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2004

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Genetics and Genomics

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Articles 1 - 30 of 130

Full-Text Articles in Life Sciences

Chromosomal Duplications And Cointegrates Generated By The Bacteriophage Lamdba Red System In Escherichia Coli K-12, Anthony R. Poteete, Anita C. Fenton, Ashwini Nadkarni Dec 2004

Chromosomal Duplications And Cointegrates Generated By The Bacteriophage Lamdba Red System In Escherichia Coli K-12, Anthony R. Poteete, Anita C. Fenton, Ashwini Nadkarni

Open Access Articles

BACKGROUND: An Escherichia coli strain in which RecBCD has been genetically replaced by the bacteriophage lambda Red system engages in efficient recombination between its chromosome and linear double-stranded DNA species sharing sequences with the chromosome. Previous studies of this experimental system have focused on a gene replacement-type event, in which a 3.5 kbp dsDNA consisting of the cat gene and flanking lac operon sequences recombines with the E. coli chromosome to generate a chloramphenicol-resistant Lac- recombinant. The dsDNA was delivered into the cell as part of the chromosome of a non-replicating lambda vector, from which it was released by ...


The Histone Fold Domain Of Cse4 Is Sufficient For Cen Targeting And Propagation Of Active Centromeres In Budding Yeast, Lisa Morey, Kelly Barnes, Yinhuai Chen, Molly Fitzgerald-Hayes, Richard E. Baker Dec 2004

The Histone Fold Domain Of Cse4 Is Sufficient For Cen Targeting And Propagation Of Active Centromeres In Budding Yeast, Lisa Morey, Kelly Barnes, Yinhuai Chen, Molly Fitzgerald-Hayes, Richard E. Baker

Open Access Articles

Centromere-specific H3-like proteins (CenH3s) are conserved across the eukaryotic kingdom and are required for packaging centromere DNA into a specialized chromatin structure required for kinetochore assembly. Cse4 is the CenH3 protein of the budding yeast Saccharomyces cerevisiae. Like all CenH3 proteins, Cse4 consists of a conserved histone fold domain (HFD) and a divergent N terminus (NT). The Cse4 NT contains an essential domain designated END (for essential N-terminal domain); deletion of END is lethal. To investigate the role of the Cse4 NT in centromere targeting, a series of deletion alleles (cse4DeltaNT) were analyzed. No part of the Cse4 NT was ...


Plag1 And Plagl2 Are Oncogenes That Induce Acute Myeloid Leukemia In Cooperation With Cbfb-Myh11, Sean F. Landrette, Ya-Huei Kuo, Karen Hensen, Sahar Barjesteh Van Waalwijk Van Doorn-Khosrovani, Paola N. Perrat, Wim J. M. Van De Ven, Ruud Delwel, Lucio H. Castilla Dec 2004

Plag1 And Plagl2 Are Oncogenes That Induce Acute Myeloid Leukemia In Cooperation With Cbfb-Myh11, Sean F. Landrette, Ya-Huei Kuo, Karen Hensen, Sahar Barjesteh Van Waalwijk Van Doorn-Khosrovani, Paola N. Perrat, Wim J. M. Van De Ven, Ruud Delwel, Lucio H. Castilla

Open Access Articles

Recurrent chromosomal rearrangements are associated with the development of acute myeloid leukemia (AML). The frequent inversion of chromosome 16 creates the CBFB-MYH11 fusion gene that encodes the fusion protein CBFbeta-SMMHC. This fusion protein inhibits the core-binding factor (CBF), resulting in a block of hematopoietic differentiation, and induces leukemia upon the acquisition of additional mutations. A recent genetic screen identified Plag1 and Plagl2 as CBF beta-SMMHC candidate cooperating proteins. In this study, we demonstrate that Plag1 and Plagl2 independently cooperate with CBF beta-SMMHC in vivo to efficiently trigger leukemia with short latency in the mouse. In addition, Plag1 and Plagl2 increased ...


Lhx9 And Lhx9alpha: Differential Biochemical Properties And Effects On Neuronal Differentiation, Bertrand Molle, Stephane Pere, Vieri Failli, Ingolf Bach, Sylvie Retaux Dec 2004

Lhx9 And Lhx9alpha: Differential Biochemical Properties And Effects On Neuronal Differentiation, Bertrand Molle, Stephane Pere, Vieri Failli, Ingolf Bach, Sylvie Retaux

Program in Gene Function and Expression Publications and Presentations

The Lhx9 LIM-homeodomain transcription factor and its truncated isoform Lhx9alpha are generated by alternative splicing of the Lhx9 gene. Here we investigated the differential functional properties of these two isoforms. Lhx9alpha, which lacks parts of the homeodomain, was unable to bind DNA in EMSA experiments, but was able to associate with CLIM cofactors in GST pull-down assays. In transfection experiments in PC12 cells, Lhx9alpha fusion constructs systematically showed a nuclear localization, as opposed to Lhx9 fusion constructs, which also localized to the cytoplasm. Moreover, Lhx9 increased NGF-induced neuronal differentiation of PC12 cells. Lhx9alpha, on the other hand, did not significantly ...


Translational Regulation Of Gene Expression, Stephanie Kervestin, Nadia Amrani Dec 2004

Translational Regulation Of Gene Expression, Stephanie Kervestin, Nadia Amrani

Open Access Articles

A report on the Cold Spring Harbor Laboratory meeting 'Translational Control', Cold Spring Harbor, USA, 7-12 September 2004.


Isolation And Characterization Of Polymorphic Microsatellite Loci In The Boll Weevil, Anthonomus Grandis Boheman (Coleoptera: Curculionidae), Kyung Seok Kim, Thomas W. Sappington Dec 2004

Isolation And Characterization Of Polymorphic Microsatellite Loci In The Boll Weevil, Anthonomus Grandis Boheman (Coleoptera: Curculionidae), Kyung Seok Kim, Thomas W. Sappington

Entomology Publications

The boll weevil (Anthonomus grandis Boheman) is a major insect pest of cotton in North America. Dispersal activity poses a threat to ongoing eradication efforts in the US, but little is known about the frequency of long-distance migration. Nuclear molecular markers are needed to assess gene flow in relation to geographical distance. A biotin-enrichment strategy was employed to develop microsatellite markers for the boll weevil. Of 23 loci isolated, 14 were polymorphic with three to 10 alleles per locus. Twelve of the polymorphic loci showed Mendelian inheritance and are likely to be useful in population genetics studies.


Phylogeography And Genetic Ancestry Of Tigers (Panthera Tigris), Shu-Jin Luo, Jae-Heup Kim, Warren E. Johnson, Joelle Van Der Walt, Janice S. Martenson, Naoya Yuhki, Dale Miquelle, Olga Uphyrkina, John M. Goodrich, Howard Quigley, R. Tilson, Gerald Brady, Paolo Martelli, Vellayan Subramaniam, Charles Mcdougal, Sun Hean, Shi-Qiang Huang, Wenshi Pan, Ullas K. Karanth, Melvin Sunquist, James L. D. Smith, Stephen J. O'Brien Dec 2004

Phylogeography And Genetic Ancestry Of Tigers (Panthera Tigris), Shu-Jin Luo, Jae-Heup Kim, Warren E. Johnson, Joelle Van Der Walt, Janice S. Martenson, Naoya Yuhki, Dale Miquelle, Olga Uphyrkina, John M. Goodrich, Howard Quigley, R. Tilson, Gerald Brady, Paolo Martelli, Vellayan Subramaniam, Charles Mcdougal, Sun Hean, Shi-Qiang Huang, Wenshi Pan, Ullas K. Karanth, Melvin Sunquist, James L. D. Smith, Stephen J. O'Brien

Biology Faculty Articles

Eight traditional subspecies of tiger (Panthera tigris), of which three recently became extinct, are commonly recognized on the basis of geographic isolation and morphological characteristics. To investigate the species' evolutionary history and to establish objective methods for subspecies recognition, voucher specimens of blood, skin, hair, and/or skin biopsies from 134 tigers with verified geographic origins or heritage across the whole distribution range were examined for three molecular markers: (1) 4.0 kb of mitochondrial DNA (mtDNA) sequence; (2) allele variation in the nuclear major histocompatibility complex class II DRB gene; and (3) composite nuclear microsatellite genotypes based on 30 ...


Association Of Dc-Sign Promoter Polymorphism With Increased Risk For Parenteral, But Not Mucosal, Acquisition Of Human Immunodeficiency Virus Type 1 Infection, Maureen P. Martin, Michael M. Lederman, Holli B. Hutcheson, James J. Goedert, George W. Nelson, Yvette Van Kooyk, Roger Detels, Susan Buchbinder, Keith Hoots, David Vlahov, Stephen J. O'Brien, Mary Carrington Dec 2004

Association Of Dc-Sign Promoter Polymorphism With Increased Risk For Parenteral, But Not Mucosal, Acquisition Of Human Immunodeficiency Virus Type 1 Infection, Maureen P. Martin, Michael M. Lederman, Holli B. Hutcheson, James J. Goedert, George W. Nelson, Yvette Van Kooyk, Roger Detels, Susan Buchbinder, Keith Hoots, David Vlahov, Stephen J. O'Brien, Mary Carrington

Biology Faculty Articles

There is considerable debate about the fundamental mechanisms that underlie and restrict acquisition of human immunodeficiency virus type 1 (HIV-1) infection. In light of recent studies demonstrating the ability of C type lectins to facilitate infection with HIV-1, we explored the potential relationship between polymorphisms in the DC-SIGN promoter and risk for acquisition of HIV-1 according to route of infection. Using samples obtained from 1,611 European-American participants at risk for parenteral (n = 713) or mucosal (n = 898) infection, we identified single-nucleotide polymorphisms in the DC-SIGN promoter using single-strand conformation polymorphism. Individuals at risk for parenterally acquired infection who had ...


A Genetic Variation Map For Chicken With 2.8 Million Single-Nucleotide Polymorphisms, Gane Ka-Shu Wong, Bin Liu, Jun Wang, Yong Zhang, Xu Yang, Zengjin Zhang, Qingshun Meng, Jun Zhou, Dawei Li, Jingjing Zhang, Peixiang Ni, Songgang Li, Longhua Ran, Heng Li, Jianguo Zhang, Ruiqiang Li, Shengting Li, Hongkun Zheng, Wei Lin, Guangyuan Li, Xiaoling Wang, Wenming Zhao, Jun Li, Chen Ye, Mingtao Dai, Jue Ruan, Yan Zhou, Yuanzhe Li, Ximiao He, Yunze Zhang, Jing Wang, Xiangang Huang, Wei Tong, Jie Chen, Jia Ye, Chen Chen, Ning Wei, Guoqing Li, Le Dong, Fengdi Land, Yongqiao Sun, Zhenpeng Zhang, Zheng Yang, Yingpu Yu, Yanqing Huang, Dandan He, Yan Xi, Dong Wei, Qiuhui Qi, Wenjie Li, Jianping Shi, Miaoheng Wang, Fei Xie, Jianjun Wang, Xiaowei Zhang, Pei Wang, Yiqiang Zhao, Ning Li, Ning Yang, Wei Dong, Songnian Hu, Changqing Zeng, Weimou Zheng, Bailin Hao, Ladeana W. Hillier, Shiaw-Pyng Yang, Wesley C. Warren, Richard K. Wilson, Mikael Brandstrom, Hans Ellegren, Richard P. M. A. Crooijmans, Jan J. Van Der Poel, Henk Bovenhuis, Martien A. M. Groenen, Ivan Ovcharenko, Laurie Gordon, Lisa Stubbs, Susan Lucas, Tijana Glavina, Andrea Aerts, Pete Kaiser, Lisa Rothwell, John R. Young, Sally Rogers, Brian A. Walker, Andy Van Hateren, Jim Kaufman, Nat Bumstead, Susan J. Lamont, Huaijun Zhou, Paul M. Hocking, David Morrice, Dirk-Jan De Koning, Andy Law, Neil Bartly, David W. Burt, Henry Hunt, Hans H. Cheng, Ulrika Gunnarsson, Per Wahlberg, Leif Andersson, Ellen Kindlund, Martti T. Tammi, Björn Andersson, Caleb Webber, Chris P. Ponting, Ian M. Overton, Paul E. Boardman, Haizhou Tang, Simon J. Hubbard, Stuart A. Wilson, Jun Yu, Jian Wang, Huanming Yang, International Chicken Polymorphism Map Consortium Dec 2004

A Genetic Variation Map For Chicken With 2.8 Million Single-Nucleotide Polymorphisms, Gane Ka-Shu Wong, Bin Liu, Jun Wang, Yong Zhang, Xu Yang, Zengjin Zhang, Qingshun Meng, Jun Zhou, Dawei Li, Jingjing Zhang, Peixiang Ni, Songgang Li, Longhua Ran, Heng Li, Jianguo Zhang, Ruiqiang Li, Shengting Li, Hongkun Zheng, Wei Lin, Guangyuan Li, Xiaoling Wang, Wenming Zhao, Jun Li, Chen Ye, Mingtao Dai, Jue Ruan, Yan Zhou, Yuanzhe Li, Ximiao He, Yunze Zhang, Jing Wang, Xiangang Huang, Wei Tong, Jie Chen, Jia Ye, Chen Chen, Ning Wei, Guoqing Li, Le Dong, Fengdi Land, Yongqiao Sun, Zhenpeng Zhang, Zheng Yang, Yingpu Yu, Yanqing Huang, Dandan He, Yan Xi, Dong Wei, Qiuhui Qi, Wenjie Li, Jianping Shi, Miaoheng Wang, Fei Xie, Jianjun Wang, Xiaowei Zhang, Pei Wang, Yiqiang Zhao, Ning Li, Ning Yang, Wei Dong, Songnian Hu, Changqing Zeng, Weimou Zheng, Bailin Hao, Ladeana W. Hillier, Shiaw-Pyng Yang, Wesley C. Warren, Richard K. Wilson, Mikael Brandstrom, Hans Ellegren, Richard P. M. A. Crooijmans, Jan J. Van Der Poel, Henk Bovenhuis, Martien A. M. Groenen, Ivan Ovcharenko, Laurie Gordon, Lisa Stubbs, Susan Lucas, Tijana Glavina, Andrea Aerts, Pete Kaiser, Lisa Rothwell, John R. Young, Sally Rogers, Brian A. Walker, Andy Van Hateren, Jim Kaufman, Nat Bumstead, Susan J. Lamont, Huaijun Zhou, Paul M. Hocking, David Morrice, Dirk-Jan De Koning, Andy Law, Neil Bartly, David W. Burt, Henry Hunt, Hans H. Cheng, Ulrika Gunnarsson, Per Wahlberg, Leif Andersson, Ellen Kindlund, Martti T. Tammi, Björn Andersson, Caleb Webber, Chris P. Ponting, Ian M. Overton, Paul E. Boardman, Haizhou Tang, Simon J. Hubbard, Stuart A. Wilson, Jun Yu, Jian Wang, Huanming Yang, International Chicken Polymorphism Map Consortium

Animal Science Publications

We describe a genetic variation map for the chicken genome containing 2.8 million single-nucleotide polymorphisms (SNPs). This map is based on a comparison of the sequences of three domestic chicken breeds (a broiler, a layer and a Chinese silkie) with that of their wild ancestor, red jungle fowl. Subsequent experiments indicate that at least 90% of the variant sites are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity is about five SNPs per kilobase for almost every possible comparison between red jungle fowl and domestic lines, between two different ...


A Bayesian Method For Finding Interactions In Genomic Studies, Wei Chen, Debashis Ghosh, Trivellore E. Raghuanthan, Sharon Kardia Nov 2004

A Bayesian Method For Finding Interactions In Genomic Studies, Wei Chen, Debashis Ghosh, Trivellore E. Raghuanthan, Sharon Kardia

The University of Michigan Department of Biostatistics Working Paper Series

An important step in building a multiple regression model is the selection of predictors. In genomic and epidemiologic studies, datasets with a small sample size and a large number of predictors are common. In such settings, most standard methods for identifying a good subset of predictors are unstable. Furthermore, there is an increasing emphasis towards identification of interactions, which has not been studied much in the statistical literature. We propose a method, called BSI (Bayesian Selection of Interactions), for selecting predictors in a regression setting when the number of predictors is considerably larger than the sample size with a focus ...


Estimation Of Genetically Effective Breeding Numbers Using A Rejection Algorithm Approach, Uma Ramakrishnan, Jay F. Storz, Barbara L. Taylor, Russell Lande Nov 2004

Estimation Of Genetically Effective Breeding Numbers Using A Rejection Algorithm Approach, Uma Ramakrishnan, Jay F. Storz, Barbara L. Taylor, Russell Lande

Jay F. Storz Publications

Polygynous mating results in nonrandom sampling of the adult male gamete pool in each generation, thereby increasing the rate of genetic drift. In principle, genetic paternity analysis can be used to infer the effective number of breeding males (Nebm). However, this requires genetic data from an exhaustive sample of candidate males. Here we describe a new approach to estimate Nebm using a rejection algorithm in association with three statistics: Euclidean distance between the frequency distributions of maternally and paternally inherited alleles, average number of paternally inherited alleles and average gene diversity of paternally inherited alleles. We quantify the ...


Finding Cancer Subtypes In Microarray Data Using Random Projections, Debashis Ghosh Oct 2004

Finding Cancer Subtypes In Microarray Data Using Random Projections, Debashis Ghosh

The University of Michigan Department of Biostatistics Working Paper Series

One of the benefits of profiling of cancer samples using microarrays is the generation of molecular fingerprints that will define subtypes of disease. Such subgroups have typically been found in microarray data using hierarchical clustering. A major problem in interpretation of the output is determining the number of clusters. We approach the problem of determining disease subtypes using mixture models. A novel estimation procedure of the parameters in the mixture model is developed based on a combination of random projections and the expectation-maximization algorithm. Because the approach is probabilistic, our approach provides a measure for the number of true clusters ...


A First Version Of The Caenorhabditis Elegans Promoterome, Denis Dupuy, Qian-Ru Li, Bart Deplancke, Mike Boxem, Tong Hao, Philippe Lamesch, Reynaldo Sequerra, Stephanie Bosak, Lynn Doucette-Stamm, Ian A. Hope, David E. Hill, Albertha J. M. Walhout, Marc Vidal Oct 2004

A First Version Of The Caenorhabditis Elegans Promoterome, Denis Dupuy, Qian-Ru Li, Bart Deplancke, Mike Boxem, Tong Hao, Philippe Lamesch, Reynaldo Sequerra, Stephanie Bosak, Lynn Doucette-Stamm, Ian A. Hope, David E. Hill, Albertha J. M. Walhout, Marc Vidal

Program in Gene Function and Expression Publications and Presentations

An important aspect of the development of systems biology approaches in metazoans is the characterization of expression patterns of nearly all genes predicted from genome sequences. Such "localizome" maps should provide information on where (in what cells or tissues) and when (at what stage of development or under what conditions) genes are expressed. They should also indicate in what cellular compartments the corresponding proteins are localized. Caenorhabditis elegans is particularly suited for the development of a localizome map since all its 959 adult somatic cells can be visualized by microscopy, and its cell lineage has been completely described. Here we ...


Newborn Screening For Cystic Fibrosis: Evaluation Of Benefits And Risks And Recommendations For State Newborn Screening Programs, Scott D. Grosse, Coleen A. Boyle, Jeffrey R. Botkin, Anne Marie Comeau, Martin Kharrazi, Margaret Rosenfeld, Benjamin S. Wilfond Oct 2004

Newborn Screening For Cystic Fibrosis: Evaluation Of Benefits And Risks And Recommendations For State Newborn Screening Programs, Scott D. Grosse, Coleen A. Boyle, Jeffrey R. Botkin, Anne Marie Comeau, Martin Kharrazi, Margaret Rosenfeld, Benjamin S. Wilfond

Genetics

In November 2003, CDC and the Cystic Fibrosis Foundation cosponsored a workshop to review the benefits and risks associated with newborn screening for cystic fibrosis (CF). This report describes new research findings and outlines the recommendations of the workshop. The peer-reviewed evidence presented at the workshop supports the clinical utility of newborn screening for CF. Demonstrated long-term benefits from early nutritional treatment as a result of newborn screening for CF include improved growth and, in one study, cognitive development. Other benefits might include reduced hospitalizations and improved survival. Mixed evidence has been reported for pulmonary outcomes. Newborn screening in the ...


Judging A Virus By Its Cover, Eva Szomolanyi-Tsuda, Raymond M. Welsh Oct 2004

Judging A Virus By Its Cover, Eva Szomolanyi-Tsuda, Raymond M. Welsh

Open Access Articles

The production of protective neutralizing antibodies occurs quickly in some viral infections but very slowly in others. In a new study, surface glycoproteins (the targets of neutralization) of 2 different viruses were genetically switched. Analysis of the neutralizing antibody response to each of the 2 parent and recombinant viruses in infected mice revealed that the speed of neutralizing antibody induction was intrinsically dependent on the surface glycoprotein and not the rest of the virus.


Apobec3g Genetic Variants And Their Influence On The Progression To Aids, Ping An, Gabriela Bleiber, Priya Duggal, George Nelson, Margaret May, Bastien Mangeat, Irene Alobwede, Didier Trono, David Vlahov, Sharyne Donfield, James J. Goedert, John Phair, Susan Buchbinder, Stephen J. O'Brien, Amalio Telenti, Cheryl Winkler Oct 2004

Apobec3g Genetic Variants And Their Influence On The Progression To Aids, Ping An, Gabriela Bleiber, Priya Duggal, George Nelson, Margaret May, Bastien Mangeat, Irene Alobwede, Didier Trono, David Vlahov, Sharyne Donfield, James J. Goedert, John Phair, Susan Buchbinder, Stephen J. O'Brien, Amalio Telenti, Cheryl Winkler

Biology Faculty Articles

The cytosine deaminase APOBEC3G, in the absence of the human immunodeficiency virus type 1 (HIV-1) accessory gene HIV-1 viral infectivity factor (vif), inhibits viral replication by introducing G→A hypermutation in the newly synthesized HIV-1 DNA negative strand. We tested the hypothesis that genetic variants of APOBEC3G may modify HIV-1 transmission and disease progression. Single nucleotide polymorphisms were identified in the promoter region (three), introns (two), and exons (two). Genotypes were determined for 3,073 study participants enrolled in six HIV-AIDS prospective cohorts. One codon-changing variant, H186R in exon 4, was polymorphic in African Americans (AA) (f < 37%) and rare in European Americans (f < 3%) or Europeans (f = 5 ...


New Alleles In Calpastatin Gene Are Associated With Meat Quality Traits In Pigs, D. C. Ciobanu, John Bastiaansen, Steven M. Lonergan, H. K. Thomsen, Jack C. M. Dekkers, Graham S. Plastow, Max F. Rothschild Oct 2004

New Alleles In Calpastatin Gene Are Associated With Meat Quality Traits In Pigs, D. C. Ciobanu, John Bastiaansen, Steven M. Lonergan, H. K. Thomsen, Jack C. M. Dekkers, Graham S. Plastow, Max F. Rothschild

Animal Science Publications

Suggestive QTL affecting raw firmness scores and average Instron force, tenderness, juiciness, and chewiness on cooked meat were mapped to pig chromosome 2 using a three-generation intercross between Berkshire and Yorkshire pigs. Based on its function and location, the calpastatin (CAST) gene was considered to be a good candidate for the observed effects. Several missense and silent mutations were identified in CASTand haplotypes covering most of the coding region were constructed and used for association analyses with meat quality traits. Results demonstrated that one CAST haplotype was significantly associated with lower Instron force and cooking loss and higher juiciness ...


Effect Of Misreported Family History On Mendelian Mutation Prediction Models, Hormuzd A. Katki Sep 2004

Effect Of Misreported Family History On Mendelian Mutation Prediction Models, Hormuzd A. Katki

Johns Hopkins University, Dept. of Biostatistics Working Papers

People with familial history of disease often consult with genetic counselors about their chance of carrying mutations that increase disease risk. To aid them, genetic counselors use Mendelian models that predict whether the person carries deleterious mutations based on their reported family history. Such models rely on accurate reporting of each member's diagnosis and age of diagnosis, but this information may be inaccurate. Commonly encountered errors in family history can significantly distort predictions, and thus can alter the clinical management of people undergoing counseling, screening, or genetic testing. We derive general results about the distortion in the carrier probability ...


The Bvg Virulence Control System Regulates Biofilm Formation In Bordetella Bronchiseptica, Yasuhiko Irie, Seema Mattoo, Ming H. Yuk Sep 2004

The Bvg Virulence Control System Regulates Biofilm Formation In Bordetella Bronchiseptica, Yasuhiko Irie, Seema Mattoo, Ming H. Yuk

Biology Faculty Publications

Bordetella species utilize the BvgAS (Bordetella virulence gene) two-component signal transduction system to sense the environment and regulate gene expression among at least three phases: a virulent Bvg+ phase, a nonvirulent Bvg phase, and an intermediate Bvgi phase. Genes expressed in the Bvg+ phase encode known virulence factors, including adhesins such as filamentous hemagglutinin (FHA) and fimbriae, as well as toxins such as the bifunctional adenylate cyclase/hemolysin (ACY). Previous studies showed that in the Bvgi phase, FHA and fimbriae continue to be expressed, but ACY expression is significantly downregulated. In this report, we determine that Bordetella bronchiseptica ...


Interaction-Dependent Gene Expression In Mla-Specified Response To Barley Powdery Mildew, Rico A. Caldo, Dan Nettleton, Roger P. Wise Sep 2004

Interaction-Dependent Gene Expression In Mla-Specified Response To Barley Powdery Mildew, Rico A. Caldo, Dan Nettleton, Roger P. Wise

Statistics Publications

Plant recognition of pathogen-derived molecules influences attack and counterattack strategies that affect the outcome of host–microbe interactions. To ascertain the global framework of host gene expression during biotrophic pathogen invasion, we analyzed in parallel the mRNA abundance of 22,792 host genes throughout 36 (genotype × pathogen × time) interactions between barley (Hordeum vulgare) and Blumeria graminis f. sp hordei (Bgh), the causal agent of powdery mildew disease. A split-split-plot design was used to investigate near-isogenic barley lines with introgressed Mla6, Mla13, and Mla1 coiled-coil, nucleotide binding site, Leu-rich repeat resistance alleles challenged with Bgh isolates 5874 (AvrMla6 and AvrMla1) and ...


Mitochondrial Diversity Analysis Of Glossina Palpalis Gambiensis From Mali And Senegal, J. G. Marquez, M. J. B. Vreysen, A. S. Robinson, S. Bado, E. S. Krafsur Sep 2004

Mitochondrial Diversity Analysis Of Glossina Palpalis Gambiensis From Mali And Senegal, J. G. Marquez, M. J. B. Vreysen, A. S. Robinson, S. Bado, E. S. Krafsur

Entomology Publications

West African riverine tsetse populations of Glossina palpalis gambiensis Vanderplank (Diptera: Glossinidae) were investigated for gene flow, inferred from mitochondrial diversity in samples of 69 flies from Senegal and 303 flies from three river drainages in Mali. Four polymorphic mitochondrial loci were scored. Mean haplotype diversities were 0.30 in Mali and 0.18 over both Mali and Senegal. These diversities estimate the probabilities that two randomly chosen tsetse have different haplotypes. Substantial rates of gene flow were detected among flies sampled along tributaries belonging to the river basins of the Senegal, Niger, and Bani in Mali. There was virtually ...


Multiple Kh Domains Of Poly C Binding Protein Are Required For Its Trans-Activation On The Proximal Promoter Of The Mu-Opioid Receptor Gene, Adnan K. Malik Sep 2004

Multiple Kh Domains Of Poly C Binding Protein Are Required For Its Trans-Activation On The Proximal Promoter Of The Mu-Opioid Receptor Gene, Adnan K. Malik

Seton Hall University Dissertations and Theses (ETDs)

The mu-opioid receptor (MOR) has been shown to mediate morphine induced analgesia, addiction, and tolerance. The expression of the major product of the MOR (MOR-1) gene has been found to be driven by two promoters, a distal promoter and a proximal promoter. The proximal promoter region has been shown in previous studies to be the major promoter for the regulation of MOR gene transcription in the adult mouse brain and embryonic development. Recent studies have shown that single-stranded DNA binding proteins (such as Poly C Binding Protein) are involved in transcriptional regulation of mouse MOR gene. Poly C binding protein ...


Significance Analysis Of Time Course Microarray Experiments, John D. Storey, Wenzhong Xiao, Jeffrey T. Leek, Ronald G. Tompkins, Ron W. Davis Aug 2004

Significance Analysis Of Time Course Microarray Experiments, John D. Storey, Wenzhong Xiao, Jeffrey T. Leek, Ronald G. Tompkins, Ron W. Davis

UW Biostatistics Working Paper Series

Characterizing the genome-wide dynamic regulation of gene expression is important and will be of much interest in the future. However, there is currently no established method for identifying differentially expressed genes in a time course study. Here we propose a significance method for analyzing time course microarray studies that can be applied to the typical types of comparisons and sampling schemes. This method is applied to two studies on humans. In one study, genes are identified that show differential expression over time in response to in vivo endotoxin administration. Using our method 7409 genes are called significant at a 1 ...


Chemical Genomics In Yeast, Charles Brenner Aug 2004

Chemical Genomics In Yeast, Charles Brenner

Open Dartmouth: Faculty Open Access Scholarship

Four recent 'chemical genomic' studies, using genome-scale collections of yeast gene deletions, have presented complementary approaches to identifying gene-drug and pathway-drug interactions.Many drugs have unknown, controversial or multiple mechanisms of action. Four recent 'chemical genomic' studies, using genome-scale collections of yeast gene deletions that were either arrayed or barcoded, have presented complementary approaches to identifying gene-drug and pathway-drug interactions.


Regulation Of Muscle Fiber Type And Running Endurance By Ppardelta, Yong-Xu Wang, Chung-Li Zhang, Ruth T. Yu, Helen K. Cho, Michael C. Nelson, Corinne R. Bayuga-Ocampo, Jungyeob Ham, Heonjoong Kang, Ronald M. Evans Aug 2004

Regulation Of Muscle Fiber Type And Running Endurance By Ppardelta, Yong-Xu Wang, Chung-Li Zhang, Ruth T. Yu, Helen K. Cho, Michael C. Nelson, Corinne R. Bayuga-Ocampo, Jungyeob Ham, Heonjoong Kang, Ronald M. Evans

Program in Gene Function and Expression Publications and Presentations

Endurance exercise training can promote an adaptive muscle fiber transformation and an increase of mitochondrial biogenesis by triggering scripted changes in gene expression. However, no transcription factor has yet been identified that can direct this process. We describe the engineering of a mouse capable of continuous running of up to twice the distance of a wild-type littermate. This was achieved by targeted expression of an activated form of peroxisome proliferator-activated receptor delta (PPARdelta) in skeletal muscle, which induces a switch to form increased numbers of type I muscle fibers. Treatment of wild-type mice with PPARdelta agonist elicits a similar type ...


A Mechanical Basis For Chromosome Function, Nancy Kleckner, Denise Zickler, Gareth H. Jones, Job Dekker, Ruth Padmore, Jim Henle, John N. Hutchinson Aug 2004

A Mechanical Basis For Chromosome Function, Nancy Kleckner, Denise Zickler, Gareth H. Jones, Job Dekker, Ruth Padmore, Jim Henle, John N. Hutchinson

Program in Gene Function and Expression Publications and Presentations

We propose that chromosome function is governed by internal mechanical forces generated by programmed tendencies for expansion of the DNA/chromatin fiber against constraining features.


The Caenorhabditis Elegans F-Box Protein Sel-10 Promotes Female Development And May Target Fem-1 And Fem-3 For Degradation By The Proteasome, Sibylle Jager, Hillel T. Schwartz, H. Robert Horvitz, Barbara Conradt Aug 2004

The Caenorhabditis Elegans F-Box Protein Sel-10 Promotes Female Development And May Target Fem-1 And Fem-3 For Degradation By The Proteasome, Sibylle Jager, Hillel T. Schwartz, H. Robert Horvitz, Barbara Conradt

Open Dartmouth: Faculty Open Access Scholarship

The Caenorhabditis elegans F-box protein SEL-10 and its human homolog have been proposed to regulate LIN-12 Notch signaling by targeting for ubiquitin-mediated proteasomal degradation LIN-12 Notch proteins and SEL-12 PS1 presenilins, the latter of which have been implicated in Alzheimer's disease. We found that sel-10 is the same gene as egl-41, which previously had been defined by gain-of-function mutations that semidominantly cause masculinization of the hermaphrodite soma. Our results demonstrate that mutations causing loss-of-function of sel-10 also have masculinizing activity, indicating that sel-10 functions to promote female development. Genetically, sel-10 acts upstream of the genes fem-1, fem-2, and fem-3 ...


Restoration Of Aspen Woodland Invaded By Western Juniper: Applications Of Partial Cutting And Prescribed Fire, Jonathon D. Bates, Richard F. Miller Aug 2004

Restoration Of Aspen Woodland Invaded By Western Juniper: Applications Of Partial Cutting And Prescribed Fire, Jonathon D. Bates, Richard F. Miller

Aspen Bibliography

No abstract provided.


Bone Marrow Microenvironmental Changes Underlie Reduced Rag-Mediated Recombination And B Cell Generation In Aged Mice, Joseph E. Labrie, Alex P. Sah, David M. Allman, Michael P. Cancro, Rachel M. Gerstein Aug 2004

Bone Marrow Microenvironmental Changes Underlie Reduced Rag-Mediated Recombination And B Cell Generation In Aged Mice, Joseph E. Labrie, Alex P. Sah, David M. Allman, Michael P. Cancro, Rachel M. Gerstein

Open Access Articles

During aging, adaptive immunity is severely compromised, due in part to decreased production of B lymphocytes and loss of immunoglobulin (Ig) diversity. However, the molecular mechanisms that underlie age-associated diminished B cell production remain unclear. Using in vivo labeling, we find that this reduction in marrow pre-B cells reflects increased attrition during passage from the pro-B to pre-B cell pool. Analyses of reciprocal bone marrow chimeras reveal that the magnitude and production rates of pre-B cells are controlled primarily by microenvironmental factors, rather than intrinsic events. To understand changes in pro-B cells that could diminish production of pre-B cells, we ...


Lestig1, An Extracellular Binding Partner For The Pollen Receptor Kinases Leprk1 And Leprk2, Promotes Pollen Tube Growth In Vitro, Weihua Tang, Dior R. Kelley, Ines Ezcurra, Robyn Cotter, Sheila Mccormick Jul 2004

Lestig1, An Extracellular Binding Partner For The Pollen Receptor Kinases Leprk1 And Leprk2, Promotes Pollen Tube Growth In Vitro, Weihua Tang, Dior R. Kelley, Ines Ezcurra, Robyn Cotter, Sheila Mccormick

Dior Kelley

As pollen tubes grow through the pistil they are thought to perceive and respond to diverse signals. The tomato pollen-specific receptor kinases LePRK1 and LePRK2 might participate in signaling during pollen tube growth. We previously showed that the extracellular domain of LePRK2 interacts with a pollen protein, LAT52, before but not after pollen germination. To determine whether LePRK2 might have different binding partner(s) after pollen germination, we characterized two more proteins that, like LAT52, were identified in yeast two-hybrid screens using the extracellular domains of LePRK1 and LePRK2 as baits. We show that LeSHY, a leucine-rich repeat protein from ...