bayesian methods were congruent. The grassland sparrows, as presently configured, are polyphyletic. Pooecetes gramineus, Amphispiza belli (but not A. …

Purification, Crystallization And Preliminary Crystallographic Analysis Of Deoxyuridine Triphosphate Nucleotidohydrolase From Arabidopsis Thaliana, Mamta Bajaj, Hideaki Moriyama

Papers in Genetics

The deoxyuridine triphosphate nucleotidohydrolase gene from Arabidopsis thaliana was expressed and the gene product was purified. Crystallization was performed by the hanging-drop vapour-diffusion method at 298 K using 2 M ammonium sulfate as the precipitant. X-ray diffraction data were collected to 2.2 Å resolution using Cu Kα radiation. The crystal belongs to the orthorhombic space group P2₁2₁2₁, with unit-cell parameters a = 69.90, b = 70.86 Å, c = 75.55 Å. Assuming the presence of a trimer in the asymmetric unit, the solvent content was 30%, with a V_M of 1.8 Å …

A Markov Random Field Model For Network-Based Analysis Of Genomic Data, Zhi Wei, Hongzhe Li

UPenn Biostatistics Working Papers

A central problem in genomic research is the identification of genes and pathways involved in diseases and other biological processes. The genes identified or the univariate test statistics are often linked to known biological pathways through gene set enrichment analysis in order to identify the pathways involved. However, most of the procedures for identifying differentially expressed genes do not utilize the known pathway information in the phase of identifying such genes. In this paper, we develop a Markov random field (MRF)-based method for identifying genes and subnetworks that are related to diseases. Such a procedure models the dependency of the …

Statistical Methods For Inference Of Genetic Networks And Regulatory Modules, Hongzhe Li

UPenn Biostatistics Working Papers

Large-scale microarray gene expression data, motif data derived from promotor sequences, genome-wide chromatin immunoprecipitation (ChIP-chip) data, DNA polymorphism data and epigenomic data provide the possibility of constructing genetic networks or biological pathways, especially regulatory networks. In this paper, we review some new statistical methods for inference of genetic networks and regulatory modules, including a threshold gradient descent procedure for inference of Gaussian graphical models, a sparse regression mixture modeling approach for inference of regulatory modules, and the varying coefficient model for identifying regulatory subnetworks by integrating microarray time-course gene expression data and motif or ChIP-chip data. We present the statistical …

Conservative Estimation Of Optimal Multiple Testing Procedures, James E. Signorovitch

Harvard University Biostatistics Working Paper Series

No abstract provided.

Statistical Evaluation Of Evidence For Clonal Allelic Alterations In Array-Cgh Experiments, Colin B. Begg, Kevin Eng, Adam Olshen, E S. Venkatraman

Memorial Sloan-Kettering Cancer Center, Dept. of Epidemiology & Biostatistics Working Paper Series

In recent years numerous investigators have conducted genetic studies of pairs of tumor specimens from the same patient to determine whether the tumors share a clonal origin. These studies have the potential to be of considerable clinical significance, especially in clinical settings where the distinction of a new primary cancer and metastatic spread of a previous cancer would lead to radically different indications for treatment. Studies of clonality have typically involved comparison of the patterns of somatic mutations in the tumors at candidate genetic loci to see if the patterns are sufficiently similar to indicate a clonal origin. More recently, …

Sequential Quantitative Trait Locus Mapping In Experimental Crosses, Jaya M. Satagopan, Saunak Sen, Gary A. Churchill

Memorial Sloan-Kettering Cancer Center, Dept. of Epidemiology & Biostatistics Working Paper Series

The etiology of complex diseases is heterogeneous. The presence of risk alleles in one or more genetic loci affects the function of a variety of intermediate biological pathways, resulting in the overt expression of disease. Hence, there is an increasing focus on identifying the genetic basis of disease by sytematically studying phenotypic traits pertaining to the underlying biological functions. In this paper we focus on identifying genetic loci linked to quantitative phenotypic traits in experimental crosses. Such genetic mapping methods often use a one stage design by genotyping all the markers of interest on the available subjects. A genome scan …

Improved Performance Of Marron Using Genetic And Pond On Using Genetic And Pond Management Strategies, Craig Lawrence Dr

Fisheries Research Contract Reports

Marron (Cherax tenuimanus) are the highest valued freshwater crayfish farmed in Australia. This project addressed the need to increase the profitability of commercial marron farms by improving growth rates and pond management strategies.

Genetic Analysis Of A Novel Pathway For D-Xylose Metabolism In Caulobacter Crescentus, Craig Stephens, Beat Christen, Thomas Fuchs, Vidyodhaya Sundaram, Kelly Watanabe, Urs Jenal

Biology

Genetic data suggest that the oligotrophic freshwater bacterium Caulobacter crescentus metabolizes D-xylose through a pathway yielding -ketoglutarate, comparable to the recently described L-arabinose degradation pathway of Azospirillum brasilense. Enzymes of the C. crescentus pathway, including an NAD -dependent xylose dehydrogenase, are encoded in the xylose-inducible xylXABCD operon (CC0823-CC0819).

The Carnegie Protein Trap Library: A Versatile Tool For Drosophila Developmental Studies, Anna Allen

Department of Biology Faculty Publications

Metazoan physiology depends on intricate patterns of gene expression that remain poorly known. Using transposon mutagenesis in Drosophila, we constructed a library of 7404 protein trap and enhancer trap lines, the Carnegie collection, to facilitate gene expression mapping at single-cell resolution. By sequencing the genomic insertion sites, determining splicing patterns downstream of the enhanced green fluorescent protein (EGFP) exon, and analyzing expression patterns in the ovary and salivary gland, we found that 600-900 different genes are trapped in our collection. A core set of 244 lines trapped different identifiable protein isoforms, while insertions likely to act as GFP-enhancer traps were …

A Hidden Markov Model For Joint Estimation Of Genotype And Copy Number In High-Throughput Snp Chips, Robert B. Scharpf, Giovanni Parmigiani, Jonathan Pevnser, Ingo Ruczinski

Johns Hopkins University, Dept. of Biostatistics Working Papers

Amplifications and deletions of chromosomal DNA, as well as copy-neutral loss of heterozygosity have been associated with diseases processes. High-throughput single nucleotide polymorphism (SNP) arrays are useful for making genome-wide estimates of copy number and genotype calls. Because neighboring SNPs in high throughput SNP arrays are likely to have dependent copy number and genotype due to the underlying haplotype structure and linkage disequilibrium, hidden Markov models (HMM) may be useful for improving genotype calls and copy number estimates that do not incorporate information from nearby SNPs. We improve previous approaches that utilize a HMM framework for inference in high throughput …

Multiple Diseases In Carrier Probability Estimation: Accounting For Surviving All Cancers Other Than Breast And Ovary In Brcapro, Hormuzd A. Katki, Amanda Blackford, Sining Chen, Giovanni Parmigiani

Johns Hopkins University, Dept. of Biostatistics Working Papers

Mendelian models can predict who carries an inherited deleterious mutation of known disease genes based on family history. For example, the BRCAPRO model is commonly used to identify families who carry mutations of BRCA1 and BRCA2, based on familial breast and ovarian cancers. These models incorporate the age of diagnosis of diseases in relatives and current age or age of death. We develop a rigorous foundation for handling multiple diseases with censoring. We prove that any disease unrelated to mutations can be excluded from the model, unless it is sufficiently common and dependent on a mutation-related disease time. Furthermore, if …

Power Boosting In Genome-Wide Studies Via Methods For Multivariate Outcomes, Mary J. Emond

UW Biostatistics Working Paper Series

Whole-genome studies are becoming a mainstay of biomedical research. Examples include expression array experiments, comparative genomic hybridization analyses and large case-control studies for detecting polymorphism/disease associations. The tactic of applying a regression model to every locus to obtain test statistics is useful in such studies. However, this approach ignores potential correlation structure in the data that could be used to gain power, particularly when a Bonferroni correction is applied to adjust for multiple testing. In this article, we propose using regression techniques for misspecified multivariate outcomes to increase statistical power over independence-based modeling at each locus. Even when the outcome …

Regressive Evolution In The Mexican Cave Tetra, Astyanax Mexicanus, Meredith E. Protas, Melissa Conrad, Joshua B. Gross, Clifford Tabin, Richard Borowsky

Collected Faculty Scholarship

Cave adapted animals generally have reduced pigmentation and eyes, but the evolutionary forces driving the reductions are unknown; Darwin famously questioned the role of natural selection in eye loss in cave fishes; “As it is difficult to imagine that eyes, although useless, could be in any way injurious to animals living in darkness, I attribute their loss wholly to disuse” [1]. We studied the genetic basis of this phenomenon in the Mexican cave tetra, Astyanax mexicanus, by mapping the quantitative trait loci (QTL) determining differences in eye/lens sizes and melanophore number between cave and surface fish. In addition, we mapped …

Data Quality Assessment Of Ungated Flow Cytometry Data In High, Nolwenn Le Meur, Anthony Rossini, Maura Gasparetto, Clay Smith, Ryan R. Brinkman, Robert Gentleman

Bioconductor Project Working Papers

Background: The recent development of semi-automated techniques for staining and analyzing flow cytometry samples has presented new challenges. Quality control and quality assessment are critical when developing new high throughput technologies and their associated information services. Our experience suggests that significant bottlenecks remain in the development of high throughput flow cytometry methods for data analysis and display. Especially, data quality control and quality assessment are crucial steps in processing and analyzing high throughput flow cytometry data.

Methods: We propose a variety of graphical exploratory data analytic tools for exploring ungated flow cytometry data. We have implemented a number of specialized …

Optimization Of Cutaneous Electrically Mediated Plasmid Dna Delivery Using Novel Electrode, L. C. Heller, M. J. Jaroszeski, D. Coppola, A. N. Mccray, J. Hickey, R. Heller

Bioelectrics Publications

The easy accessibility of skin makes it an excellent target for gene transfer protocols. To take advantage of skin as a target for gene transfer, it is important to establish an efficient and reproducible delivery system. Electroporation is an established technique for enhancing plasmid delivery to many tissues in vivo. A critical component of this technique is the electrode configuration. Electroporation parameters were optimized for transgene expression with minimal tissue damage with a novel electrode. The highest transgene expression and efficiency of individual cell transformation with minimal damage was produced with eight 150 ms pulses at field strength of …

Conflict Between Translation Initiation And Elongation In Vertebrate Mitochondrial Genomes, Xuhua Xia, Huang Huang, Malisa Carullo, Esther Betran, Estuko N. Moriyama

Papers in Genetics

The strand-biased mutation spectrum in vertebrate mitochondrial genomes results in an AC-rich L-strand and a GT-rich H-strand. Because the L-strand is the sense strand of 12 protein-coding genes out of the 13, the third codon position is overall strongly AC-biased. The wobble site of the anticodon of the 22 mitochondrial tRNAs is either U or G to pair with the most abundant synonymous codon, with only one exception. The wobble site of Met-tRNA is C instead of U, forming the Watson- Crick match with AUG instead of AUA, the latter being much more frequent than the former. This has been …

Hemoglobin Function And Physiological Adaptation To Hypoxia In High-Altitude Mammals, Jay F. Storz

Jay F. Storz Publications

Understanding the biochemical mechanisms that enable high-altitude animals to survive and function under conditions of hypoxic stress can provide important insights into the nature of physiological adaptation. Evidence from a number of high-altitude vertebrates indicates that modifications of hemoglobin function typically play a key role in mediating an adaptive response to chronic hypoxia. Because much is known about structure– function relationships of mammalian hemoglobins and their physiological role in oxygen transport, the study of hemoglobin variation in high-altitude mammals holds much promise for understanding the nature of adaptation to hypoxia from the level of blood biochemistry to the level of …

The Study Of Adaptation And Speciation In The Genomic Era, Jay F. Storz, Hopi E. Hoekstra

Jay F. Storz Publications

The availability of complete genome sequences and genetic linkage maps for a growing number of mammalian species is opening up exciting new opportunities for studies of evolutionary change in natural populations. For example, multilocus mapping approaches hold the promise of identifying the specific genetic changes that underlie ecological adaptation and reproductive isolation. The fact that many of the genomic resources that have been developed for Mus and Rattus are transferable to other muroid rodents means that roughly 25% of all mammalian species can now be considered ‘‘genome-enabled’’ study organisms to varying degrees. The transferability of genomic resources between model organisms …

The Genome-Enabled Electronic Medical Record., M A Hoffman

Manuscripts, Articles, Book Chapters and Other Papers

The integration of patient-specific genomic information into the electronic medical record (EMR) will create many opportunities to improve patient care. Key to the successful incorporation of genomic information into the EMR will be the development of laboratory information systems capable of appropriately formatting molecular diagnostic and cytogenetic findings in the EMR. Due to the lack of granular genomics-related content in existing medical vocabularies, the adoption of new standards for describing clinically significant genomic information will be an important step toward recognizing the genome-enabled EMR. Appropriate capture of patient-specific genomic results in the EMR will generate new opportunities to utilize this …

Group Scad Regression Analysis For Microarray Time Course Gene Expression Data, Lifeng Wang, Guang Chen, Hongzhe Li Phd

UPenn Biostatistics Working Papers

Since many important biological systems or processes are dynamic systems, it is important to study the gene expression patterns over time in a genomic scale in order to capture the dynamic behavior of gene expression. Microarray technologies have made it possible to measure the gene expression levels of essentially all the genes during a given biological process. In order to determine the transcriptional factors involved in gene regulation during a given biological process, we propose to develop a functional response model with varying coefficients in order to model the transcriptional effects on gene expression levels and to develop a group …

The Yeast Orthologue Of Grasp65 Forms A Complex With A Coiled-Coil Protein That Contributes To Er To Golgi Traffic, Rudy Behnia, Francis A. Barr, John J. Flanagan, Charles Barlowe, Sean Munro

Dartmouth Scholarship

The mammalian Golgi protein GRASP65 is required in assays that reconstitute cisternal stacking and vesicle tethering. Attached to membranes by an N-terminal myristoyl group, it recruits the coiled-coil protein GM130. The relevance of this system to budding yeasts has been unclear, as they lack an obvious orthologue of GM130, and their only GRASP65 relative (Grh1) lacks a myristoylation site and has even been suggested to act in a mitotic checkpoint. In this study, we show that Grh1 has an N-terminal amphipathic helix that is N-terminally acetylated and mediates association with the cis-Golgi. We find that Grh1 forms a complex with …

Following Temperature Stress, Export Of Heat Shock Mrna Occurs Efficiently In Cells With Mutations In Genes Normally Important For Mrna Export, Christiane Rollenhagen, Christine A. Hodge, Charles N. Cole

Dartmouth Scholarship

Heat shock leads to accumulation of polyadenylated RNA in nuclei of Saccharomyces cerevisiae cells, transcriptional induction of heat shock genes, and efficient export of polyadenylated heat shock mRNAs. These studies were conducted to examine the requirements for export of mRNA following heat shock. We used in situ hybridization to detect SSA4 mRNA (encoding Hsp70) and flow cytometry to measure the amount of Ssa4p-green fluorescent protein (GFP) produced following heat shock. Npl3p and Yra1p are mRNA-binding proteins recruited to nascent mRNAs and are essential for proper mRNA biogenesis and export. Heat shock mRNA was exported efficiently in temperature-sensitive npl3, yra1 …

A Proposal For Robust Temperature Compensation Of Circadian Rhythms, Christian I. Hong, Emery D. Conrad, John J. Tyson

Dartmouth Scholarship

The internal circadian rhythms of cells and organisms coordinate their physiological properties to the prevailing 24-h cycle of light and dark on earth. The mechanisms generating circadian rhythms have four defining characteristics: they oscillate endogenously with period close to 24 h, entrain to external signals, suffer phase shifts by aberrant pulses of light or temperature, and compensate for changes in temperature over a range of 10°C or more. Most theoretical descriptions of circadian rhythms propose that the underlying mechanism generates a stable limit cycle oscillation (in constant darkness or dim light), because limit cycles quite naturally possess the first three …