Life Sciences Commons^™

Gene Response Profiles For Daphnia Pulex Exposed To The Environmental Stressor Cadmium Reveals Novel Crustacean Metallothioneins, Joseph R. Shaw, John K. Colbourne, Jennifer C. Davey, Stephen P. Glaholt, Thomas H. Hampton, Celia Y. Chen, Carol L. Folt, Joshua W. Hamilton

Dartmouth Scholarship

Genomic research tools such as microarrays are proving to be important resources to study the complex regulation of genes that respond to environmental perturbations. A first generation cDNA microarray was developed for the environmental indicator species Daphnia pulex, to identify genes whose regulation is modulated following exposure to the metal stressor cadmium. Our experiments revealed interesting changes in gene transcription that suggest their biological roles and their potentially toxicological features in responding to this important environmental contaminant.

Genome-Wide Transcriptional Profiling Of The Cyclic Amp-Dependent Signaling Pathway During Morphogenic Transitions Of Candida Albicans, Yong-Sun Bahn, Matthew Molenda, Janet F. Staab, Courtney A. Lyman, Laura J. Gordon, Paula Sundstrom

Dartmouth Scholarship

Candida albicans is an opportunistic human fungal pathogen that causes systemic candidiasis as well as superficial mucosal candidiasis. In response to the host environment, C. albicans transitions between yeast and hyphal forms. In particular, hyphal growth is important in facilitating adhesion and invasion of host tissues, concomitant with the expression of various hypha-specific virulence factors. In previous work, we showed that the cyclic AMP (cAMP) signaling pathway plays a crucial role in morphogenic transitions and virulence of C. albicans by studying genes encoding adenylate cyclase-associated protein (CAP1) and high-affinity phosphodiesterase (PDE2) (Y. S. Bahn, J. Staab, and P. Sundstrom, Mol. …

Non-Standard Sources In A Standardized World: Responsible Practice And Ethics Of Acquiring Turtle Specimens For Scientific Use, Edgar Lehr, Russell Burke, Linda Ford, Steve Mockford, Peter Pritchard, Jose Rosado, Darrell Senneke, Bryan Stuart

Edgar Lehr

No abstract provided.

Assessing Population Level Genetic Instability Via Moving Average, Samuel Mcdaniel, Rebecca Betensky, Tianxi Cai

Harvard University Biostatistics Working Paper Series

No abstract provided.

The Small Rna Repertoire Of Dictyostelium Discoideum And Its Regulation By Components Of The Rnai Pathway, Andrea Hinas, Johan Reimegård, E. Gerhart H. Wagner, Wolfgang Nellen, Victor R. Ambros, Fredrik Soderbum

Dartmouth Scholarship

Small RNAs play crucial roles in regulation of gene expression in many eukaryotes. Here, we report the cloning and characterization of 18–26 nt RNAs in the social amoeba Dictyostelium discoideum . This survey uncovered developmentally regulated microRNA candidates whose biogenesis, at least in one case, is dependent on a Dicer homolog, DrnB. Furthermore, we identified a large number of 21 nt RNAs originating from the DIRS-1 retrotransposon, clusters of which have been suggested to constitute centromeres. Small RNAs from another retrotransposon, Skipper, were significantly up-regulated in strains depleted of the second Dicer-like protein, DrnA, and a putative RNA-dependent RNA polymerase, …

A Hidden Spatial-Temporal Markov Random Field Model For Network-Based Analysis Of Time Course Gene Expression Data, Zhi Wei, Hongzhe Li

UPenn Biostatistics Working Papers

Microarray time course (MTC) gene expression data are commonly collected to study the dynamic nature of biological processes. One important problem is to identify genes that show different expression profiles over time and pathways that are perturbed during a given biological process. While methods are available to identify the genes with differential expression levels over time, there is a lack of methods that can incorporate the pathway information in identifying the pathways being modified/activated during a biological process. In this paper, we develop a hidden spatial-temporal Markov random field (hstMRF)-based method for identifying genes and subnetworks that are related to …

Role Of Actin Cytoskeletal Dynamics In Activation Of The Cyclic Amp Pathway And Hwp1 Gene Expression In Candida Albicans, Michael J. Wolyniak, Paula Sundstrom

Dartmouth Scholarship

Changes in gene expression during reversible bud-hypha transitions of the opportunistic fungal pathogen Candida albicans permit adaptation to environmental conditions that are critical for proliferation in host tissues. Our previous work has shown that the hypha-specific adhesin gene HWP1 is up-regulated by the cyclic AMP (cAMP) signaling pathway. However, little is known about the potential influences of determinants of cell morphology on HWP1 gene expression. We found that blocking hypha formation with cytochalasin A, which destabilizes actin filaments, and with latrunculin A, which sequesters actin monomers, led to a loss of HWP1 gene expression. In contrast, high levels of HWP1 …

Fully Codon-Optimized Luciferase Uncovers Novel Temperature Characteristics Of The Neurospora Clock, Van D. Gooch, Arun Mehra, Luis F. Larrondo, Julie Fox, Melissa Touroutoutoudis, Jennifer J. Loros, Jay C. Dunlap

Dartmouth Scholarship

We report the complete reconstruction of the firefly luciferase gene, fully codon optimized for expression in Neurospora crassa. This reporter enhances light output by approximately 4 log orders over that with previously available versions, now producing light that is visible to the naked eye and sufficient for monitoring the activities of many poorly expressed genes. Time lapse photography of strains growing in race tubes, in which the frq or eas/ccg-2 promoter is used to drive luciferase, shows the highest levels of luciferase activity near the growth front and newly formed conidial bands. Further, we have established a sorbose medium colony …

The Yeast Integral Membrane Protein Apq12 Potentially Links Membrane Dynamics To Assembly Of Nuclear Pore Complexes, John J. Scarcelli, Christin A. Hodge, Charles N. Cole

Dartmouth Scholarship

Although the structure and function of components of the nuclear pore complex (NPC) have been the focus of many studies, relatively little is known about NPC biogenesis. In this study, we report that Apq12 is required for efficient NPC biogenesis in Saccharomyces cerevisiae. Apq12 is an integral membrane protein of the nuclear envelope (NE) and endoplasmic reticulum. Cells lacking Apq12 are cold sensitive for growth, and a subset of their nucleoporins (Nups), those that are primarily components of the cytoplasmic fibrils of the NPC, mislocalize to the cytoplasm. APQ12 deletion also causes defects in NE morphology. In the absence of …

A Serratia Marcescens Oxyr Homolog Mediates Surface Attachment And Biofilm Formation, Robert M. Q. Shanks, Nicholas A. Stella, Eric J. Kalivoda, Megan R. Doe

Dartmouth Scholarship

OxyR is a conserved bacterial transcription factor with a regulatory role in oxidative stress response. From a genetic screen for genes that modulate biofilm formation in the opportunistic pathogen Serratia marcescens, mutations in an oxyR homolog and predicted fimbria structural genes were identified. S. marcescens oxyR mutants were severely impaired in biofilm formation, in contrast to the hyperbiofilm phenotype exhibited by oxyR mutants of Escherichia coli and Burkholderia pseudomallei. Further analysis revealed that OxyR plays a role in the primary attachment of cells to a surface. Similar to what is observed in other bacterial species, S. marcescens OxyR …

Sheep Updates 2007 - Part 2, Ian Mcfarland, Catherine Stockman, Anne Barnes, David Pethick, Jenny Davis, Brett Thompson, Ron Leng, Sally Pieruzzini, Elizabeth Jackson, Mohammed Quaddus, Nazrul Islam, John Stanton, Melanie Dowling

Sheep Updates

This session covers six papers from different authors:

CONCURRENT SESSIONS

FINISHING LAMB AND BEEF

1. Precision Feedlot Lamb, Ian McFarland, Department of Agriculture and Food, Western Australia

2. Feeding sheep under high heat load did not decrease intake of feedlot rations, Catherine Stockman, Department of Agriculture and Food, Western Australia & Murdoch University, Anne Barnes, Murdoch University David Pethick, Murdoch University

3. Taking the stress out of fifishing lambs and cattle - EasyFeed solutions, Jenny Davis, Brett Thomson, Milne AgriGroup, Welshpool WA, Ron Leng, Emeritus Professor, University of New England, Armidale, NSW

WOOL

4. DAFWA …

A Novel Ensemble Learning Method For De Novo Computational Identification Of Dna Binding Sites, Arijit Chakravarty, Jonathan M. Carlson, Radhika S. Khetani, Robert H H. Gross

Dartmouth Scholarship

Despite the diversity of motif representations and search algorithms, the de novo computational identification of transcription factor binding sites remains constrained by the limited accuracy of existing algorithms and the need for user-specified input parameters that describe the motif being sought.ResultsWe present a novel ensemble learning method, SCOPE, that is based on the assumption that transcription factor binding sites belong to one of three broad classes of motifs: non-degenerate, degenerate and gapped motifs. SCOPE employs a unified scoring metric to combine the results from three motif finding algorithms each aimed at the discovery of one of these classes of motifs. …

Assessment Of A Cgh-Based Genetic Instability, David A. Engler, Yiping Shen, J F. Gusella, Rebecca A. Betensky

Harvard University Biostatistics Working Paper Series

No abstract provided.

Survival Analysis With Large Dimensional Covariates: An Application In Microarray Studies, David A. Engler, Yi Li

Harvard University Biostatistics Working Paper Series

Use of microarray technology often leads to high-dimensional and low- sample size data settings. Over the past several years, a variety of novel approaches have been proposed for variable selection in this context. However, only a small number of these have been adapted for time-to-event data where censoring is present. Among standard variable selection methods shown both to have good predictive accuracy and to be computationally efficient is the elastic net penalization approach. In this paper, adaptation of the elastic net approach is presented for variable selection both under the Cox proportional hazards model and under an accelerated failure time …

Regulation Of Meiotic Cohesion And Chromosome Core Morphogenesis During Pachytene In Drosophila Oocytes, Radhika S. Khetani, Sharon E. Bickel

Dartmouth Scholarship

During meiosis, cohesion between sister chromatids is required for normal levels of homologous recombination, maintenance of chiasmata and accurate chromosome segregation during both divisions. In Drosophila, null mutations in the ord gene abolish meiotic cohesion, although how ORD protein promotes cohesion has remained elusive. We show that SMC subunits of the cohesin complex colocalize with ORD at centromeres of ovarian germ-line cells. In addition, cohesin SMCs and ORD are visible along the length of meiotic chromosomes during pachytene and remain associated with chromosome cores following DNase I digestion. In flies lacking ORD activity, cohesin SMCs fail to accumulate at oocyte …

Bifa, A Cyclic-Di-Gmp Phosphodiesterase, Inversely Regulates Biofilm Formation And Swarming Motility By Pseudomonas Aeruginosa Pa14, Sherry L. Kuchma, Kimberly M. Brothers, Judith H. Merritt, Nicole T. Liberati, Frederick M. Ausubel, George A. O'Toole

Dartmouth Scholarship

The intracellular signaling molecule, cyclic-di-GMP (c-di-GMP), has been shown to influence bacterial behaviors, including motility and biofilm formation. We report the identification and characterization of PA4367, a gene involved in regulating surface-associated behaviors in Pseudomonas aeruginosa. The PA4367 gene encodes a protein with an EAL domain, associated with c-di-GMP phosphodiesterase activity, as well as a GGDEF domain, which is associated with a c-di-GMP-synthesizing diguanylate cyclase activity. Deletion of the PA4367 gene results in a severe defect in swarming motility and a hyperbiofilm phenotype; thus, we designate this gene bifA, for biofilm formation. We show that BifA localizes to the inner …

Crystal Structure Of The Vibrio Cholerae Quorum-Sensing Regulatory Protein Hapr, Rukman S. De Silva, Gabriela Kovacikova, Wei Lin, Ronald K. Taylor, Karen Skorupski, F. Jon Kull

Dartmouth Scholarship

Quorum sensing in Vibrio cholerae involves signaling between two-component sensor protein kinases and the response regulator LuxO to control the expression of the master regulator HapR. HapR, in turn, plays a central role in regulating a number of important processes, such as virulence gene expression and biofilm formation. We have determined the crystal structure of HapR to 2.2-Å resolution. Its structure reveals a dimeric, two-domain molecule with an all-helical structure that is strongly conserved with members of the TetR family of transcriptional regulators. The N-terminal DNA-binding domain contains a helix-turn-helix DNA-binding motif and alteration of certain residues in this domain …

Coordinated Regulation Of Myc Trans-Activation Targets By Polycomb And The Trithorax Group Protein Ash1, Julie M. Goodliffe, Michael D. Cole, Eric Wieschaus

Dartmouth Scholarship

The Myc oncoprotein is a transcriptional regulator whose function is essential for normal development. Myc is capable of binding to 10% of the mammalian genome, and it is unclear how a developing embryo controls the DNA binding of its abundant Myc proteins in order to avoid Myc's potential for inducing tumorigenesis.To identify chromatin binding proteins with a potential role in controlling Myc activity, we established a genetic assay for dMyc activity in Drosophila. We conducted a genome-wide screen using this assay, and identified the Trithorax Group protein Ash1 as a modifier of dMyc activity. Ash1 is a histone methyltransferase known …

Population Genetics Of Black Bear (Ursus Americanus), Amanda K. Thibodeau

Honors College

DNA analysis is a ubiquitous tool to identify variation within populations. By using microsatellites, highly variable genetic loci distributed throughout the entire nuclear genome, genetic characteristics can be identified in the population. Genetic variation in the black bear, Ursus americanus, was characterized through samples gathered from the Maine population. In total, five loci were characterized for analysis. In order to aid in wildlife forensic cases, I examined genetic variations in black bears. The range of observed heterozygosity for the population sample was 0.729-0.871; the number of alleles per locus ranged from 7 to 15. Sampling the population and determining the …

Membrane Association And Multimerization Of Tcpt, The Cognate Atpase Ortholog Of The Vibrio Cholerae Toxin-Coregulated-Pilus Biogenesis Apparatus, Shital A. Tripathi, Ronald K. Taylor

Dartmouth Scholarship

The toxin-coregulated pilus (TCP) is one of the major virulence factors of Vibrio cholerae. Biogenesis of this type 4 pilus (Tfp) requires a number of structural components encoded by the tcp operon. TcpT, the cognate putative ATPase, is required for TCP biogenesis and all TCP-mediated functions. We studied the stability and localization of TcpT in cells containing in-frame deletions in each of the tcp genes. TcpT was detectable in each of the biogenesis mutants except the ΔtcpT strain. TcpT was localized to the inner membrane (IM) in a TcpR-dependent manner. TcpR is a predicted bitopic inner membrane protein …

Short Telomeres In Short-Lived Males: What Are The Molecular And Evolutionary Causes?, Stephanie Jemielity, Masayuki Kimura, Karen M. Parker, Joel D. Parker, Xiaojian Cao, Abraham Aviv, Laurent Keller

Joel D Parker

Telomere length regulation is an important aspect of cell maintenance in eukaryotes, since shortened telomeres can lead to a number of defects, including impaired cell division. Although telomere length is correlated with lifespan in some bird species, its possible role in aging and lifespan determination is still poorly understood. Here we investigate telomere dynamics (changes in telomere length and attrition rate) and telomerase activity in the ant Lasius niger, a species in which different groups of individuals have evolved extraordinarily different lifespans. We found that somatic tissues of the short-lived males had dramatically shorter telomeres than those of the much …

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 …

Inverse Regulation Of Biofilm Formation And Swarming Motility By Pseudomonas Aeruginosa Pa14, Nicky C. Caiazza, Judith H. Merritt, Kimberly M. Brothers, George A. O'Toole

Dartmouth Scholarship

We previously reported that SadB, a protein of unknown function, is required for an early step in biofilm formation by the opportunistic pathogen Pseudomonas aeruginosa. Here we report that a mutation in sadB also results in increased swarming compared to the wild-type strain. Our data are consistent with a model in which SadB inversely regulates biofilm formation and swarming motility via its ability both to modulate flagellar reversals in a viscosity-dependent fashion and to influence the production of the Pel exopolysaccharide. We also show that SadB is required to properly modulate flagellar reversal rates via chemotaxis cluster IV (CheIV cluster). …

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 …

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 …

2006 Lowbush Blueberry Project Reports, Kristi Crowe, Alfred A. Bushway, Rodney J. Bushway, Vivian Ch Wu, Brian Perkins, Pam Small, Darrell Donahue, Frank Drummond, Judith Collins, Floyd Dowell, Dorothy J. Klimis-Zacas, Mary Ellen Camire, Gordon Starr, David E. Yarborough, S Hoffmann, Daniel J. Bell, Seanna L. Annis, Tamara Levitsky, Loretta Kreider, Kristen Mcgovern, K Frost, John M. Smagula, Qian Wang, Kerry Fl Guiseppe

Wild Blueberry Research Reports

The 2006 edition of the Lowbush Blueberry Project Reports was prepared for the Wild Blueberry Commission of Maine and the Wild Blueberry Advisory Committee by researchers at the University of Maine, Orono. Projects in this report include:

1. Evaluation of Emerging Disinfection Technologies for Wild Blueberry Processing

2. Incorporation of wild blueberry puree into a soy-based burger and its effect on sensory and chemical properties of the broiled burgers

3. Infestation Detection using NIRS

4. Mechanism of Action through which Wild Blueberries affect Arterial Functional Properties in Normotensive and Spontaneously Hypertensive Rats

5. Practical Microbial Control Approach for Wild Blueberries …

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 …