gene order

Summary

Summary: The sequential location of genes on a chromosome.

Top Publications

  1. pmc The complete mitochondrial genome and novel gene arrangement of the unique-headed bug Stenopirates sp. (Hemiptera: Enicocephalidae)
    Hu Li
    Department of Entomology, China Agricultural University, Beijing, China
    PLoS ONE 7:e29419. 2012
  2. ncbi The complete chloroplast genome sequence of Pelargonium x hortorum: organization and evolution of the largest and most highly rearranged chloroplast genome of land plants
    Timothy W Chumley
    The University of Texas at Austin, TX, USA
    Mol Biol Evol 23:2175-90. 2006
  3. ncbi Extensive rearrangements in the chloroplast genome of Trachelium caeruleum are associated with repeats and tRNA genes
    Rosemarie C Haberle
    Section of Integrative Biology and Institute of Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
    J Mol Evol 66:350-61. 2008
  4. ncbi Gene rearrangements and evolution of tRNA pseudogenes in the mitochondrial genome of the parrotfish (Teleostei: Perciformes: Scaridae)
    Kohji Mabuchi
    Ocean Research Institute, University of Tokyo, 1 15 1 Minamidai, Nakano Ku, Tokyo 164 8639, Japan
    J Mol Evol 59:287-97. 2004
  5. ncbi Data mining pathogen genomes using GeneOrder and CoreGenes and CGUG: gene order, synteny and in silico proteomes
    Padmanabhan Mahadevan
    Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA E mail
    Int J Comput Biol Drug Des 2:100-14. 2009
  6. pmc Gene order and chromosome dynamics coordinate spatiotemporal gene expression during the bacterial growth cycle
    Patrick Sobetzko
    School of Engineering and Science, Jacobs University Bremen, D 28759 Bremen, Germany
    Proc Natl Acad Sci U S A 109:E42-50. 2012
  7. pmc Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps
    Haibao Tang
    Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
    Genome Res 18:1944-54. 2008
  8. pmc Support for multiple classes of local expression clusters in Drosophila melanogaster, but no evidence for gene order conservation
    Claudia C Weber
    Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
    Genome Biol 12:R23. 2011
  9. ncbi Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events
    John E Bowers
    Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
    Nature 422:433-8. 2003
  10. ncbi Comparison of the genomes of two Xanthomonas pathogens with differing host specificities
    A C R da Silva
    Departamento de Bioquimica, Instituto de Quimica, Av Prof Lineu Prestes 748, Sao Paulo, SP, Brazil
    Nature 417:459-63. 2002

Research Grants

Detail Information

Publications286 found, 100 shown here

  1. pmc The complete mitochondrial genome and novel gene arrangement of the unique-headed bug Stenopirates sp. (Hemiptera: Enicocephalidae)
    Hu Li
    Department of Entomology, China Agricultural University, Beijing, China
    PLoS ONE 7:e29419. 2012
    ..The gene order differs substantially from other known insect mitochondrial genomes, with rearrangements of both tRNA genes and ..
  2. ncbi The complete chloroplast genome sequence of Pelargonium x hortorum: organization and evolution of the largest and most highly rearranged chloroplast genome of land plants
    Timothy W Chumley
    The University of Texas at Austin, TX, USA
    Mol Biol Evol 23:2175-90. 2006
    ..We propose simple models that account for the major rearrangements with a minimum of 8 IR boundary changes and 12 inversions in addition to several insertions of duplicated sequence...
  3. ncbi Extensive rearrangements in the chloroplast genome of Trachelium caeruleum are associated with repeats and tRNA genes
    Rosemarie C Haberle
    Section of Integrative Biology and Institute of Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
    J Mol Evol 66:350-61. 2008
    Chloroplast genome organization, gene order, and content are highly conserved among land plants. We sequenced the chloroplast genome of Trachelium caeruleum L...
  4. ncbi Gene rearrangements and evolution of tRNA pseudogenes in the mitochondrial genome of the parrotfish (Teleostei: Perciformes: Scaridae)
    Kohji Mabuchi
    Ocean Research Institute, University of Tokyo, 1 15 1 Minamidai, Nakano Ku, Tokyo 164 8639, Japan
    J Mol Evol 59:287-97. 2004
    ..In the typical gene order of vertebrates, a tRNA-gene cluster between ND1 and ND2 genes includes tRNA(Ile) (I), tRNA(Gln) (Q), and tRNA(..
  5. ncbi Data mining pathogen genomes using GeneOrder and CoreGenes and CGUG: gene order, synteny and in silico proteomes
    Padmanabhan Mahadevan
    Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA E mail
    Int J Comput Biol Drug Des 2:100-14. 2009
    ..GeneOrder, CoreGenes and CGUG are web-based 'on-the-fly' tools that examine gene order and synteny, as well as proteomes for comparative genomics and for drug discovery and design targets...
  6. pmc Gene order and chromosome dynamics coordinate spatiotemporal gene expression during the bacterial growth cycle
    Patrick Sobetzko
    School of Engineering and Science, Jacobs University Bremen, D 28759 Bremen, Germany
    Proc Natl Acad Sci U S A 109:E42-50. 2012
    ....
  7. pmc Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps
    Haibao Tang
    Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
    Genome Res 18:1944-54. 2008
    ..Comparative analysis of inferred homologous genes derived from this model shows patterns of preferential gene retention or loss after polyploidy and reveals large variability of nucleotide substitution rates among plant nuclear genomes...
  8. pmc Support for multiple classes of local expression clusters in Drosophila melanogaster, but no evidence for gene order conservation
    Claudia C Weber
    Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
    Genome Biol 12:R23. 2011
    b>Gene order in eukaryotic genomes is not random, with genes with similar expression profiles tending to cluster...
  9. ncbi Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events
    John E Bowers
    Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
    Nature 422:433-8. 2003
    Conservation of gene order in vertebrates is evident after hundreds of millions of years of divergence, but comparisons of the Arabidopsis thaliana sequence to partial gene orders of other angiosperms (flowering plants) sharing common ..
  10. ncbi Comparison of the genomes of two Xanthomonas pathogens with differing host specificities
    A C R da Silva
    Departamento de Bioquimica, Instituto de Quimica, Av Prof Lineu Prestes 748, Sao Paulo, SP, Brazil
    Nature 417:459-63. 2002
    ..More than 80% of genes are shared, and gene order is conserved along most of their respective chromosomes...
  11. pmc Transfer RNA gene arrangement and codon usage in vertebrate mitochondrial genomes: a new insight into gene order conservation
    Takashi P Satoh
    Collection Center, National Museum of Nature and Science, 3 23 1 Hyakunincho, Shinjuku ku, Tokyo 169 0073, Japan
    BMC Genomics 11:479. 2010
    ..It remains unclear, however, whether such long-term persistence is a consequence of some constraints on the gene order.
  12. pmc The complete mitochondrial genome of the bag-shelter moth Ochrogaster lunifer (Lepidoptera, Notodontidae)
    Paola Salvato
    Department of Public Health, Comparative Pathology and Veterinary Hygiene, University of Padova, Agripolis, Viale dell Universita 16, 35020 Legnaro, Italy
    BMC Genomics 9:331. 2008
    ..Thus advance of lepidopteran mitogenomics deeply requires new genomes derived from a broad taxon sampling. In present work we describe the mitochondrial genome of the moth Ochrogaster lunifer...
  13. pmc The architecture and complete sequence of mitochondrial genome of an assassin bug Agriosphodrus dohrni (Hemiptera: Reduviidae)
    Hu Li
    Department of Entomology, China Agricultural University, Beijing 100193, China
    Int J Biol Sci 7:792-804. 2011
    ..dimidiata and Valentia hoffmanni, exhibited highly conserved genome architectures including genome contents, gene order, nucleotide composition, codon usage, amino acid composition, as well as genome asymmetry...
  14. ncbi The chloroplast genome sequence of the green alga Pseudendoclonium akinetum (Ulvophyceae) reveals unusual structural features and new insights into the branching order of chlorophyte lineages
    Jean Francois Pombert
    Departement de Biochimie et de Microbiologie, Universite Laval, Quebec G1K 7P4, Canada
    Mol Biol Evol 22:1903-18. 2005
    ..We favor the latter hypothesis because it is strongly supported by phylogenetic analyses of gene order data and by independent structural evidence based on shared gene losses and rearrangement break points within ..
  15. pmc Ecdysozoan mitogenomics: evidence for a common origin of the legged invertebrates, the Panarthropoda
    Omar Rota-Stabelli
    Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
    Genome Biol Evol 2:425-40. 2010
    ..Tardigrada mitochondrial genomes resemble those of the arthropods in term of the gene order and strand asymmetry, whereas Onychophora genomes are characterized by numerous gene order rearrangements and ..
  16. pmc A fragmented metazoan organellar genome: the two mitochondrial chromosomes of Hydra magnipapillata
    Oliver Voigt
    Courant Research Center Geobiology, Georg August Universitat Gottingen, Goldschmidtstr, 3, 37077 Gottingen, Germany
    BMC Genomics 9:350. 2008
    ..Here, we present the whole mt genome sequence from the hydrozoan Hydra magnipapillata, comprising the first sequence of a fragmented metazoan mt genome encoded on two linear mt chromosomes (mt1 and mt2)...
  17. ncbi A nonribosomal peptide synthetase gene (mgoA) of Pseudomonas syringae pv. syringae is involved in mangotoxin biosynthesis and is required for full virulence
    Eva Arrebola
    Departamento de Microbiologia, Facultad de Ciencias, Universidad de Malaga, Malaga, Spain
    Mol Plant Microbe Interact 20:500-9. 2007
    ..syringae pv. syringae. The involvement of an NRPS in the production of an antimetabolite toxin from P. syringae inhibiting ornithine acetyltransferase activity is proposed...
  18. ncbi Transcriptional coupling of neighboring genes and gene expression noise: evidence that gene orientation and noncoding transcripts are modulators of noise
    Guang Zhong Wang
    Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom
    Genome Biol Evol 3:320-31. 2011
    ..We conclude that gene orientation and transcription of ncRNAs are candidate modulators of noise...
  19. ncbi Complete mtDNA sequences of two millipedes suggest a new model for mitochondrial gene rearrangements: duplication and nonrandom loss
    Dennis V Lavrov
    Department of Biology, University of Michigan, Ann Arbor, USA
    Mol Biol Evol 19:163-9. 2002
    ..The proposed mechanism has important implications for phylogenetic inferences that are drawn on the basis of gene arrangement comparisons...
  20. pmc The complete mitochondrial genomes of three parasitic nematodes of birds: a unique gene order and insights into nematode phylogeny
    Guo hua Liu
    State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, 730046, People s Republic of China
    BMC Genomics 14:414. 2013
    ....
  21. ncbi Karyotype evolution in monitor lizards: cross-species chromosome mapping of cDNA reveals highly conserved synteny and gene order in the Toxicofera clade
    Kornsorn Srikulnath
    Laboratory of Animal Genetics, Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo cho, Chikusa ku, Nagoya, 464 8601, Japan
    Chromosome Res 21:805-19. 2013
    ..salvator macromaculatus and V. exanthematicus. Morphologic differences in chromosomes 6-8 between the two species could have resulted from pericentric inversion or centromere repositioning...
  22. ncbi The complete mitochondrial genome of Symphylella sp. (Myriapoda: Symphyla): Extensive gene order rearrangement and evidence in favor of Progoneata
    Yonghua Gai
    Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China Nanjing Institute of Geology and Palaeontology, Chinese Academy of Science, Nanjing 210008, China
    Mol Phylogenet Evol 49:574-85. 2008
    ..With respect to the ancestral arthropod mitochondrial gene order, two protein-coding genes, the rRNAs and 10 of the tRNAs appear to be rearranged...
  23. ncbi Analysis of gene order evolution beyond single-copy genes
    Nadia El-Mabrouk
    Département d informatique et de recherche opérationnelle, Universite de Montreal, Montreal, QC, Canada
    Methods Mol Biol 855:397-429. 2012
    ....
  24. ncbi Mycobacteriophages: genes and genomes
    Graham F Hatfull
    Pittsburgh Bacteriophage Institute, Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
    Annu Rev Microbiol 64:331-56. 2010
    ..Mycobacteriophages have provided key tools for tuberculosis genetics, and new methods for simple construction of mycobacteriophage recombinants will facilitate postgenomic explorations into mycobacteriophage biology...
  25. ncbi Complete mitochondrial genomes of two Japanese precious corals, Paracorallium japonicum and Corallium konojoi (Cnidaria, Octocorallia, Coralliidae): notable differences in gene arrangement
    Kouji Uda
    Laboratories of Biochemistry, Faculty of Science, Kochi University, Kochi 780 8520, Japan
    Gene 476:27-37. 2011
    ..sequences belonging to species in the subclass Octocorallia indicated that within the subclass, at least three gene order rearrangement events occurred during evolution...
  26. ncbi The mitochondrial genome of the butterfly Papilio xuthus (Lepidoptera: Papilionidae) and related phylogenetic analyses
    Xia Feng
    Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, No 1, Wenyuan Road, 210046, Nanjing, Jiangsu, People s Republic of China
    Mol Biol Rep 37:3877-88. 2010
    ..The genome has a typical gene order identical to other lepidopteran species...
  27. pmc Sessile snails, dynamic genomes: gene rearrangements within the mitochondrial genome of a family of caenogastropod molluscs
    Timothy A Rawlings
    Cape Breton University, 1250 Grand Lake Road, Sydney, NS B1P 6L2, Canada
    BMC Genomics 11:440. 2010
    ..In contrast, more limited sampling within the Phylum Mollusca has revealed an unusually high number of gene order arrangements...
  28. ncbi The complete mitochondrial genome of the yellow coaster, Acraea issoria (Lepidoptera: Nymphalidae: Heliconiinae: Acraeini): sequence, gene organization and a unique tRNA translocation event
    Jing Hu
    College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
    Mol Biol Rep 37:3431-8. 2010
    ..There are some short microsatellite-like repeat regions (e.g., (TA)(9), polyA and polyT) scattered in the control region, however, the conspicuous macro-repeats units commonly found in other insect species are absent...
  29. ncbi Two circular chromosomes of unequal copy number make up the mitochondrial genome of the rotifer Brachionus plicatilis
    Koushirou Suga
    Nagasaki Industrial Promotion Foundation, Omura, Japan
    Mol Biol Evol 25:1129-37. 2008
    ..b>Gene order is not conserved between B...
  30. pmc Genome sequences of three agrobacterium biovars help elucidate the evolution of multichromosome genomes in bacteria
    Steven C Slater
    Virginia Bioinformatics Institute, Washington St, MC 0477, Blacksburg, VA 24060, USA
    J Bacteriol 191:2501-11. 2009
    ..In contrast, secondary chromosomes share smaller percentages of genes, and conserved gene order is restricted to short blocks...
  31. pmc Comparative and phylogenomic studies on the mitochondrial genomes of Pentatomomorpha (Insecta: Hemiptera: Heteroptera)
    Jimeng Hua
    Department of Zoology and Developmental Biology, Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, PR China
    BMC Genomics 9:610. 2008
    ....
  32. pmc Genetic mapping in a natural population of collared flycatchers (Ficedula albicollis): conserved synteny but gene order rearrangements on the avian Z chromosome
    Niclas Backstrom
    Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE 752 36 Uppsala, Sweden
    Genetics 174:377-86. 2006
    ..Interestingly, the rate of recombination on the Z chromosome of collared flycatchers was only approximately 50% that of chicken, challenging the widely held view that birds generally have high recombination rates...
  33. pmc Fragile regions and not functional constraints predominate in shaping gene organization in the genus Drosophila
    Marcin von Grotthuss
    Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92697, USA
    Genome Res 20:1084-96. 2010
    ..Both gene order conservation and breakpoint reuse can result from the existence of functional constraints on where chromosomal ..
  34. pmc Unusual conservation of mitochondrial gene order in Crassostrea oysters: evidence for recent speciation in Asia
    Jianfeng Ren
    Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
    BMC Evol Biol 10:394. 2010
    ..iredalei and Saccostrea mordax) for a comprehensive analysis...
  35. pmc Complete chloroplast genome sequence of a tree fern Alsophila spinulosa: insights into evolutionary changes in fern chloroplast genomes
    Lei Gao
    Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, PR China
    BMC Evol Biol 9:130. 2009
    ..Availability of cp genome sequence from a tree fern will facilitate interpretation of the evolutionary changes of fern cp genomes. Here we have sequenced the complete cp genome of a scaly tree fern Alsophila spinulosa (Cyatheaceae)...
  36. ncbi The evolution of chloroplast genome structure in ferns
    Paul G Wolf
    Department of Biology, and Ecology Center, Utah State University, Logan, UT 84322, USA
    Genome 53:731-8. 2010
    ..However, in a major group of plants, the ferns, a unique plastome structure has evolved. The gene order in ferns has been explained by a series of genomic inversions relative to the plastome organization of seed ..
  37. pmc A survey of sRNA families in α-proteobacteria
    Coral Del Val
    CITIC UGR, Centro de Investigación en Tecnologías de la Información y de las Comunicaciones de la Universidad de Granada, Granada, Spain
    RNA Biol 9:119-29. 2012
    ..meliloti 1021. The distribution patterns of these sRNA families suggest major contributions of vertical inheritance and extensive ancestral duplication events to the evolution of sRNAs in plant-interacting bacteria...
  38. ncbi Mitochondrial genomes from the lichenized fungi Peltigera membranacea and Peltigera malacea: features and phylogeny
    Basil Britto Xavier
    Department of Life and Environmental Sciences, University of Iceland, 101 Reykjavik, Iceland
    Fungal Biol 116:802-14. 2012
    ..representatives of the class Lecanoromycetes, close to Leotiomycetes, Dothidiomycetes, and Sordariomycetes, in contrast to phylogenies found using nuclear genes...
  39. pmc Construction of an oncolytic herpes simplex virus that precisely targets hepatocellular carcinoma cells
    Xinping Fu
    Department of Biology and Biochemistry, Center for Nuclear Receptors and Cell Signaling, University of Houston, Houston, Texas 77204, USA
    Mol Ther 20:339-46. 2012
    ..Designated liver-cancer specific oncolytic virus (LCSOV), it was highly selective in killing HCC cells and in shrinking HCC xenografts. We conclude that LCSOV is a highly specific oncolytic virus that can precisely target HCC...
  40. pmc Mitogenomic sequences and evidence from unique gene rearrangements corroborate evolutionary relationships of myctophiformes (Neoteleostei)
    Jan Y Poulsen
    Natural History Collections, University Museum of Bergen, University of Bergen, Allegaten 41, P O Box 7800, Bergen N 5020, Norway
    BMC Evol Biol 13:111. 2013
    ..This study attempts to resolve major myctophiform phylogenies from both mitogenomic sequences and corroborating evidence in the form of unique mitochondrial gene order rearrangements.
  41. ncbi Evolution of the mitochondrial genome: protist connections to animals, fungi and plants
    Charles E Bullerwell
    Department of Biochemistry and Molecular Biology, Dalhousie University, Room 8F 2, Sir Charles Tupper Medical Building, 5850 College Street, Halifax, Nova Scotia B3H 1X5, Canada
    Curr Opin Microbiol 7:528-34. 2004
    ....
  42. ncbi The chloroplast genomes of the green algae Pedinomonas minor, Parachlorella kessleri, and Oocystis solitaria reveal a shared ancestry between the Pedinomonadales and Chlorellales
    Monique Turmel
    Departement de Biochimie et de Microbiologie, Universite Laval, Québec Québec Canada
    Mol Biol Evol 26:2317-31. 2009
    ..Our results further emphasize the importance of secondary reduction at both the cellular and genome levels during chlorophyte evolution...
  43. pmc A gene-based linkage map for Bicyclus anynana butterflies allows for a comprehensive analysis of synteny with the lepidopteran reference genome
    Patricia Beldade
    Institute of Biology, Leiden University, Leiden, The Netherlands
    PLoS Genet 5:e1000366. 2009
    ..This is discussed in relation to the identification of the loci contributing to color pattern evolution in butterflies...
  44. pmc The posttranslocation chaperone PrsA2 contributes to multiple facets of Listeria monocytogenes pathogenesis
    Francis Alonzo
    UIC Department of Microbiology and Immunology MC790, Chicago, IL 60612 7344, USA
    Infect Immun 77:2612-23. 2009
    ..PrsA2 is thus distinct from PrsA1 in its unique requirement for the stability and full activity of L. monocytogenes-secreted factors that contribute to host infection...
  45. ncbi Multiple rearrangements in mitochondrial genomes of Isopoda and phylogenetic implications
    Fabian Kilpert
    Institute of Evolutionary Biology and Ecology, Rheinische Friedrich Wilhelms Universitat Bonn, Bonn, Germany
    Mol Phylogenet Evol 64:106-17. 2012
    In this study, we analyse the evolutionary dynamics and phylogenetic implications of gene order rearrangements in five newly sequenced mitochondrial (mt) genomes and four published mt genomes of isopod crustaceans...
  46. pmc Genome and proteome analysis of 7-7-1, a flagellotropic phage infecting Agrobacterium sp H13-3
    Andrew M Kropinski
    Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, ON, NIG 3W4, Canada
    Virol J 9:102. 2012
    ..Here we describe the complete genomic sequence of 69,391 base pairs of this unusual bacteriophage...
  47. ncbi Inference of the phylogenetic position of the phylum Deferribacteres from gene order comparison
    Takashi Kunisawa
    Department of Applied Biological Sciences, Science University of Tokyo, Noda, Japan
    Antonie Van Leeuwenhoek 99:417-22. 2011
    The phylogenetic placement of the phylum Deferribacteres was investigated on the basis of gene order comparisons of completely sequenced bacterial genomes...
  48. pmc The mitochondrial genome of the lycophyte Huperzia squarrosa: the most archaic form in vascular plants
    Yang Liu
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
    PLoS ONE 7:e35168. 2012
    ..It also has the least rearranged gene order in comparison to the chondromes of other vascular plants...
  49. ncbi Chromatin structure and the regulation of gene expression: the lessons of PEV in Drosophila
    Jack R Girton
    Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
    Adv Genet 61:1-43. 2008
    ..Current studies of PEV are focusing on defining the complex patterns of modifier gene activity and the sequence of events that leads to the dynamic interplay between heterochromatin and euchromatin...
  50. pmc Complete DNA sequences of the plastid genomes of two parasitic flowering plant species, Cuscuta reflexa and Cuscuta gronovii
    Helena T Funk
    Department of Cell Biology, Philipps University Marburg, Karl von Frisch Str, D 35032 Marburg, Germany
    BMC Plant Biol 7:45. 2007
    ..reflexa to a restricted photosynthetic activity and degenerated chloroplasts in C. gronovii to an achlorophyllous state in E. virginiana...
  51. ncbi eGOB: eukaryotic Gene Order Browser
    Marcela Dávila López
    Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, SE 405 30 Goteborg, Sweden
    Bioinformatics 27:1150-1. 2011
    ..Here, we present the eukaryotic Gene Order Browser with information on the order of protein and non-coding RNA (ncRNA) genes of 74 different eukaryotic ..
  52. ncbi Complete mitochondrial genome sequences of the three pelagic chaetognaths Sagitta nagae, Sagitta decipiens and Sagitta enflata
    Hiroomi Miyamoto
    Ocean Research Institute, University of Tokyo, Tokyo, 164 8639, Japan
    Comp Biochem Physiol Part D Genomics Proteomics 5:65-72. 2010
    ..The gene order of this cluster was also assumed to be the ancestral state of the phylum.
  53. pmc Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics
    A H Paterson
    Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
    Proc Natl Acad Sci U S A 101:9903-8. 2004
    ..Additional ancient duplication events probably remain to be discovered in other angiosperm lineages...
  54. pmc A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome
    Guillaume Blanc
    Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland
    Genome Res 13:137-44. 2003
    ....
  55. pmc Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements
    Frank Jühling
    Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16 18, D 04107 Leipzig, Germany
    Nucleic Acids Res 40:2833-45. 2012
    ..Direct evidence for several recent Tandem Duplication-Random Loss events is gained, demonstrating that this mechanism has an impact on the appearance of new mitochondrial gene orders...
  56. pmc Comparative genomics of multidrug resistance-encoding IncA/C plasmids from commensal and pathogenic Escherichia coli from multiple animal sources
    Claudia Fernandez-Alarcon
    Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St Paul, Minnesota, United States of America
    PLoS ONE 6:e23415. 2011
    ....
  57. pmc Phylogeny and mitochondrial gene order variation in Lophotrochozoa in the light of new mitogenomic data from Nemertea
    Lars Podsiadlowski
    Abteilung Evolutionsbiologie, Institut fur Evolutionsbiologie und Okologie, Universitat Bonn, Germany
    BMC Genomics 10:364. 2009
    ..g. Mollusca, Brachiozoa or Platyhelminthes. Mitochondrial genomes contributed well with sequence data and gene order characters to the deep metazoan phylogeny debate.
  58. pmc The complete mitochondrial genome of the Asiatic cavity-nesting honeybee Apis cerana (Hymenoptera: Apidae)
    Hong Wei Tan
    State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
    PLoS ONE 6:e23008. 2011
    ..The complete mtDNA sequence of A. cerana provides additional genetic markers for studying population genetics, systematics and phylogeographics of honeybees...
  59. ncbi Numerous gene rearrangements in the mitochondrial genome of the wallaby louse, Heterodoxus macropus (Phthiraptera)
    R Shao
    Department of Microbiology and Parasitology, and Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
    Mol Biol Evol 18:858-65. 2001
    ..The large number of gene rearrangements in the mt genome of H. macropus is unprecedented for an arthropod...
  60. ncbi QseBC controls flagellar motility, fimbrial hemagglutination and intracellular virulence in fish pathogen Edwardsiella tarda
    Xin Wang
    State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, PR China
    Fish Shellfish Immunol 30:944-53. 2011
    ..Our results revealed that the QseBC system modified the virulence-related surface structures (flagellum, fimbriae and secretion system) and that hormone might stimulate the virulence of the pathogen in fish...
  61. pmc Conservation of the biotin regulon and the BirA regulatory signal in Eubacteria and Archaea
    Dmitry A Rodionov
    State Scientific Center GosNIIGenetika, Moscow 113545, Russia
    Genome Res 12:1507-16. 2002
    ..BirA is the first example of a transcriptional regulator with a conserved binding signal in eubacteria and archaea...
  62. pmc Identification of mammalian orthologs using local synteny
    Jin Jun
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
    BMC Genomics 10:630. 2009
    ..have been most successfully implemented in fungal genomes and have long been used in prokaryotic genomes, where gene order is far less variable than in vertebrates...
  63. pmc High-density linkage mapping and evolution of paralogs and orthologs in Salix and Populus
    Sofia Berlin
    Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences, PO Box 7090, SE 750 07 Uppsala, Sweden
    BMC Genomics 11:129. 2010
    ..The marker positions in the two genomes were used to study genome evolution since the divergence of the two lineages some 45 mya...
  64. pmc Complete DNA sequences of the mitochondrial genomes of the pathogenic yeasts Candida orthopsilosis and Candida metapsilosis: insight into the evolution of linear DNA genomes from mitochondrial telomere mutants
    Peter Kosa
    Department of Biochemistry, Faculty of Natural Sciences, Comenius University Mlynska dolina, CH 1 and B 1, 842 15, Bratislava, Slovak Republic
    Nucleic Acids Res 34:2472-81. 2006
    ....
  65. pmc Identification and characterization of catabolic para-nitrophenol 4-monooxygenase and para-benzoquinone reductase from Pseudomonas sp. strain WBC-3
    Jun Jie Zhang
    Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
    J Bacteriol 191:2703-10. 2009
    ..J. Moonen, N. M. Kamerbeek, A. H. Westphal, S. A. Boeren, D. B. Janssen, M. W. Fraaije, and W. J. van Berkel, J. Bacteriol. 190:5190-5198, 2008), suggesting that the genes involved in PNP degradation are physically linked...
  66. pmc Discovery of stable and variable differences in the Mycobacterium avium subsp. paratuberculosis type I, II, and III genomes by pan-genome microarray analysis
    Elena Castellanos
    Centro de Vigilancia Sanitaria Veterinaria, Departamento Sanidad Animal, Universidad Complutense, Madrid, Spain
    Appl Environ Microbiol 75:676-86. 2009
    ..Quantitative PCR demonstrated that variation in vGI signals could be associated with colony growth rate and morphology...
  67. ncbi Complete mitochondrial genome of brown marmorated stink bug Halyomorpha halys (Hemiptera: Pentatomidae), and phylogenetic relationships of hemipteran suborders
    Wonhoon Lee
    Insect Biosystematics Laboratory, Research Institute for Agricultural and Life Sciences, Department of Agricultural Biotechnology, Seoul National University, Korea
    Mol Cells 28:155-65. 2009
    ..The mitochondrial gene arrangements of the 20 genomes=are also consistent with our results...
  68. ncbi Complete mitochondrial genome of the small brown planthopper, Laodelphax striatellus (Delphacidae: Hemiptera), with a novel gene order
    Nan Song
    Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, China
    Zoolog Sci 26:851-60. 2009
    ..striatellus mitogenome is identical to other completely sequenced insect mitogenomes, while the gene order is different from the common arrangement found in most insects: five tRNA genes and three PCGs in the L...
  69. pmc The determinants of gene order conservation in yeasts
    Juan F Poyatos
    Logic of Genomic Systems Laboratory, Spanish National Biotechnology Centre, Centro Superior de Investigaciones Científicas CSIC, Darwin 3, Campus de Cantoblanco, Madrid 28049, Spain
    Genome Biol 8:R233. 2007
    ....
  70. pmc Chloroplast DNA rearrangements in Campanulaceae: phylogenetic utility of highly rearranged genomes
    Mary E Cosner
    Department of Plant Biology, Ohio State University, Columbus OH 43210, USA
    BMC Evol Biol 4:27. 2004
    ..Taxonomic treatments vary widely and little phylogenetic work has been done in the family. Gene order in the chloroplast genome usually varies little among vascular plants...
  71. ncbi A novel rearrangement in the mitochondrial genome of tongue sole, Cynoglossus semilaevis: control region translocation and a tRNA gene inversion
    Xiaoyu Kong
    Marine Biodiversity Collection of South China Sea, Laboratory of Marine Bioresource Sustainable Utilization, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, China
    Genome 52:975-84. 2009
    ..The remaining gene order is identical to that of typical fish mitogenomes...
  72. ncbi The analysis of the complete mitochondrial genome of Lecanicillium muscarium (synonym Verticillium lecanii) suggests a minimum common gene organization in mtDNAs of Sordariomycetes: phylogenetic implications
    Vassili N Kouvelis
    Department of Genetics and Biotechnology, Faculty of Biology, University of Athens, Panepistemiopolis, Athens 157 01, Greece
    Fungal Genet Biol 41:930-40. 2004
    ..All genes are transcribed from the same DNA strand. Gene order comparison with all available complete fungal mtDNAs-representatives of all four Phyla are included-revealed ..
  73. ncbi The mitochondrial genome of the olive fly Bactrocera oleae: two haplotypes from distant geographical locations
    F Nardi
    Department of Evolutionary Biology, University of Siena, Siena, Italy
    Insect Mol Biol 12:605-11. 2003
    ..The differences are mostly transitions (26) and synonymous substitutions in PCGs (21). The two new sequences are compared with others already present in the database...
  74. pmc High rate of chimeric gene origination by retroposition in plant genomes
    Wen Wang
    CAS Max Plank Junior Research Group, Key Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
    Plant Cell 18:1791-802. 2006
    ..These observations suggest that retroposition is an important mechanism that governs gene evolution in rice and other grass species...
  75. ncbi The complete mitochondrial genome of the vascular wilt fungus Verticillium dahliae: a novel gene order for Verticillium and a diagnostic tool for species identification
    Malena P Pantou
    Department of Genetics and Biotechnology, Faculty of Biology, University of Athens, Panepistemiopolis, Greece
    Curr Genet 50:125-36. 2006
    ..b>Gene order comparisons of V...
  76. pmc Conservation and functional significance of gene topology in the genome of Caenorhabditis elegans
    Nansheng Chen
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Genome Res 16:606-17. 2006
    ....
  77. ncbi An unusual source of apparent mitochondrial heteroplasmy: duplicate mitochondrial control regions in Thalassarche albatrosses
    Cathryn L Abbott
    School of Botany and Zoology, The Australian National University, Canberra ACT 0200, Australia
    Mol Ecol 14:3605-13. 2005
    ....
  78. pmc Genome survey sequencing of the wine spoilage yeast Dekkera (Brettanomyces) bruxellensis
    Megan Woolfit
    Department of Genetics, Smurfit Institute, Trinity College Dublin, Dublin 2, Ireland
    Eukaryot Cell 6:721-33. 2007
    ..These data provide a resource for further analyses of the population genetics and evolution of D. bruxellensis and of the genetic bases of its physiological capabilities...
  79. pmc SynBlast: assisting the analysis of conserved synteny information
    Jörg Lehmann
    Bioinformatics Group, Department of Computer Science, University of Leipzig, Härtelstrasse 16 18, D 04107 Leipzig, Germany
    BMC Bioinformatics 9:351. 2008
    ..This situation can be improved in many cases by including conserved synteny information...
  80. ncbi Order and disorder in bacterial genomes
    Eduardo P C Rocha
    Unité Génétique des Génomes Bactériens, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
    Curr Opin Microbiol 7:519-27. 2004
    ..As a result, the clash between elements generating rearrangements and chromosome organization is a classic case of evolutionary conflict...
  81. pmc Gene content and virtual gene order of barley chromosome 1H
    Klaus F X Mayer
    Munich Information Center for Protein Sequences Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany
    Plant Physiol 151:496-505. 2009
    ..Thus, integration of genomic, transcriptomic, and synteny-derived information represents a major step toward developing reference sequences of chromosomes and complete genomes of the most important plant tribe for mankind...
  82. pmc Multidrug-resistant Salmonella enterica serovar paratyphi A harbors IncHI1 plasmids similar to those found in serovar typhi
    Kathryn E Holt
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    J Bacteriol 189:4257-64. 2007
    ..Our data show that these serovar Typhi and Paratyphi A IncHI1 plasmids share highly conserved core DNA and have acquired similar mobile elements encoding antibiotic resistance genes in past decades...
  83. ncbi The biosynthesis and regulation of bacterial prodiginines
    Neil R Williamson
    Department of Biochemistry, Tennis Court Road, University of Cambridge, UK
    Nat Rev Microbiol 4:887-99. 2006
    ..However, research into the biology of pigment production will stimulate interest in the bioengineering of strains to synthesize useful prodiginine derivatives...
  84. ncbi The mitochondrial DNA of land plants: peculiarities in phylogenetic perspective
    Volker Knoop
    IZMB Institut für Zelluläre und Molekulare Botanik, Universitat Bonn, Kirschallee 1, Bonn, Germany
    Curr Genet 46:123-39. 2004
    ..This review attempts to summarize the unique aspects of land plant mitochondrial evolution from a phylogenetic perspective...
  85. pmc Characterization of novel components of the baculovirus per os infectivity factor complex
    Ke Peng
    Laboratory of Virology, Wageningen University, Wageningen, The Netherlands
    J Virol 86:4981-8. 2012
    ..Three other proteins, AC5, AC68, and AC108 (homologue of SF58), were also found by the proteomic analysis to be associated with the PIF complex. Finally the functional significance of the PIF protein interactions is discussed...
  86. ncbi Comparative genomics and phylogeny of the IncI1 plasmids: a common plasmid type among porcine enterotoxigenic Escherichia coli
    Timothy J Johnson
    Department of Veterinary and Biomedical Sciences, University of Minnesota, 1971 Commonwealth Avenue, 205 Veterinary Science, St Paul, MN 55108, USA
    Plasmid 66:144-51. 2011
    ..Furthermore, the high occurrence of IncI1 and IncA/C plasmids among clinical E. coli from commercial swine facilities is indicative of extensive horizontal gene transfer among porcine ETEC...
  87. pmc Analyses of the extent of shared synteny and conserved gene orders between the genome of Fugu rubripes and human 20q
    Sarah F Smith
    Fugu Genomics, United Kingdom Human Genome Mapping Project Resource Centre, Wellcome Genome Campus, Hinxton Hall, Hinxton, Cambridgeshire, CB10 1SB, United Kingdom
    Genome Res 12:776-84. 2002
    ....
  88. pmc Mycobacteriophage Marvin: a new singleton phage with an unusual genome organization
    Catherine Mageeney
    Cabrini College, Department of Science, Radnor, Pennsylvania, USA
    J Virol 86:4762-75. 2012
    ....
  89. pmc The mechanism of Bacillus anthracis intracellular germination requires multiple and highly diverse genetic loci
    Soumitra Barua
    Department of Microbiology and Immunology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, USA
    Infect Immun 77:23-31. 2009
    ..Collectively, these findings provide insight into the mechanisms supporting B. anthracis germination within host cells...
  90. pmc Molecular characterization of a variant of Bacillus anthracis-specific phage AP50 with improved bacteriolytic activity
    Shanmuga Sozhamannan
    Naval Medical Research Center, Silver Spring, Maryland 20910, USA
    Appl Environ Microbiol 74:6792-6. 2008
    ..Spontaneous AP50c-resistant B. anthracis mutants exhibit a mucoid colony phenotype...
  91. ncbi The first complete mitochondrial genome sequences of Amblypygi (Chelicerata: Arachnida) reveal conservation of the ancestral arthropod gene order
    Kathrin Fahrein
    Department of Biology, Koenigin Luise Str 1 3, D 14195 Berlin, Germany
    Genome 52:456-66. 2009
    ..Mitochondrial genomes provide an additional large data set of phylogenetic information (sequences, gene order, RNA secondary structure), but in arachnids, mitochondrial genome data are missing for some of the major orders...
  92. pmc Autoregulation of convergent RNAi genes in fission yeast
    Monika Gullerova
    Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
    Genes Dev 25:556-68. 2011
    ..Our results emphasize the significance of gene orientation for correct RNAi gene expression, and suggest a role for cell cycle-dependent formation of RNAi CG heterochromatin in cellular integrity...
  93. ncbi An association study between polymorphism of L1CAM gene and schizophrenia in a Japanese sample
    A Kurumaji
    Department of Neuropsychiatry, Tokyo Medical and Dental University School of Medicine, Japan
    Am J Med Genet 105:99-104. 2001
    ..These results suggest that the polymorphism in intron 25 plays a role in the genetic predisposition of male schizophrenia in the Japanese sample...
  94. pmc Bacterial syntenies: an exact approach with gene quorum
    Yves Pol Deniélou
    INRIA Grenoble Rhone Alpes, team BAMBOO, 655 avenue de l Europe, 38334 Montbonnot Cedex, France
    BMC Bioinformatics 12:193. 2011
    ..The automatic identification of syntenies across multiple species is a key step in comparative genomics that helps biologists shed light both on evolutionary and functional problems...
  95. ncbi The complete sequence and gene organization of the mitochondrial genome of the gadilid scaphopod Siphonondentalium lobatum (Mollusca)
    Hermann Dreyer
    Institute of Zoology, University of Vienna, Althanstr 14, A 1090 Vienna, Austria
    Mol Phylogenet Evol 31:605-17. 2004
    ..different from all other known molluscan mitochondrial genomes and shows low similarity even to an unpublished gene order of a dentaliid scaphopod...
  96. ncbi The complete mitochondrial genome of Setaria digitata (Nematoda: Filarioidea): Mitochondrial gene content, arrangement and composition compared with other nematodes
    Lalani Yatawara
    Department of Environmental Health Sciences, Kochi Medical School, Oko, Nankoku City, Japan
    Mol Biochem Parasitol 173:32-8. 2010
    ..This genome contains a high A+T (75.1%) content and low G+C content (24.9%). The mt gene order for S. digitata is the same as those for O. volvulus, D. immitis and B...
  97. ncbi Rare genomic changes and mitochondrial sequences provide independent support for congruent relationships among the sea spiders (Arthropoda, Pycnogonida)
    Susan E Masta
    Department of Biology, Portland State University, Portland, OR 97207, USA
    Mol Phylogenet Evol 57:59-70. 2010
    ..b>Gene order and tRNA secondary structure characters provide independent lines of evidence for these inferred phylogenetic ..
  98. ncbi Contracaecum rudolphii B: gene content, arrangement and composition of its complete mitochondrial genome compared with Anisakis simplex s.l
    Rui Qing Lin
    State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, PR China
    Exp Parasitol 130:135-40. 2012
    ..This genome contains a high A+T (70.5%) content. The mt gene order for C. rudolphii B is the same as those for A. simplex s.l...
  99. pmc Conservation of gene order and content in the circular chromosomes of 'Candidatus Liberibacter asiaticus' and other Rhizobiales
    L David Kuykendall
    Molecular Plant Pathology Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America
    PLoS ONE 7:e34673. 2012
    ..Liberibacter asiaticus' genes not shared with other Rhizobiales are of bacteriophage origin. 'Ca. Liberibacter asiaticus' shares 11 genes with only Sinorhizobium meliloti and 12 genes are shared with only Bartonella henselae...
  100. pmc Distinctive mitochondrial genome of Calanoid copepod Calanus sinicus with multiple large non-coding regions and reshuffled gene order: useful molecular markers for phylogenetic and population studies
    Wang Minxiao
    KLMEES and JBMERS, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
    BMC Genomics 12:73. 2011
    ..As they are genome-level informative, mitochondrial DNA sequences can be used as markers for population genetic studies and phylogenetic studies...
  101. ncbi The complete mitochondrial genome of the grand jackknife clam, Solen grandis (Bivalvia: Solenidae): a novel gene order and unusual non-coding region
    Yang Yuan
    Fisheries College, Ocean University of China, Qingdao, China
    Mol Biol Rep 39:1287-92. 2012
    Molluscs in general, and bivalves in particular, exhibit an extraordinary degree of mitochondrial gene order variation when compared with other metazoans...

Research Grants62

  1. Genomic Mechanisms of Chromosomal Rearrangements in Drosophila Pseudoobscura
    Stephen W Schaeffer; Fiscal Year: 2013
    ..Genes that show differential expression or protein variation may be manipulated in future experiments designed to understand the molecular genetic basis that underpins inversion evolution. ..
  2. Structural studies of Togaviruses
    Michael G Rossmann; Fiscal Year: 2013
    ..Alphaviruses and Rubella virus constitute the Togavirus family because of their similarity in gene order and morphology...
  3. Data-driven Computational Modeling of the Growth and Spread of Viruses
    John Yin; Fiscal Year: 2010
    ..model using experimental data from a panel of recombinant VSV strains, and (3) employ the model to predict how gene order affects VSV growth...
  4. Regulation of sleep-like behavior in C. elegans
    DAVID MENASSAH RAIZEN; Fiscal Year: 2013
    ..In addition, we will assess the gene order relationship between egl-4 and pde-4 is regulating sensory gating...
  5. TEST OF NEUTRAL MOLECULAR EVOLUTION
    Martin Kreitman; Fiscal Year: 1999
    ..In(3R)a is a fixed inversion (84F-93F) between D. melanogaster and D. simulans. D. simulans has the ancestral gene order. Recombination on chromosome 3 is suppressed near the centromere (from 81-84), so genes near the breakpoints of ..
  6. INVESTIGATION Of HUMAN COMPLEMENT
    CHESTER ALPER; Fiscal Year: 1999
    ..variation in C2, BF, C4A, C4B, 21-OHA and 21-OHB and related DNA at define the overall size, gene copy number, gene order, and the extent of deletions and insertions in the class III MHC regions of extended and non-extended MHC ..
  7. CELLULAR MECHANISMS OF DRUG REACTIONS IN SCHIZOPHRENIA
    Edmond Yunis; Fiscal Year: 1999
    ..constellations; a,b,c,d,e microsatellites, n intron of TNFB and -308 of promoter region of TNFa) (given in the gene order b,a,n,c, -308, e,d) within the major histocompatibility complex (MHC) are associated with the HLA CA markers...
  8. System Dynamics of the Salmonella Virulence Regulatory Network
    Christopher A Voigt; Fiscal Year: 2012
    ..In Aim 1, the refactored system will be used as a platform to determine how gene order and translational coupling impact the robustness of the cluster to perturbations in expression levels...
  9. Baboon Model for Genetics of Human Generalized Epilepsy
    Jeff Williams; Fiscal Year: 2007
    ..The evolutionary proximity of baboon and human, and the high degree of conservation of gene order between these species, imply that genetic factors identified in the baboon genome will be directly relevant to ..
  10. Structure and activity of Escherichia coli chromosome
    Arkady Khodursky; Fiscal Year: 2007
    ..abstract_text> ..
  11. MOLECULAR BIOLOGY OF B-CELL CHRONIC LYMPHOCYTIC LEUKEMIA
    Elizabeth Newcomb; Fiscal Year: 1993
    ..This study will identify the transforming activity associated with B-CLL disease. Understanding the genetic mechanism of oncogene activation in B- CLL disease may have potential for improved patient diagnosis and treatment...
  12. Remodeling SARS Coronavirus Genome Regulatory Networks
    Ralph Baric; Fiscal Year: 2004
    ..Moreover, we and others have shown that coronaviruses tolerate gene order rearrangements, but as a consequence are attenuated in replication efficiency and pathogenesis...
  13. REVERSE GENETICS WITH A CORONAVIRUS INFECTIOUS CONSTRUCT
    Ralph Baric; Fiscal Year: 2004
    ..we will use reverse genetics and the full length TGE construct to systematically address the role of gene order, cis and trans acting regulatory sequences, and N gene function in coronavirus transcription and replication...
  14. SYSTEMIC AND MUCOSAL IMMUNITY IN ECTOTHERMS
    CRAIG LOBB; Fiscal Year: 2000
    ..These analyses will determine the patterns of gene utilization, the junctional diversity within the encoded CDR3 region, and the interrelationships of genomic organization and developmental expression. ..
  15. ZEBRAFISH MAP FOR COMPARATIVE AND FUNCTIONAL GENOMICS
    WILLIAM TALBOT; Fiscal Year: 2002
    ..between zebrafish and human genomes by identifying the boundaries of conserved chromosomal segments and defining gene order within these segments...
  16. LEISHMANIA GENOME
    Kenneth Stuart; Fiscal Year: 1999
    ..two Leishmania species to establish the basis for chromosome size differences and examine conservation of gene order. The investigators will determine and analyze the sequence of the mapped chromosomes...
  17. MAXIMUM LIKELIHOOD MAPPING OF THE HUMAN CHROMOSOMES
    Bronya Keats; Fiscal Year: 1992
    ..statistical methods will be applied to updating linkage information on pairwise recombination fractions and on gene order, determined from multilocus analyses, in the construction of the linkage maps ...
  18. GENETIC DETERMINATES
    Howard Jacob; Fiscal Year: 1999
    ..2. Convert regions of interest in the rat to human homologs. Conservation of gene order and use of radiation hybrids will facilitate the quick transition to genetic markers for genotyping in humans. 3...
  19. Control of Mammalian Meiotic Recombination
    Terry Ashley; Fiscal Year: 2007
    ..Genetic linkage maps provide information on gene order and crossover frequency but not on the influence of chromosome structure on recombination, while chiasmata ..
  20. Canine Brain Tumors - A New Model for Gene Discovery
    Matthew Breen; Fiscal Year: 2006
    ..Humans and dogs have similar physiology, share extensive genome homology with a high degree of preserved gene order, and are exposed to the same environment...
  21. EVOLUTIONARY MOLECULAR GENETICS OF MITOCHONDRIAL DNA
    WESLEY BROWN; Fiscal Year: 1990
    ..The groups chosen include, respectively, the causative agents of schistosomiasis and their intermediate hosts. Knowledge of the biology of these organisms may ultimately lead to methods of control...
  22. Data-driven Computational Modeling of the Growth and Spread of Viruses
    John Yin; Fiscal Year: 2007
    ..model using experimental data from a panel of recombinant VSV strains, and (3) employ the model to predict how gene order affects VSV growth...
  23. Locus-linked Regulatory Motifs of Globin Gene Switching
    KENNETH PETERSON; Fiscal Year: 2004
    ..sequences involved in activation, silencing and competition for interaction with the locus control region (LCR), gene order, and distance from the LCR...
  24. LINKAGE DISEQUILIBRIUM IN DNA POLYMORPHISMS
    Lynn Jorde; Fiscal Year: 1990
    ..physical distance between closely linked RFLPs? Linkage disequilibrium values have recently been used to infer gene order. This assumes a uniform inverse relationship between disequilibrium and the recombination fraction between loci...
  25. DNA METHYLATION IN T CELL DEVELOPMENT AND FUNCTION
    Christopher Wilson; Fiscal Year: 2004
    ..2) The increased numbers of TCRgammabeta thymocytes will reflect either increased locus accessibility and rearrangement of the relevant gammabeta TCR genes or reduced Notch signaling. ..
  26. GENE MAPPING AND GENOME ORGANIZATION IN MAMMALS
    Joseph Nadeau; Fiscal Year: 1992
    ..The mouse will be used as a model for analyzing gene location, clarifying gene order on specific chromosomal segments, and characterizing the patterns of synteny and linkage conservation during ..
  27. CUMULATIVE MULTILOCUS MAP OF MOUSE CHROMOSOME 5
    VERNE CHAPMAN; Fiscal Year: 1993
    A well-defined genetic map of the mouse genome that establishes gene order in an unambiguous manner and accurately estimates recombinational distances between genes is an important tool for analyzing the molecular basis of mutational ..
  28. IMMUNOGLOBULIN GENE ARRANGEMENT/EXPRESSION IN LEUKEMIA
    Dario Campana; Fiscal Year: 2005
    ..The development of new automated MRD assays and the identification of new markers of leukemia should improve residual disease evaluation and thereby improve risk-directed therapy selection for every child with ALL. ..
  29. LINKAGE ANALYSIS AND MULTIPLE LOCI
    Mark Skolnick; Fiscal Year: 1991
    ..can be divided into two phases: 1) initial assignment of a gene to a chromosomal region, and 2) assignment of gene order and map distance of the disease locus to all of the markers...
  30. HUMAN T COMPLEX TESTES-EXPRESSED GENES & MALE STERILITY
    Lee Silver; Fiscal Year: 1992
    ..The gene order of human chromosome 6 will be compared with that of mouse chromosome 17 to formulate models for chromosomal ..
  31. GENE SEQUENCES ACTIVATING GAMMA-GLOBIN GENE TRANSCRIPTON
    Robert Williamson; Fiscal Year: 1980
    ..The predicted gene order has been confirmed, and polymorphisms were used to distinguish between the two gamma-globin genes and between ..
  32. MARINER TRANSPOSONS OF MAMMALS
    Hugh Robertson; Fiscal Year: 2001
    ..It will also reveal how occasionally particular copies of transposons can become integral parts of their host genetic complements. ..
  33. Gustatory and olfactory receptors of Anopheles gambiae
    Hugh Robertson; Fiscal Year: 2006
    ..This work will also contribute to our overall understanding of the molecular basis of chemoreception in insects and other animals. [unreadable] [unreadable]..
  34. Characterization of sar-agr Interactions in S. aureus
    AMBROSE LIN YAU CHEUNG; Fiscal Year: 2010
    ..Our goal is to understand how SarA controls target gene and how other intracellular regulators affect SarA expression in S. aureus. ..
  35. Dimension Reduction Approaches for Genome-wide Association Testing
    Andrew Clark; Fiscal Year: 2008
    ..Of particular interest will be the tuning model parameters to optimize the balance of false positive and false negative inferences. [unreadable] [unreadable] [unreadable] [unreadable]..
  36. Regulation and function of cGMP in the nervous system
    David B Morton; Fiscal Year: 2011
    ..Viagra and other pharmacological treatments for erectile disfunction are probably just the tip of the iceberg for compounds that target cGMP mediated processes. ..
  37. Desmosomal components and epithelial cell fate decision
    MY MAHONEY; Fiscal Year: 2008
    ..Determining the molecular mechanisms by which desmoglein 2 affects tumor growth and development has the potential of identifying new targets for therapeutic cancer treatments. [unreadable] [unreadable] [unreadable]..
  38. Comparative genetics of Lesch-Nyhan disease
    James Thomas; Fiscal Year: 2008
    ..unreadable] [unreadable] [unreadable]..
  39. Determinants of RNA virus evolution
    ISABEL NOVELLA; Fiscal Year: 2009
    ....
  40. Phylogenetic Analysis with Complex Genome Rearrangement Events
    Jijun Tang; Fiscal Year: 2009
    ..A new type of data based on gene order and gene content within whole genomes has attracted increasing interest from researchers in the past several ..
  41. Inferring the Roadmap of Bacterial Gene Transfer
    Jeffrey Lawrence; Fiscal Year: 2009
    ..This framework will allow us to test the hypothesis that gene transfer occurs more often between more closely related lineages. ..
  42. Metagenomic analysis of the human virome
    Eric L Delwart; Fiscal Year: 2010
    ..This metagenomic survey of non-human nucleic acids in humans will therefore begin the task of determining the full range of viral diversity in humans. ..
  43. Genomic Approaches to Improve Transfusion Therapy in SCD Patients
    Marion E Reid; Fiscal Year: 2010
    ..We believe that data generated from this project will have an immediate impact in improving the transfusion of patients with SCD. (End of Abstract) ..
  44. The Genetics of Female Reproductive Aging
    Tara Matise; Fiscal Year: 2008
    ..Finally, enhancing our understanding of reproductive senescence may facilitate improvements in technologies used for assisted reproduction. [unreadable] [unreadable] [unreadable]..
  45. Rat, a regulator of autolysis in S. aureus
    Ambrose Cheung; Fiscal Year: 2008
    ..Our long-term goal is to promote autolysis with an anti-Rat or pro-SarV strategy without developing an untoward impact on virulence. ..
  46. MICROBIAL METABOLISM OF REDUCED PHOSPHORUS COMPOUNDS
    WILLIAM METCALF; Fiscal Year: 2008
    ..unreadable] [unreadable]..
  47. REGULATION OF BRAIN PEPTIDE BIOSYNTHESIS
    Michael Bannon; Fiscal Year: 2003
    ....
  48. INTEGRATION AND EXCISION OF PROPHAGES IN TUBERCULOSIS
    Graham Hatfull; Fiscal Year: 2003
    ..tuberculoses to determine whether they have functional recombination systems; whether they act as Genetic Transfer Agents; and whether they play a role in virulence of M. tuberculosis. ..
  49. Desmoglein 2 Function in Cell Adhesion and Pemphigus
    MY MAHONEY; Fiscal Year: 2003
    ..To this end, the ultimate goal is to find a means to upregulate Dsg2 in the epidermis as a therapeutic approach to pemphigus. ..
  50. MECHANISM OF PHAGE L5 INTEGRATION AND EXCISION
    Graham Hatfull; Fiscal Year: 2002
    ..In addition to Providing new insights into the mechanism of recombination these studies will offer new tools for mycobacterial genetics and a greater understanding of mycobacterial physiology. ..
  51. REPLICATION AND ENCAPSIDATION OF NODAVIRUS RNAS
    L Ball; Fiscal Year: 2004
    ....
  52. Genome-Wide Analysis of Gene Duplication in Vertebrates
    MARIE DURAND; Fiscal Year: 2004
    ....
  53. Gene Duplication and Genome Evolution
    Austin Hughes; Fiscal Year: 2004
    ..5) Examining the role of transposable elements in duplication of genomic segments by testing for nonrandom association between these elements and putatively duplicated blocks in the yeast genome. ..
  54. CMT Peripheral Neuropathy: IV. Genes and Pathogenesis
    JAMES LUPSKI; Fiscal Year: 2005
    ..abstract_text> ..
  55. The Genetic Epidemiology of Asthma in Costa Rica
    Scott Weiss; Fiscal Year: 2005
    ..Thus, this proposal will greatly contribute to our understanding of the pathogenesis of a significant public health problem among Hispanic Americans: bronchial asthma. ..
  56. Methionine Recycling Pathways in Klebsiella
    Jeffrey Lawrence; Fiscal Year: 2006
    ..In this way, characterization of these pathways sheds light on the evolution of complex metabolism, and on the selective forces that lead to gene acquisition, gene loss, and genome change. ..
  57. Nickel Metabolism in Helicobacter pylori
    Robert Maier; Fiscal Year: 2006
    ..The role of a DNA binding and nickel-sensing protein (NikR) is of particular interest as it may play a global regulatory role in metal homeostasis, in turn affecting many processes of cell metabolism. ..
  58. Replication and processing of baculovirus genomes
    GEORGE ROHRMANN; Fiscal Year: 2005
    ..From these studies, major advances in the elucidation of this important and possibly novel replication system are expected. ..
  59. DNA SEQUENCES INVOLVED IN THE HEAVY CHAIN SWITCH
    Wesley Dunnick; Fiscal Year: 2006
    ..We will examine the role of the orientation of switch sequences, and hence the role of the unusual complexes between germline transcripts and switch region DNA, in Aim 4. ..
  60. RNAi-mediated Silencing of Mutant Superoxide Dismutase
    MICHELE MAXWELL; Fiscal Year: 2006
    ..In addition, the therapeutic potential of RNAi will be assessed using viral delivery of shRNA to the spinal cords of mutant SOD1 transgenic mice. ..
  61. GENE THERAPY FOR HURLERS DISEASE
    Donald Kohn; Fiscal Year: 2001
    ..Successful tolerance induction in murine and canine models of MPS I will be an Important step toward application of gene therapy in human patients. ..