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2006

Genetics and Genomics

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Articles 1 - 30 of 211

Full-Text Articles in Life Sciences

Analysis Of Genetic Mutations In The 7a7b Open Reading Frame Of Coronavirus Of Cheetahs (Acinonyx Jubatus), Melissa Kennedy, E Moore, R Wilkes, S Citino, Stephen Kania Jan 2012

Analysis Of Genetic Mutations In The 7a7b Open Reading Frame Of Coronavirus Of Cheetahs (Acinonyx Jubatus), Melissa Kennedy, E Moore, R Wilkes, S Citino, Stephen Kania

Melissa A. Kennedy

OBJECTIVE: To analyze the 7a7b genes of the feline coronavirus (FCoV) of cheetahs, which are believed to play a role in virulence of this virus. SAMPLE POPULATION: Biologic samples collected during a 4-year period from 5 cheetahs at the same institution and at 1 time point from 4 cheetahs at different institutions. PROCEDURES: Samples were first screened for FCoV via a reverse transcription-PCR procedure involving primers that encompassed the 3'-untranslated region. Samples that yielded positive assay results were analyzed by use of primers that targeted the 7a7b open reading frames. The nucleotide sequences of the 7a7b amplification products were ...


Pulmonary Fibroblasts Stimulate The Proliferation Of Cell Lines From Human Lung Adenocarcinomas, Maria Cekanova, T Masi, Howard Plummer, M Majidi, P Fedorocko, Hildegard Schuller Aug 2011

Pulmonary Fibroblasts Stimulate The Proliferation Of Cell Lines From Human Lung Adenocarcinomas, Maria Cekanova, T Masi, Howard Plummer, M Majidi, P Fedorocko, Hildegard Schuller

Howard K. Plummer III

Human lung cancer cell lines are widely used to test anticancer drugs. These in-vitro tests, however, preclude the detection of responses to paracrine factors from surrounding stroma. We have cocultured pulmonary fibroblasts CCD-19Lu, from a healthy donor, or HLF-A, from a patient with epidermoid carcinoma of the lung, with two human pulmonary adenocarcinoma cell lines to test the hypothesis that the fibroblasts stimulate the growth of the tumor cells. Both fibroblast cell lines significantly increased the proliferation of the pulmonary adenocarcinoma cell lines in 3-(4,5-dimethylthiazol-2yl)-2,5-diphenyl tetrazolium bromide assays, with HLF-A fibroblasts yielding the most pronounced responses ...


Evaluation Of Canine Serum For The Presence Of Anti-Retinal Antibodies In Sudden Acquired Retinal Dengeneration Syndrome, R Keller, Stephen Kania, Diane Hendrix, Daniel Ward, K Abrams May 2011

Evaluation Of Canine Serum For The Presence Of Anti-Retinal Antibodies In Sudden Acquired Retinal Dengeneration Syndrome, R Keller, Stephen Kania, Diane Hendrix, Daniel Ward, K Abrams

Diane Hendrix

Objective: To determine the presence of serum antiretinal antibodies in sudden acquired retinal degeneration syndrome (SARDS) affected dogs and the size of the antigen to which these antibodies bind via the use of enzyme-linked immunosorbent assay (ELISA) and Western blot immunoassays. Animals studied: Serum was collected from 13 dogs affected by SARDS and five dogs with normal ocular examinations. Procedures: All serum samples were subjected to ELISA with saline-soluble canine retinal tissue and Western blot analyses with SDS solubilized normal canine retinal tissue as the antigen. Antirecoverin (23 kDa) and antiheat shock cognate (65 kDa) antibodies were used as positive ...


Evaluation Of Canine Serum For The Presence Of Anti-Retinal Antibodies In Sudden Acquired Retinal Dengeneration Syndrome, R Keller, Stephen Kania, Diane Hendrix, Daniel Ward, K Abrams Feb 2011

Evaluation Of Canine Serum For The Presence Of Anti-Retinal Antibodies In Sudden Acquired Retinal Dengeneration Syndrome, R Keller, Stephen Kania, Diane Hendrix, Daniel Ward, K Abrams

Daniel A. Ward

Objective: To determine the presence of serum antiretinal antibodies in sudden acquired retinal degeneration syndrome (SARDS) affected dogs and the size of the antigen to which these antibodies bind via the use of enzyme-linked immunosorbent assay (ELISA) and Western blot immunoassays. Animals studied: Serum was collected from 13 dogs affected by SARDS and five dogs with normal ocular examinations. Procedures: All serum samples were subjected to ELISA with saline-soluble canine retinal tissue and Western blot analyses with SDS solubilized normal canine retinal tissue as the antigen. Antirecoverin (23 kDa) and antiheat shock cognate (65 kDa) antibodies were used as positive ...


The Plant Structure Ontology, A Unified Vocabulary Of Anatomy And Morphology Of A Flowering Plant, Katica Ilic, Elizabeth A. Kellogg, Pankaj Jaiswal, Felipe Zapata, Peter F. Stevens, Leszek P. Vincent, Shulamit Avraham, Leonore Reiser, Anuradha Pujar, Martin M. Sachs, Noah T. Whitman, Susan R. Mccouch, Mary L. Schaeffer, Doreen H. Ware, Lincoln D. Stein, Seung Y. Rhee Dec 2006

The Plant Structure Ontology, A Unified Vocabulary Of Anatomy And Morphology Of A Flowering Plant, Katica Ilic, Elizabeth A. Kellogg, Pankaj Jaiswal, Felipe Zapata, Peter F. Stevens, Leszek P. Vincent, Shulamit Avraham, Leonore Reiser, Anuradha Pujar, Martin M. Sachs, Noah T. Whitman, Susan R. Mccouch, Mary L. Schaeffer, Doreen H. Ware, Lincoln D. Stein, Seung Y. Rhee

Peter Stevens

Formal description of plant phenotypes and standardized annotation of gene expression and protein localization data require uniform terminology that accurately describes plant anatomy and morphology. This facilitates cross species comparative studies and quantitative comparison of phenotypes and expression patterns. A major drawback is variable terminology that is used to describe plant anatomy and morphology in publications and genomic databases for different species. The same terms are sometimes applied to different plant structures in different taxonomic groups. Conversely, similar structures are named by their species-specific terms. To address this problem, we created the Plant Structure Ontology (PSO), the first generic ontological ...


Activated Checkpoint Kinase 2 Provides A Survival Signal For Tumor Cells, Jagadish C. Ghosh, Takehiko Dohi, Christopher M. Raskett, Timothy F. Kowalik, Dario C. Altieri Dec 2006

Activated Checkpoint Kinase 2 Provides A Survival Signal For Tumor Cells, Jagadish C. Ghosh, Takehiko Dohi, Christopher M. Raskett, Timothy F. Kowalik, Dario C. Altieri

Open Access Articles

Tumor cells often become resistant to DNA damage-based therapy; however, the underlying mechanisms are not yet understood. Here, we show that tumor cells exposed to DNA damage counteract cell death by releasing the antiapoptotic protein, survivin, from mitochondria. This is independent of p53, and requires activated checkpoint kinase 2 (Chk2), a putative tumor suppressor. Molecular or genetic targeting of Chk2 prevents the release of survivin from mitochondria, enhances DNA damage-induced tumor cell apoptosis, and inhibits the growth of resistant in vivo tumors. Therefore, activated Chk2 circumvents its own tumor-suppressive functions by promoting tumor cell survival. Inhibiting Chk2 in combination with ...


Caenorhabditis Briggsae Methods, Scott Everet Baird, Helen M. Chamberlin Dec 2006

Caenorhabditis Briggsae Methods, Scott Everet Baird, Helen M. Chamberlin

Biological Sciences Faculty Publications

Caenorhabditis briggsae is being developed in parallel to C. elegans as a model system, primarily for the study of evolution. Like C. elegans, C. briggsae is a protandrous hermaphrodite and like C. elegans, its genome has been sequenced. From this point, these two model systems diverge. The development, behavior, and physiology of C. elegans have been characterized through tens of thousands of genetic and molecular studies. Genetic and molecular characterizations of C. briggsae are relatively few. Experimental resources in C. elegans include a high density recombination map that is well integrated with the genome sequence. The C. briggsae recombination map ...


Structure Of The Yeast Histone H3-Asf1 Interaction: Implications For Chaperone Mechanism, Species-Specific Interactions, And Epigenetics, Andrew J. Antczak, Toshiaki Tsubota, Paul D. Kaufman, James M. Berger Dec 2006

Structure Of The Yeast Histone H3-Asf1 Interaction: Implications For Chaperone Mechanism, Species-Specific Interactions, And Epigenetics, Andrew J. Antczak, Toshiaki Tsubota, Paul D. Kaufman, James M. Berger

Program in Gene Function and Expression Publications and Presentations

BACKGROUND: The histone H3/H4 chaperone Asf1 (anti-silencing function 1) is required for the establishment and maintenance of proper chromatin structure, as well as for genome stability in eukaryotes. Asf1 participates in both DNA replication-coupled (RC) and replication-independent (RI) histone deposition reactions in vitro and interacts with complexes responsible for both pathways in vivo. Asf1 is known to directly bind histone H3, however, high-resolution structural information about the geometry of this interaction was previously unknown. RESULTS: Here we report the structure of a histone/histone chaperone interaction. We have solved the 2.2 A crystal structure of the conserved N-terminal ...


Cbfbeta Reduces Cbfbeta-Smmhc-Associated Acute Myeloid Leukemia In Mice, Susan Ann Heilman, Ya-Huei Kuo, Chantal S. Goudswaard, Peter J. Valk, Lucio H. Castilla Dec 2006

Cbfbeta Reduces Cbfbeta-Smmhc-Associated Acute Myeloid Leukemia In Mice, Susan Ann Heilman, Ya-Huei Kuo, Chantal S. Goudswaard, Peter J. Valk, Lucio H. Castilla

Open Access Articles

The gene encoding for core-binding factor beta (CBFbeta) is altered in acute myeloid leukemia samples with an inversion in chromosome 16, expressing the fusion protein CBFbeta-SMMHC. Previous studies have shown that this oncoprotein interferes with hematopoietic differentiation and proliferation and participates in leukemia development. In this study, we provide evidence that Cbfbeta modulates the oncogenic function of this fusion protein. We show that Cbfbeta plays an important role in proliferation of hematopoietic progenitors expressing Cbfbeta-SMMHC in vitro. In addition, Cbfbeta-SMMHC-mediated leukemia development is accelerated in the absence of Cbfbeta. These results indicate that the balance between Cbfbeta and Cbfbeta-SMMHC directly ...


Use Of Hidden Markov Models For Qtl Mapping, Karl W. Broman Dec 2006

Use Of Hidden Markov Models For Qtl Mapping, Karl W. Broman

Johns Hopkins University, Dept. of Biostatistics Working Papers

An important aspect of the QTL mapping problem is the treatment of missing genotype data. If complete genotype data were available, QTL mapping would reduce to the problem of model selection in linear regression. However, in the consideration of loci in the intervals between the available genetic markers, genotype data is inherently missing. Even at the typed genetic markers, genotype data is seldom complete, as a result of failures in the genotyping assays or for the sake of economy (for example, in the case of selective genotyping, where only individuals with extreme phenotypes are genotyped). We discuss the use of ...


Genomeblast: A Web Tool For Small Genome Comparison, Guoqing Lu, Liying Jiang, Resa M. K. Helikar, Thaine W. Rowley, Luwen Zhang, Xianfeng Chen, Etsuko N. Moriyama Dec 2006

Genomeblast: A Web Tool For Small Genome Comparison, Guoqing Lu, Liying Jiang, Resa M. K. Helikar, Thaine W. Rowley, Luwen Zhang, Xianfeng Chen, Etsuko N. Moriyama

Biology Faculty Publications

Background: Comparative genomics has become an essential approach for identifying homologous gene candidates and their functions, and for studying genome evolution. There are many tools available for genome comparisons. Unfortunately, most of them are not applicable for the identification of unique genes and the inference of phylogenetic relationships in a given set of genomes.

Results: GenomeBlast is a Web tool developed for comparative analysis of multiple small genomes. A new parameter called "coverage" was introduced and used along with sequence identity to evaluate global similarity between genes. With GenomeBlast, the following results can be obtained: (1) unique genes in each ...


Review Of "Plant Exploration For Longwood Gardens" By T. Aniśko, Nicholas J. Kaplinsky Dec 2006

Review Of "Plant Exploration For Longwood Gardens" By T. Aniśko, Nicholas J. Kaplinsky

Biology Faculty Works

No abstract provided.


Analysis Of Bulked And Redundant Accessions Of Brassica Germplasm Using Assignment Tests Of Microsatellite Markers, Von Mark V. Cruz, John D. Nason, Richard Luhman, Laura F. Marek, Randy C. Shoemaker, E. Charles Brummer, Candice A. C. Gardner Dec 2006

Analysis Of Bulked And Redundant Accessions Of Brassica Germplasm Using Assignment Tests Of Microsatellite Markers, Von Mark V. Cruz, John D. Nason, Richard Luhman, Laura F. Marek, Randy C. Shoemaker, E. Charles Brummer, Candice A. C. Gardner

Ecology, Evolution and Organismal Biology Publications

This study was conducted to determine if Brassica germplasm bulks created and maintained by the USDA-ARS North Central Plant Introduction Station (NCRPIS) were made with genetically indistinguishable component accessions and to examine newly identified putative duplicate accessions to determine if they can be bulked. Using ten microsatellite primer pairs, we genotyped two bulks of B. rapa L. ssp. dichotoma (Roxb.) Hanelt comprising four accessions and three bulks of B. rapa L. ssp. trilocularis (Roxb.) Hanelt comprising fourteen accessions, as well as four pairs of putatively duplicate accessions of B.␣napus L. Assignment tests on ten individual plants per accession were ...


A Sex-Linked Allele, Autosomal Modifiers And Temperature-Dependence Appear To Regulate Melanism In Male Mosquitofish (Gambusia Holbrooki), Lisa Horth Dec 2006

A Sex-Linked Allele, Autosomal Modifiers And Temperature-Dependence Appear To Regulate Melanism In Male Mosquitofish (Gambusia Holbrooki), Lisa Horth

Biological Sciences Faculty Publications

About 1% of male mosquitofish (Gambusia holbrooki) express melanic (mottled-black) body coloration, which differs dramatically from the wild-type, silvery-gray coloration. Here, I report on the genetic inheritance pattern of melanic coloration, which indicates Y-linkage, and at least one autosomal modifier. Phenotypic expression of melanism is also affected by temperature. Expression is constitutive ( temperature insensitive) in some populations, inducible ( temperature sensitive) in others. Constitutive and inducible expression occur among geographically proximal populations. However, males from any single population demonstrate the same constitutive or inducible expression pattern as one another. The F1 males from inter-population crosses demonstrate temperature-related expression patterns like their ...


Wild And Aquaculture Populations Of The Eastern Oyster Compared Using Microsatellites, J Carlsson, Cl Morrison, Ks Reece Dec 2006

Wild And Aquaculture Populations Of The Eastern Oyster Compared Using Microsatellites, J Carlsson, Cl Morrison, Ks Reece

VIMS Articles

Five new microsatellite markers were developed for the eastern oyster (Crassostrea virginica), and allelic variability was compared between a wild Chesapeake Bay population (James River) and a hatchery strain (DEBY (TM)). All loci amplified readily and demonstrated allelic variability with the number of alleles ranging from 16 to 36 in the wild population and from 11 to 19 in the DEBY (TM) strain. Average observed and expected heterozygosities were estimated at 0.66 and 0.80 in the hatchery sample. The corresponding estimates were 0.91 and 0.75 in the wild sample. Results indicated lower genetic variability in the ...


Semiparametric Regression Of Multi-Dimensional Genetic Pathway Data: Least Squares Kernel Machines And Linear Mixed Models, Dawei Liu, Xihong Lin, Debashis Ghosh Nov 2006

Semiparametric Regression Of Multi-Dimensional Genetic Pathway Data: Least Squares Kernel Machines And Linear Mixed Models, Dawei Liu, Xihong Lin, Debashis Ghosh

Harvard University Biostatistics Working Paper Series

No abstract provided.


Limited Functional Redundancy And Oscillation Of Cyclins In Multinucleated Ashbya Gossypii Fungal Cells, A. Katrin Hungerbuehler, Peter Philippsen, Amy S. Gladfelter Nov 2006

Limited Functional Redundancy And Oscillation Of Cyclins In Multinucleated Ashbya Gossypii Fungal Cells, A. Katrin Hungerbuehler, Peter Philippsen, Amy S. Gladfelter

Open Dartmouth: Faculty Open Access Scholarship

Cyclin protein behavior has not been systematically investigated in multinucleated cells with asynchronous mitoses. Cyclins are canonical oscillating cell cycle proteins, but it is unclear how fluctuating protein gradients can be established in multinucleated cells where nuclei in different stages of the division cycle share the cytoplasm. Previous work in A. gossypii, a filamentous fungus in which nuclei divide asynchronously in a common cytoplasm, demonstrated that one G1 and one B-type cyclin do not fluctuate in abundance across the division cycle. We have undertaken a comprehensive analysis of all G1 and B-type cyclins in A. gossypii to determine whether any ...


Trefoil Family Factor 2 Is Expressed In Murine Gastric And Immune Cells And Controls Both Gastrointestinal Inflammation And Systemic Immune Responses, Evelyn A. Kurt-Jones, Lucheng Cao, Frantisek Sandor, Arlin B. Rogers, Mark T. Whary, Prashant R. Nambiar, Anna M. Cerny, Glennice N. Bowen, Jing Yan, Shigeo Takaishi, Alfred L. Chi, George W. Reed, Jeanmarie Houghton, James G. Fox, Timothy C. Wang Nov 2006

Trefoil Family Factor 2 Is Expressed In Murine Gastric And Immune Cells And Controls Both Gastrointestinal Inflammation And Systemic Immune Responses, Evelyn A. Kurt-Jones, Lucheng Cao, Frantisek Sandor, Arlin B. Rogers, Mark T. Whary, Prashant R. Nambiar, Anna M. Cerny, Glennice N. Bowen, Jing Yan, Shigeo Takaishi, Alfred L. Chi, George W. Reed, Jeanmarie Houghton, James G. Fox, Timothy C. Wang

Open Access Articles

Trefoil family factor 2 (TFF2), also known as spasmolytic peptide, is a low-molecular-weight protein that is upregulated in gastric tissues infected with Helicobacter or having other inflammatory conditions, but a precise function is yet to be elucidated. The role of TFF2 in the development of gastritis, colitis, and inflammatory cytokine responses was examined both in vivo and in vitro using wild-type and TFF2 knockout mice. TFF2 knockout and wild-type mice were infected with Helicobacter felis (H. felis) to induce gastritis. Colitis was induced in TFF2 knockout and wild-type mice by administering dextran sodium sulfate (DSS) in drinking water. Histopathology, clinical ...


Multiple Testing With An Empirical Alternative Hypothesis, James E. Signorovitch Nov 2006

Multiple Testing With An Empirical Alternative Hypothesis, James E. Signorovitch

Harvard University Biostatistics Working Paper Series

An optimal multiple testing procedure is identified for linear hypotheses under the general linear model, maximizing the expected number of false null hypotheses rejected at any significance level. The optimal procedure depends on the unknown data-generating distribution, but can be consistently estimated. Drawing information together across many hypotheses, the estimated optimal procedure provides an empirical alternative hypothesis by adapting to underlying patterns of departure from the null. Proposed multiple testing procedures based on the empirical alternative are evaluated through simulations and an application to gene expression microarray data. Compared to a standard multiple testing procedure, it is not unusual for ...


Penalized Likelihood And Bayesian Methods For Sparse Contingency Tables: An Analysis Of Alternative Splicing In Full-Length Cdna Libraries, Corinne Dahinden, Giovanni Parmigiani, Mark C. Emerick, Peter Buhlmann Nov 2006

Penalized Likelihood And Bayesian Methods For Sparse Contingency Tables: An Analysis Of Alternative Splicing In Full-Length Cdna Libraries, Corinne Dahinden, Giovanni Parmigiani, Mark C. Emerick, Peter Buhlmann

Johns Hopkins University, Dept. of Biostatistics Working Papers

We develop methods to perform model selection and parameter estimation in loglinear models for the analysis of sparse contingency tables to study the interaction of two or more factors. Typically, datasets arising from so-called full-length cDNA libraries, in the context of alternatively spliced genes, lead to such sparse contingency tables. Maximum Likelihood estimation of log-linear model coefficients fails to work because of zero cell entries. Therefore new methods are required to estimate the coefficients and to perform model selection. Our suggestions include computationally efficient penalization (Lasso-type) approaches as well as Bayesian methods using MCMC. We compare these procedures in a ...


Prepms: Tof Ms Data Graphical Preprocessing Tool, Yuliya V. Karpievitch, Elizabeth G. Hill, Adam J. Smolka, Jeffrey S. Morris, Kevin R. Coombes, Keith A. Baggerly, Jonas S. Almeida Nov 2006

Prepms: Tof Ms Data Graphical Preprocessing Tool, Yuliya V. Karpievitch, Elizabeth G. Hill, Adam J. Smolka, Jeffrey S. Morris, Kevin R. Coombes, Keith A. Baggerly, Jonas S. Almeida

Jeffrey S. Morris

We introduce a simple-to-use graphical tool that enables researchers to easily prepare time-of-flight mass spectrometry data for analysis. For ease of use, the graphical executable provides default parameter settings experimentally determined to work well in most situations. These values can be changed by the user if desired. PrepMS is a stand-alone application made freely available (open source), and is under the General Public License (GPL). Its graphical user interface, default parameter settings, and display plots allow PrepMS to be used effectively for data preprocessing, peak detection, and visual data quality assessment.


Complete Dna Sequence, Comparative Genomics, And Prevalence Of An Inchi2 Plasmid Occurring Among Extraintestinal Pathogenic Escherichia Coli Isolates, Timothy J. Johnson, Yvonne Wannemuehler, Jennifer A. Scaccianoce, Sara J. Johnson, Lisa K. Nolan Nov 2006

Complete Dna Sequence, Comparative Genomics, And Prevalence Of An Inchi2 Plasmid Occurring Among Extraintestinal Pathogenic Escherichia Coli Isolates, Timothy J. Johnson, Yvonne Wannemuehler, Jennifer A. Scaccianoce, Sara J. Johnson, Lisa K. Nolan

Veterinary Microbiology and Preventive Medicine Publications

We have sequenced a large plasmid that occurs among avian pathogenicEscherichia coli isolates. This plasmid, pAPEC-O1-R, is a 241,387-bp IncHI2 plasmid which is cotransmissible via bacterial conjugation with a ColBM virulence plasmid, encodes resistance to eight antimicrobial agents, and appears to occur at low rates among extraintestinal E. coli isolates.


The Fat Cadherin Acts Through The Hippo Tumor-Suppressor Pathway To Regulate Tissue Size, Maria Willecke, Fisun Hamaratoglu, Madhuri Kango-Singh, Ryan Udan, Chiao-Lin Chen, Chunyao Tao, Xinwei Zhang, Georg Halder Nov 2006

The Fat Cadherin Acts Through The Hippo Tumor-Suppressor Pathway To Regulate Tissue Size, Maria Willecke, Fisun Hamaratoglu, Madhuri Kango-Singh, Ryan Udan, Chiao-Lin Chen, Chunyao Tao, Xinwei Zhang, Georg Halder

Biology Faculty Publications

Background: The Hippo tumor-suppressor pathway has emerged as a key signaling pathway that controls tissue size in Drosophila. Merlin, the Drosophila homolog of the human Neurofibromatosis type-2 (NF2) tumor-suppressor gene, and the related protein Expanded are the most upstream components of the Hippo pathway identified so far. However, components acting upstream of Expanded and Merlin, such as transmembrane receptors, have not yet been identified.

Results: Here, we report that the protocadherin Fat acts as an upstream component in the Hippo pathway. Fat is a known tumor-suppressor gene in Drosophila, and fat mutants have severely overgrown imaginal discs. We found that ...


Lobe And Serrate Are Required For Cell Survival During Early Eye Development In Drosophila, Amit Singh, Xiao Shi, Kwang-Wook Choi Nov 2006

Lobe And Serrate Are Required For Cell Survival During Early Eye Development In Drosophila, Amit Singh, Xiao Shi, Kwang-Wook Choi

Biology Faculty Publications

Organogenesis involves an initial surge of cell proliferation, leading to differentiation. This is followed by cell death in order to remove extra cells. During early development, there is little or no cell death. However, there is a lack of information concerning the genes required for survival during the early cell-proliferation phase. Here, we show that Lobe (L) and the Notch (N) ligand Serrate (Ser), which are both involved in ventral eye growth, are required for cell survival in the early eye disc. We observed that the loss-of-ventral-eye phenotype in L or Ser mutants is due to the induction of cell ...


Genetic Analysis Of White Marlin (Tetrapturus Albidus) Stock Structure, Je Graves, Jr Mcdowell Nov 2006

Genetic Analysis Of White Marlin (Tetrapturus Albidus) Stock Structure, Je Graves, Jr Mcdowell

VIMS Articles

The genetic basis of stock structure of white marlin (Tetrapturus albidus Poey, 1860) was inferred from analyses of five tetranucleotide repeat microsatellite loci (n = 214) and the mitochondrial (mt)DNA control region (n = 99) of white marlin from four geographic regions in the Atlantic Ocean. Considerable genetic variation was present in all collections for all molecular markers. Analysis of replicate collections taken in different years from three regions revealed no significant differences in the distribution of allele frequencies among years within regions. The value of global F-statistics for both multilocus microsatellite data and mtDNA control region sequences approached significance (0 ...


Validity, Identification, And Distribution Of The Roundscale Spearfish, Tetrapturus Georgii (Teleostei: Istiophoridae): Morphological And Molecular Evidence, Mahmood S. Shivji, Jennifer E. Magnussen, Lawrence R. Beerkircher, George Hinteregger, Dennis W. Lee, Joseph E. Serafy, Eric D. Prince Nov 2006

Validity, Identification, And Distribution Of The Roundscale Spearfish, Tetrapturus Georgii (Teleostei: Istiophoridae): Morphological And Molecular Evidence, Mahmood S. Shivji, Jennifer E. Magnussen, Lawrence R. Beerkircher, George Hinteregger, Dennis W. Lee, Joseph E. Serafy, Eric D. Prince

Marine & Environmental Sciences Faculty Articles

The roundscale spearfish, Tetrapturus georgii Lowe, 1840, is known only from four specimens from the Mediterranean and eastern North Atlantic. Additional specimens have not been identified since 1961, making the validity and distribution of this species unclear. Analysis of 16 billfish specimens from the western North Atlantic on the basis of scale morphology, anus position, and mitochondrial DNA confirms the validity of this species and extends its distribution. Mid-lateral scales are soft, notably rounded anteriorly, and bear 2–3 points distinct from those of the sympatric longbill spearfish (Tetrapturus pfluegeri Robins and de Sylva, 1963) and white marlin (Tetrapturus albidus ...


The Allantois And Chorion, When Isolated Before Circulation Or Chorio-Allantoic Fusion, Have Hematopoietic Potential, Brandon M. Zeigler, Daisuke Sugiyama, Michael Chen, Yalin Guo, K. M. Downs, N. A. Speck Nov 2006

The Allantois And Chorion, When Isolated Before Circulation Or Chorio-Allantoic Fusion, Have Hematopoietic Potential, Brandon M. Zeigler, Daisuke Sugiyama, Michael Chen, Yalin Guo, K. M. Downs, N. A. Speck

Open Dartmouth: Faculty Open Access Scholarship

The chorio-allantoic placenta forms through the fusion of the allantois (progenitor tissue of the umbilical cord), with the chorionic plate. The murine placenta contains high levels of hematopoietic stem cells, and is therefore a stem cell niche. However, it is not known whether the placenta is a site of hematopoietic cell emergence, or whether hematopoietic cells originate from other sites in the conceptus and then colonize the placenta. Here, we show that the allantois and chorion, isolated prior to the establishment of circulation, have the potential to give rise to myeloid and definitive erythroid cells following explant culture. We further ...


Nonparametric Pathway-Based Regression Models For Analysis Of Genomic Data, Zhi Wei, Hongzhe Li Oct 2006

Nonparametric Pathway-Based Regression Models For Analysis Of Genomic Data, Zhi Wei, Hongzhe Li

Hongzhe Li

High-throughout genomic data provide an opportunity for identifying pathways and genes that are related to various clinical phenotypes. Besides these genomic data, another valuable source of data is the biological knowledge about genes and pathways that might be related to the phenotypes of many complex diseases. Databases of such knowledge are often called the metadata. In microarray data analysis, such metadata are currently explored in post hoc ways by gene set enrichment analysis but have hardly been utilized in the modeling step. We propose to develop and evaluate a pathway-based gradient descent boosting procedure for nonparametric pathways-based regression(NPR) analysis ...


Group Additive Regression Models For Genomic Data Analysis, Yihui Luan, Hongzhe Li Oct 2006

Group Additive Regression Models For Genomic Data Analysis, Yihui Luan, Hongzhe Li

Hongzhe Li

One important problem in genomic research is to identify genomic features such as gene expression data or DNA single nucleotide polymorphisms (SNPs) that are related to clinical phenotypes. Often these genomic data can be naturally divided into biologically meaningful groups such as genes belonging to the same pathways or SNPs within genes. In this paper, we propose group additive regression models and a group gradient descent boosting procedure for identifying groups of genomic features that are related to clinical phenotypes. Our simulation results show that by dividing the variables into appropriate groups, we can obtain better identification of the group ...


Estimating Genome-Wide Copy Number Using Allele Specific Mixture Models, Wenyi Wang , Benilton Caravalho, Nate Miller, Jonathan Pevsner, Aravinda Chakravarti, Rafael A. Irizarry Oct 2006

Estimating Genome-Wide Copy Number Using Allele Specific Mixture Models, Wenyi Wang , Benilton Caravalho, Nate Miller, Jonathan Pevsner, Aravinda Chakravarti, Rafael A. Irizarry

Johns Hopkins University, Dept. of Biostatistics Working Papers

Genomic changes such as copy number alterations are thought to be one of the major underlying causes of human phenotypic variation among normal and disease subjects [23,11,25,26,5,4,7,18]. These include chromosomal regions with so-called copy number alterations: instead of the expected two copies, a section of the chromosome for a particular individual may have zero copies (homozygous deletion), one copy (hemizygous deletions), or more than two copies (amplifications). The canonical example is Down syndrome which is caused by an extra copy of chromosome 21. Identification of such abnormalities in smaller regions has been of ...