Genetics and Genomics Commons^™

Bayesian Analysis Of Cell-Cycle Gene Expression Data, Chuan Zhou, Jon Wakefield, Linda Breeden

UW Biostatistics Working Paper Series

The study of the cell-cycle is important in order to aid in our understanding of the basic mechanisms of life, yet progress has been slow due to the complexity of the process and our lack of ability to study it at high resolution. Recent advances in microarray technology have enabled scientists to study the gene expression at the genome-scale with a manageable cost, and there has been an increasing effort to identify cell-cycle regulated genes. In this chapter, we discuss the analysis of cell-cycle gene expression data, focusing on a model-based Bayesian approaches. The majority of the models we describe …

The Relationship Between Frq-Protein Stability And Temperature Compensation In The Neurospora Circadian Clock, Peter Ruoff, Jennifer J. Loros, Jay C. Dunlap

Dartmouth Scholarship

Temperature compensation is an important property of all biological clocks. In Neurospora crassa, negative-feedback regulation on the frequency (frq) gene's transcription by the FRQ protein plays a central role in the organism's circadian pacemaker. Earlier model calculations predicted that the stability of FRQ should determine the period length of Neurospora's circadian rhythm as well as the rhythm's temperature compensation. Here, we report experimental FRQ protein stabilities in frq mutants at 20 degrees C and 25 degrees C, and estimates of overall activation energies for mutant FRQ protein degradation. The results are consistent with earlier model predictions, i.e., temperature compensation of …

The Role Of An Explicit Causal Framework In Affected Sib Pair Designs With Covariates , Constantine E. Frangakis, Fan Li, Betty Q. Doan

Johns Hopkins University, Dept. of Biostatistics Working Papers

The affected sib/relative pair (ASP/ARP) design is often used with covariates to find genes that can cause a disease in pathways other than through those covariates. However, such "covariates" can themselves have genetic determinants, and the validity of existing methods has so far only been argued under implicit assumptions. We propose an explicit causal formulation of the problem using potential outcomes and principal stratification. The general role of this formulation is to identify and separate the meaning of the different assumptions that can provide valid causal inference in linkage analysis. This separation helps to (a) develop better methods under explicit …

[Accepted Article Manuscript Version (Postprint)] Identification And Functional Characterization Of Arabidopsis Peroxin4 And The Interacting Protein Peroxin22, Bethany Zolman, Melanie Monroe-Augustus, Illeana Silva, Bonnie Bartel

Biology Department Faculty Works

Peroxins are genetically defined as proteins necessary for peroxisome biogenesis. By screening for reduced response to indole-3-butyric acid, which is metabolized to active auxin in peroxisomes, we isolated an Arabidopsis thaliana peroxin4 (pex4) mutant. This mutant displays sucrose-dependent seedling development and reduced lateral root production, characteristics of plant peroxisome malfunction. We used yeast two-hybrid analysis to determine that PEX4, an apparent ubiquitinconjugating enzyme, interacts with a previously unidentified Arabidopsis protein, PEX22. A pex4 pex22 double mutant enhanced pex4 defects, confirming that PEX22 is a peroxin. Expression of both Arabidopsis genes together complemented yeast pex4 or pex22 mutant defects, whereas expression …

Bayer Ag V. Housey Pharmaceuticals: Protection For Biotechnological Research Tools Under Section 271(G) Found Wanting, Matthew Barthalow

The University of New Hampshire Law Review

[Excerpt] "Research tools, a subset of biotechnological inventions protected by process patents, are “tools that scientists use in the laboratory, including cell lines, monoclonal antibodies, reagents, animal models, growth factors, combinatorial chemistry and DNA libraries, clones and cloning tools (such as PCR), methods, laboratory equipment and machines.” Many companies base their business models on the ability to find pharmaceutical products using their proprietary drug discovery research tools. Research tools used for drug discovery ‘include bioinformatic methods for identifying the interaction of certain proteins and their association with disease, methods for confirming protein targets, screening assays to identify molecules active against …

Community Analysis Of A Mercury Hot Spring Supports Occurrence Of Domain-Specific Forms Of Mercuric Reductase, Jessica Simbahan, Elizabeth Kurth, James Schelert, Amanda Dillman, Estuko N. Moriyama, Stevan Jovanovich, Paul H. Blum

Papers in Genetics

Mercury is a redox-active heavy metal that reacts with active thiols and depletes cellular antioxidants. Active resistance to the mercuric ion is a widely distributed trait among bacteria and results from the action of mercuric reductase (MerA). Protein phylogenetic analysis of MerA in bacteria indicated the occurrence of a second distinctive form of MerA among the archaea, which lacked an N-terminal metal recruitment domain and a C-terminal active tyrosine. To assess the distribution of the forms of MerA in an interacting community comprising members of both prokaryotic domains, studies were conducted at a naturally occurring mercuryrich geothermal environment. Geochemical analyses …

Genetic And Molecular Analysis Of Phytochromes From The Filamentous Fungus Neurospora Crassa, Allan C. Froehlich, Bosl Noh, Richard D. Vierstra, Jennifer Loros, Jay C. Dunlap

Dartmouth Scholarship

Phytochromes (Phys) comprise a superfamily of red-/far-red-light-sensing proteins. Whereas higher-plant Phys that control numerous growth and developmental processes have been well described, the biochemical characteristics and functions of the microbial forms are largely unknown. Here, we describe analyses of the expression, regulation, and activities of two Phys in the filamentous fungus Neurospora crassa. In addition to containing the signature N-terminal domain predicted to covalently associate with a bilin chromophore, PHY-1 and PHY-2 contain C-terminal histidine kinase and response regulator motifs, implying that they function as hybrid two-component sensor kinases activated by light. A bacterially expressed N-terminal fragment of PHY-2 covalently …

Optimal Feature Selection For Nearest Centroid Classifiers, With Applications To Gene Expression Microarrays, Alan R. Dabney, John D. Storey

UW Biostatistics Working Paper Series

Nearest centroid classifiers have recently been successfully employed in high-dimensional applications. A necessary step when building a classifier for high-dimensional data is feature selection. Feature selection is typically carried out by computing univariate statistics for each feature individually, without consideration for how a subset of features performs as a whole. For subsets of a given size, we characterize the optimal choice of features, corresponding to those yielding the smallest misclassification rate. Furthermore, we propose an algorithm for estimating this optimal subset in practice. Finally, we investigate the applicability of shrinkage ideas to nearest centroid classifiers. We use gene-expression microarrays for …

A New Approach To Intensity-Dependent Normalization Of Two-Channel Microarrays, Alan R. Dabney, John D. Storey

UW Biostatistics Working Paper Series

A two-channel microarray measures the relative expression levels of thousands of genes from a pair of biological samples. In order to reliably compare gene expression levels between and within arrays, it is necessary to remove systematic errors that distort the biological signal of interest. The standard for accomplishing this is smoothing "MA-plots" to remove intensity-dependent dye bias and array-specific effects. However, MA methods require strong assumptions. We review these assumptions and derive several practical scenarios in which they fail. The "dye-swap" normalization method has been much less frequently used because it requires two arrays per pair of samples. We show …

Principal Component Analysis For Predicting Transcription-Factor Binding Motifs From Array-Derived Data, Yunlong Liu, Matthew P Vincenti, Hiroki Yokota

Dartmouth Scholarship

The responses to interleukin 1 (IL-1) in human chondrocytes constitute a complex regulatory mechanism, where multiple transcription factors interact combinatorially to transcription-factor binding motifs (TFBMs). In order to select a critical set of TFBMs from genomic DNA information and an array-derived data, an efficient algorithm to solve a combinatorial optimization problem is required. Although computational approaches based on evolutionary algorithms are commonly employed, an analytical algorithm would be useful to predict TFBMs at nearly no computational cost and evaluate varying modelling conditions. Singular value decomposition (SVD) is a powerful method to derive primary components of a given matrix. Applying SVD …

An Introduction To Low-Level Analysis Methods Of Dna Microarray Data, Wolfgang Huber, Anja Von Heydebreck, Martin Vingron

Bioconductor Project Working Papers

This article gives an overview over the methods used in the low--level analysis of gene expression data generated using DNA microarrays. This type of experiment allows to determine relative levels of nucleic acid abundance in a set of tissues or cell populations for thousands of transcripts or loci simultaneously. Careful statistical design and analysis are essential to improve the efficiency and reliability of microarray experiments throughout the data acquisition and analysis process. This includes the design of probes, the experimental design, the image analysis of microarray scanned images, the normalization of fluorescence intensities, the assessment of the quality of microarray …

Empirical Analysis Of The Str Profiles Resulting From Conceptual Mixtures, David R. Paoletti, Travis E. Doom, Carissa M. Krane, Michael L. Raymer, Dan E. Krane

Biology Faculty Publications

Samples containing DNA from two or more individuals can be difficult to interpret. Even ascertaining the number of contributors can be challenging and associated uncertainties can have dramatic effects on the interpretation of testing results. Using an FBI genotypes dataset, containing complete genotype information from the 13 Combined DNA Index System (CODIS) loci for 959 individuals, all possible mixtures of three individuals were exhaustively and empirically computed. Allele sharing between pairs of individuals in the original dataset, a randomized dataset and datasets of generated cousins and siblings was evaluated as were the number of loci that were necessary to reliably …

The Case For Selection At Ccr5-Δ32, Pardis Sabeti, Emily C. Walsh, Stephen F. Schaffner, Patrick Varilly, Ben Fry, Holli Hutcheson, Mike Cullen, Tarjei S. Mikkelsen, Jessica Roy, Nick Patterson, Richard Cooper, David Reich, David Altshuler, Stephen J. O'Brien, Eric S. Lander

Biology Faculty Articles

The C-C chemokine receptor 5, 32 base-pair deletion (CCR5-Δ32) allele confers strong resistance to infection by the AIDS virus HIV. Previous studies have suggested that CCR5-Δ32 arose within the past 1,000 y and rose to its present high frequency (5%–14%) in Europe as a result of strong positive selection, perhaps by such selective agents as the bubonic plague or smallpox during the Middle Ages. This hypothesis was based on several lines of evidence, including the absence of the allele outside of Europe and long-range linkage disequilibrium at the locus. We reevaluated this evidence with the benefit …

When Should Judges Admit Or Compel Genetic Tests?, Diane E. Hoffmann, Karen H. Rothenberg

Faculty Scholarship

No abstract provided.

Ordering Genetic Algorithm Genomes With Reconstructability Analysis: Discrete Models, Stephen Shervais, Martin Zwick

Complex Systems Faculty Publications and Presentations

The building block hypothesis implies that genetic algorithm effectiveness is influenced by the relative location of epistatic genes on the chromosome. We demonstrate this with a discrete-valued problem, based on Kauffman’s NK model, and show that information-theoretic reconstructability analysis can be used to decide on optimal gene ordering.

Feature-Specific Penalized Latent Class Analysis For Genomic Data, E. Andres Houseman, Brent A. Coull, Rebecca A. Betensky

Harvard University Biostatistics Working Paper Series

No abstract provided.

A Pseudolikelihood Approach For Simultaneous Analysis Of Array Comparative Genomic Hybridizations (Acgh), David A. Engler, Gayatry Mohapatra, David N. Louis, Rebecca Betensky

Harvard University Biostatistics Working Paper Series

DNA sequence copy number has been shown to be associated with cancer development and progression. Array-based Comparative Genomic Hybridization (aCGH) is a recent development that seeks to identify the copy number ratio at large numbers of markers across the genome. Due to experimental and biological variations across chromosomes and across hybridizations, current methods are limited to analyses of single chromosomes. We propose a more powerful approach that borrows strength across chromosomes and across hybridizations. We assume a Gaussian mixture model, with a hidden Markov dependence structure, and with random effects to allow for intertumoral variation, as well as intratumoral clonal …

Simultaneous And Exact Interval Estimates For The Contrast Of Two Groups Based On An Extremely High Dimensional Response Variable: Application To Mass Spec Data Analysis, Yuhyun Park, Sean R. Downing, Cheng Li Dr., William C. Hahn, Philip W. Kantoff, L. J. Wei

Harvard University Biostatistics Working Paper Series

No abstract provided.

The Optimal Discovery Procedure: A New Approach To Simultaneous Significance Testing, John D. Storey

UW Biostatistics Working Paper Series

Significance testing is one of the main objectives of statistics. The Neyman-Pearson lemma provides a simple rule for optimally testing a single hypothesis when the null and alternative distributions are known. This result has played a major role in the development of significance testing strategies that are used in practice. Most of the work extending single testing strategies to multiple tests has focused on formulating and estimating new types of significance measures, such as the false discovery rate. These methods tend to be based on p-values that are calculated from each test individually, ignoring information from the other tests. As …

The Optimal Discovery Procedure For Large-Scale Significance Testing, With Applications To Comparative Microarray Experiments, John D. Storey, James Y. Dai, Jeffrey T. Leek

UW Biostatistics Working Paper Series

As much of the focus of genetics and molecular biology has shifted toward the systems level, it has become increasingly important to accurately extract biologically relevant signal from thousands of related measurements. The common property among these high-dimensional biological studies is that the measured features have a rich and largely unknown underlying structure. One example of much recent interest is identifying differentially expressed genes in comparative microarray experiments. We propose a new approach aimed at optimally performing many hypothesis tests in a high-dimensional study. This approach estimates the Optimal Discovery Procedure (ODP), which has recently been introduced and theoretically shown …

The Use Of Transcriptomics To Address Questions In Behaviour: Production Of A Suppression Subtractive Hybridisation Library From Dominance Hierarchies Of Rainbow Trout, Lynne U. Sneddon, Javier Margareto, Andrew R. Cossins

Ethology Collection

Microarrays, or gene chips, are transforming the way that gene expression is measured by allowing us to determine the expression of thousands of genes from a sample. This gives immense power to examine gene expression on a global scale within individual animals and between animals. The scope for analysing complex animal functions at the molecular level is within our grasp. Relatively few studies have examined complex behaviours and correlated them with gene expression in the central nervous system. Here, we review the use of microarray technology in the dissection of behaviour and focus specifically on dominance status. A cDNA library …

Cpg Oligodeoxynucleotides Stimulate Cord Blood Mononuclear Cells To Produce Immunoglobulins., Cheri D Landers, Subbarao Bondada

Microbiology, Immunology, and Molecular Genetics Faculty Publications

CpG oligodeoxynucleotides (ODNs) stimulate adult B cells leading to cellular proliferation and immunoglobulin production. It is unknown if CpG-ODNs similarly stimulate neonatal human B cells. Neonates have immature immune responses and are poorly responsive to thymus independent antigens such as polysaccharides. We determined umbilical cord cells' response to CpG-ODNs. Adult and umbilical cord B cells produced similar amounts of IgM (adult 1371 +/- 352 vs. cord 1873 +/- 1084 ng/ml) in response to CpG-ODN stimulation. Although CpG-ODN was able to stimulate adult IgG and IgA production, cord cells produced less IgG (153 +/- 58 vs. 10 +/- 2.5 ng/ml) and …

Atypical Pkciota Contributes To Poor Prognosis Through Loss Of Apical-Basal Polarity And Cyclin E Overexpression In Ovarian Cancer, Astrid M. Eder, Xiaomei Sui, Daniel G. Rosen, Laura K. Nolden, Kwai Wa Cheng, John P. Lahad, Madhuri Kango-Singh, Karen H. Lu, Carla L. Warneke, Edward N. Atkinson, Isabelle Bedrosian, Khandan Keyomarsi, Wen-Lin Kuo, Joe W. Gray, Jerry C. P. Yin, Jinsong Liu, Georg Halder, Gordon B. Mills

Biology Faculty Publications

We show that atypical PKCι, which plays a critical role in the establishment and maintenance of epithelial cell polarity, is genomically amplified and overexpressed in serous epithelial ovarian cancers. Furthermore, PKCι protein is markedly increased or mislocalized in all serous ovarian cancers. An increased PKCι DNA copy number is associated with decreased progression-free survival in serous epithelial ovarian cancers. In a Drosophila in vivo epithelial tissue model, overexpression of persistently active atypical PKC results in defects in apical-basal polarity, increased Cyclin E protein expression, and increased proliferation. Similar to the Drosophila model, increased PKCι proteins levels are associated with …

Characterization Of The Yeast Ionome: A Genome-Wide Analysis Of Nutrient Mineral And Trace Element Homeostasis In Saccharomyces Cerevisiae, David J. Eide, Suzanne Clark, T . Murlidharan Nair, Mathias Gehl, Michael Gribskov, Mary Lou Guerinot, Jeffrey Harper

Dartmouth Scholarship

Nutrient minerals are essential yet potentially toxic, and homeostatic mechanisms are required to regulate their intracellular levels. We describe here a genome-wide screen for genes involved in the homeostasis of minerals in Saccharomyces cerevisiae. Using inductively coupled plasma-atomic emission spectroscopy (ICP-AES), we assayed 4,385 mutant strains for the accumulation of 13 elements (calcium, cobalt, copper, iron, potassium, magnesium, manganese, nickel, phosphorus, selenium, sodium, sulfur, and zinc). We refer to the resulting accumulation profile as the yeast 'ionome'.

Metaheuristic Applications And Their Solutions Quality, Dr. Zahid Hussain

International Conference on Information and Communication Technologies

Over the past few decades, a wide variety of classes of combinatorial problems (e.g. the assignment problem, the knapsack problem, the vehicle routing problem, etc.) have emerged - from such areas as management science, telecommunication, AI, VLSI design and many others. Many large combinatorial problems are NP-hard problems because of the combinatorial growth of their solution search space with the problem size. Such problems are commonly solved by some version of a prominent metaheuristic (e.g. Genetic Algorithms, Tabu Search, Simulated Annealing and etc.). These heuristics seek good but approximate solutions at a reasonable computational cost. These heuristics are of stochastic …

C-Jun N-Terminal Kinase (Jnk) Is Required For Survival And Proliferation Of B-Lymphoma Cells, Murali Gururajan, Roger Chui, Anbu K. Karuppannan, Jiyuan Ke, C. Darrell Jennings, Subbarao Bondada

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Several primary murine and human B lymphomas and cell lines were found to constitutively express high levels of the activated form of c-jun N-terminal kinase (JNK), a member of the mitogen-activated protein (MAP) kinase family. Proliferation of murine B lymphomas CH31, CH12.Lx, BKS-2, and WEHI-231 and the human B lymphomas BJAB, RAMOS, RAJI, OCI-Ly7, and OCI-Ly10 was strongly inhibited by SP600125, an anthrapyrazolone inhibitor of JNK, in a dose-dependent manner. The lymphoma cells underwent apoptosis and arrested at the G2/M phase of cell cycle. Furthermore, JNK-specific small interfering RNA (siRNA) inhibited the growth of both murine and human B lymphomas. …

Application Of A Multiple Testing Procedure Controlling The Proportion Of False Positives To Protein And Bacterial Data, Merrill D. Birkner, Alan E. Hubbard, Mark J. Van Der Laan

U.C. Berkeley Division of Biostatistics Working Paper Series

Simultaneously testing multiple hypotheses is important in high-dimensional biological studies. In these situations, one is often interested in controlling the Type-I error rate, such as the proportion of false positives to total rejections (TPPFP) at a specific level, alpha. This article will present an application of the E-Bayes/Bootstrap TPPFP procedure, presented in van der Laan et al. (2005), which controls the tail probability of the proportion of false positives (TPPFP), on two biological datasets. The two data applications include firstly, the application to a mass-spectrometry dataset of two leukemia subtypes, AML and ALL. The protein data measurements include intensity and …

Analysis Of Affymetrix Genechip Data Using Amplified Rna, Leslie Cope, Scott M. Hartman, Hinrich W.H. Gohlmann, Jay P. Tiesman, Rafael A. Irizarry

Johns Hopkins University, Dept. of Biostatistics Working Papers

The standard method of target synthesis for hybridization to Affymetrix GeneChip® expression microarrays requires a relatively large amount of input total RNA (1-15 micrograms). When small biological samples are collected by microdissection or other methods, amplification techniques are required to provide sufficient target for hybridization to expression arrays. One amplification technique used is to perform two successive rounds of T7-based in vitro transcription. However, the use of random primers required to re-generate cDNA from the first round transcription reaction results in shortened copies of the cDNA, and ultimately the cRNA, transcripts from which the 5' end is missing. In this …

Digenic Control Of Colouration In The Two-Spot Gourami Trichogaster Trichopterus Trichopterus, Jack Frankel

Department of Biology Faculty Publications

Labyrinth  fishes  of  the  families  Anabantidae,  Belontiidae,Helostomatidae,  and  Osphronemidae  comprise the  tradi-tional  anabantoids,  a  group  of  about  80  relatively  small African  and  southeast  Asian  species (Linke  1991).  Many of  the  anabantoids  are  popular  with  aquarium  hobbyists because of their interesting reproductive behaviours, with males of most species brooding eggs in their mouths or in floating bubble nests (Vevers 1980; Linke 1991; Axelrod and Vorderwinkler 1995; Mills 2000). They have also beenthe focus of several environmental, morphological, and gene-tic  investigations  (Sommer  1982;  Gosline  1985;  Waki-yama  et  al. 1997;  Frankel  1992,  2001).  The  two-spot gourami,   Trichogaster  trichopterus  trichopterus  Pallas (Osphronemidae),  is  one …

Group 13 Hox Proteins Interact With The Mh2 Domain Of R-Smads And Modulate Smad Transcriptional Activation Functions Independent Of Hox Dna Binding Capability, Thomas M. Williams, Melissa E. Williams, Joanne H. Heaton, Thomas D. Gelehrter, Jeffrey W. Innis

Biology Faculty Publications

Interactions with co-factors provide a means by which HOX proteins exert specificity. To identify candidate protein interactors of HOXA13, we created and screened an E11.5–E12.5, distal limb bud yeast two-hybrid prey library. Among the interactors, we isolated the BMP-signaling effector Smad5, which interacted with the paralogous HOXD13 but not with HOXA11 or HOXA9, revealing unique interaction capabilities of the AbdB-like HOX proteins. Using deletion mutants, we determined that the MH2 domain of Smad5 is necessary for HOXA13 interaction.

This is the first report demonstrating an interaction between HOX proteins and the MH2 domain of Smad proteins. HOXA13 and HOXD13 …