conserved sequence

Summary

Summary: A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.

Top Publications

  1. ncbi Initial sequencing and analysis of the human genome
    E S Lander
    Whitehead Institute for Biomedical Research, Center for Genome Research, Cambridge, Massachusetts 02142, USA
    Nature 409:860-921. 2001
  2. pmc Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
    Mitchell Guttman
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 458:223-7. 2009
  3. ncbi Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
    J Castresana
    European Molecular Biology Laboratory, Heidelberg, Germany
    Mol Biol Evol 17:540-52. 2000
  4. pmc Mauve: multiple alignment of conserved genomic sequence with rearrangements
    Aaron C E Darling
    Department of Computer Science, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
    Genome Res 14:1394-403. 2004
  5. pmc Human MicroRNA targets
    Bino John
    Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, New York, USA
    PLoS Biol 2:e363. 2004
  6. pmc Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Ewan Birney
    Nature 447:799-816. 2007
  7. ncbi MatInspector and beyond: promoter analysis based on transcription factor binding sites
    K Cartharius
    Genomatix Software GmbH Landsberger Strasse 6, 80339 München, Germany
    Bioinformatics 21:2933-42. 2005
  8. ncbi Role for a bidentate ribonuclease in the initiation step of RNA interference
    E Bernstein
    Cold Spring Harbor Laboratory, New York 11724, USA
    Nature 409:363-6. 2001
  9. pmc Detection of nonneutral substitution rates on mammalian phylogenies
    Katherine S Pollard
    Gladstone Institutes, University of California, San Francisco, San Francisco, California 94158, USA
    Genome Res 20:110-21. 2010
  10. pmc A mammalian microRNA expression atlas based on small RNA library sequencing
    Pablo Landgraf
    Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Box 186, The Rockefeller University, New York, NY 10021, USA
    Cell 129:1401-14. 2007

Detail Information

Publications276 found, 100 shown here

  1. ncbi Initial sequencing and analysis of the human genome
    E S Lander
    Whitehead Institute for Biomedical Research, Center for Genome Research, Cambridge, Massachusetts 02142, USA
    Nature 409:860-921. 2001
    ..We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence...
  2. pmc Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
    Mitchell Guttman
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 458:223-7. 2009
    ..Together, these results define a unique collection of functional lincRNAs that are highly conserved and implicated in diverse biological processes...
  3. ncbi Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
    J Castresana
    European Molecular Biology Laboratory, Heidelberg, Germany
    Mol Biol Evol 17:540-52. 2000
    ....
  4. pmc Mauve: multiple alignment of conserved genomic sequence with rearrangements
    Aaron C E Darling
    Department of Computer Science, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
    Genome Res 14:1394-403. 2004
    ..We have evaluated the quality of Mauve alignments and drawn comparison to other methods through extensive simulations of genome evolution...
  5. pmc Human MicroRNA targets
    Bino John
    Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, New York, USA
    PLoS Biol 2:e363. 2004
    ..microrna.org. Our analysis suggests that miRNA genes, which are about 1% of all human genes, regulate protein production for 10% or more of all human genes...
  6. pmc Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Ewan Birney
    Nature 447:799-816. 2007
    ..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function...
  7. ncbi MatInspector and beyond: promoter analysis based on transcription factor binding sites
    K Cartharius
    Genomatix Software GmbH Landsberger Strasse 6, 80339 München, Germany
    Bioinformatics 21:2933-42. 2005
    ..The next steps in promoter analysis can be tackled only with reliable predictions, e.g. finding phylogenetically conserved patterns or identifying higher order combinations of sites in promoters of co-regulated genes...
  8. ncbi Role for a bidentate ribonuclease in the initiation step of RNA interference
    E Bernstein
    Cold Spring Harbor Laboratory, New York 11724, USA
    Nature 409:363-6. 2001
    ..The enzyme has a distinctive structure, which includes a helicase domain and dual RNase III motifs. Dicer also contains a region of homology to the RDE1/QDE2/ARGONAUTE family that has been genetically linked to RNAi...
  9. pmc Detection of nonneutral substitution rates on mammalian phylogenies
    Katherine S Pollard
    Gladstone Institutes, University of California, San Francisco, San Francisco, California 94158, USA
    Genome Res 20:110-21. 2010
    ..We also describe new "Conservation" tracks in the UCSC Genome Browser that display both phyloP and phastCons scores for genome-wide alignments of 44 vertebrate species...
  10. pmc A mammalian microRNA expression atlas based on small RNA library sequencing
    Pablo Landgraf
    Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Box 186, The Rockefeller University, New York, NY 10021, USA
    Cell 129:1401-14. 2007
    ..We also propose a subclassification scheme for miRNAs for assisting future experimental and computational functional analyses...
  11. pmc ChIP-seq accurately predicts tissue-specific activity of enhancers
    Axel Visel
    Genomics Division, MS 84 171, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Nature 457:854-8. 2009
    ....
  12. ncbi Computational identification of plant microRNAs and their targets, including a stress-induced miRNA
    Matthew W Jones-Rhoades
    Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA
    Mol Cell 14:787-99. 2004
    ..The expression of miR395, the sulfurylase-targeting miRNA, increases upon sulfate starvation, showing that miRNAs can be induced by environmental stress...
  13. pmc Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
    Adam Siepel
    Center for Biomolecular Science and Engineering, University of California, Santa Cruz, Santa Cruz, California 95064, USA
    Genome Res 15:1034-50. 2005
    ..Noncoding HCEs also show strong statistical evidence of an enrichment for RNA secondary structure...
  14. ncbi Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA
    A E Pasquinelli
    Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston 02114, USA
    Nature 408:86-9. 2000
    ..elegans and Drosophila, at 48 hours after fertilization in zebrafish, and in adult stages of annelids and molluscs. The let-7 regulatory RNA may control late temporal transitions during development across animal phylogeny...
  15. ncbi Initial sequencing and comparative analysis of the mouse genome
    Robert H Waterston
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 420:520-62. 2002
    ....
  16. ncbi Identification of novel genes coding for small expressed RNAs
    M Lagos-Quintana
    Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, , Germany
    Science 294:853-8. 2001
    ..This suggests that sequence-specific, posttranscriptional regulatory mechanisms mediated by small RNAs are more general than previously appreciated...
  17. pmc Distribution and intensity of constraint in mammalian genomic sequence
    Gregory M Cooper
    Department of Genetics, Stanford University, Stanford, California 94305, USA
    Genome Res 15:901-13. 2005
    ..We anticipate that GERP and the types of analyses it facilitates will provide further insights and improved annotation for the human genome as mammalian genome sequence data become richer...
  18. ncbi The transcriptional landscape of the mammalian genome
    P Carninci
    Science 309:1559-63. 2005
    ..The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development...
  19. ncbi An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans
    N C Lau
    Whitehead Institute for Biomedical Research, and Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA
    Science 294:858-62. 2001
    ..The abundance of these tiny RNAs, their expression patterns, and their evolutionary conservation imply that, as a class, miRNAs have broad regulatory functions in animals...
  20. ncbi Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae
    James E Galagan
    The Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, Massachusetts 02142, USA
    Nature 438:1105-15. 2005
    ..These results enhance our understanding of these widely studied fungi as well as provide new insight into eukaryotic genome evolution and gene regulation...
  21. pmc The genome of the Western clawed frog Xenopus tropicalis
    Uffe Hellsten
    Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
    Science 328:633-6. 2010
    ..The genome exhibits substantial shared synteny with human and chicken over major parts of large chromosomes, broken by lineage-specific chromosome fusions and fissions, mainly in the mammalian lineage...
  22. pmc Origin and evolution of spliceosomal introns
    Igor B Rogozin
    National Center for Biotechnology Information NLM NIH, 8600 Rockville Pike, Bldg, 38A, Bethesda, MD 20894, USA
    Biol Direct 7:11. 2012
    ....
  23. pmc Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaea L.)
    Chuan Zhi Zhao
    High Tech Research Center, Shandong Academy of Agricultural Sciences, Key Laboratory of Crop Genetic Improvement and Biotechnology, Huanghuaihai, Ministry of Agriculture, Jinan 250100, PR China
    BMC Plant Biol 10:3. 2010
    ..Increasing investigations have been performed on important agricultural crops including soybean, conifers, and Phaselous vulgaris but no studies have been reported on discovering peanut miRNAs using a cloning strategy...
  24. ncbi Attributes of short linear motifs
    Norman E Davey
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Mol Biosyst 8:268-81. 2012
    ..Finally, the most interesting conclusions are examined in regard to their functional consequences...
  25. ncbi Identification of grapevine microRNAs and their targets using high-throughput sequencing and degradome analysis
    Vitantonio Pantaleo
    Istituto di Virologia Vegetale, Consiglio Nazionale delle Ricerche, Torino, Italy
    Plant J 62:960-76. 2010
    ..Finally, 112 target mRNAs of known and 44 target mRNAs of new grapevine-specific miRNAs were identified by genomic-scale high-throughput sequencing of miRNA cleaved mRNAs...
  26. pmc ChIP-Seq identification of weakly conserved heart enhancers
    Matthew J Blow
    Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
    Nat Genet 42:806-10. 2010
    ..These results provide evidence for a large population of poorly conserved heart enhancers and suggest that the evolutionary conservation of embryonic enhancers can vary depending on tissue type...
  27. pmc Comparative genomics of the neglected human malaria parasite Plasmodium vivax
    Jane M Carlton
    The Institute for Genomic Research J Craig Venter Institute, 9704 Medical Research Drive, Rockville, Maryland 20850, USA
    Nature 455:757-63. 2008
    ..Completion of the P. vivax genome provides the scientific community with a valuable resource that can be used to advance investigation into this neglected species...
  28. pmc Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs
    J Graham Ruby
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Genome Res 17:1850-64. 2007
    ....
  29. ncbi ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information
    Fabian Glaser
    The George S Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
    Bioinformatics 19:163-4. 2003
    ..We present a new web server, ConSurf, which automates these algorithmic tools. ConSurf may be used for high-throughput characterization of functional regions in proteins...
  30. pmc Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences
    Michael F Berger
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    Cell 133:1266-76. 2008
    ..Our results provide an unprecedented level of resolution in the analysis of this simple domain structure and suggest that variation in sequence recognition may be a factor in its functional diversity and evolutionary success...
  31. ncbi CLANS: a Java application for visualizing protein families based on pairwise similarity
    Tancred Frickey
    Max Planck Institut fuer Entwicklungsbiologie, Spemannstrasse 35, 72076 Tuebingen, Germany
    Bioinformatics 20:3702-4. 2004
    ..AVAILABILITY: CLANS can be downloaded at http://protevo.eb.tuebingen.mpg.de/download...
  32. ncbi Conservation and divergence of plant microRNA genes
    Baohong Zhang
    The Institute of Environmental and Human Health TIEHH, and Department of Environmental Toxicology, Texas Tech University, Lubbock, TX 79409 1163, USA
    Plant J 46:243-59. 2006
    ..Regulation of gene expression by miRNAs appears to have existed at the earliest stages of plant evolution and has been tightly constrained (functionally) for more than 425 million years...
  33. ncbi An extensive class of small RNAs in Caenorhabditis elegans
    R C Lee
    Dartmouth Medical School, Department of Genetics, Hanover, NH 03755, USA
    Science 294:862-4. 2001
    ..elegans larval development, and three of them have apparent homologs in mammals and/or insects. Small noncoding RNAs of the miRNA class appear to be numerous and diverse...
  34. pmc Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis
    Blake C Meyers
    Department of Vegetable Crops, University of California, Davis, California 95616, USA
    Plant Cell 15:809-34. 2003
    ..The observed diversity of these NBS-LRR proteins indicates the variety of recognition molecules available in an individual genotype to detect diverse biotic challenges...
  35. pmc The Arabidopsis basic/helix-loop-helix transcription factor family
    Gabriela Toledo-Ortiz
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    Plant Cell 15:1749-70. 2003
    ..These data are consistent, in principle, with the operation of this combinatorial mechanism in Arabidopsis...
  36. pmc MicroRNA targeting specificity in mammals: determinants beyond seed pairing
    Andrew Grimson
    Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Mol Cell 27:91-105. 2007
    ..Because it predicts site efficacy without recourse to evolutionary conservation, the model also identifies effective nonconserved sites and siRNA off-targets...
  37. ncbi Genome sequence, comparative analysis and haplotype structure of the domestic dog
    Kerstin Lindblad-Toh
    Broad Institute of Harvard and MIT, 320 Charles Street, Cambridge, Massachusetts 02141, USA
    Nature 438:803-19. 2005
    ..The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health...
  38. ncbi The amphioxus genome and the evolution of the chordate karyotype
    Nicholas H Putnam
    Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
    Nature 453:1064-71. 2008
    ..These genome-scale events shaped the vertebrate genome and provided additional genetic variation for exploitation during vertebrate evolution...
  39. pmc High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes
    Noah Fahlgren
    Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
    PLoS ONE 2:e219. 2007
    ..We suggest that MIRNA genes are undergoing relatively frequent birth and death, with only a subset being stabilized by integration into regulatory networks...
  40. pmc Evolutionary conservation of sequence and secondary structures in CRISPR repeats
    Victor Kunin
    DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
    Genome Biol 8:R61. 2007
    ..It has been recently shown that CRISPR provides acquired resistance against viruses in prokaryotes...
  41. ncbi Evolutionary rate in the protein interaction network
    Hunter B Fraser
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    Science 296:750-2. 2002
    ..We confirm one predicted outcome of this process-namely, that interacting proteins evolve at similar rates...
  42. ncbi Natural selection on human microRNA binding sites inferred from SNP data
    Kevin Chen
    Center for Comparative Functional Genomics, Department of Biology, New York University, New York, New York 10003, USA
    Nat Genet 38:1452-6. 2006
    ..selection in humans is stronger on computationally predicted conserved miRNA binding sites than on other conserved sequence motifs in 3' UTRs, thus providing independent support for the target prediction model and explicitly ..
  43. pmc Segmental structure of the Brassica napus genome based on comparative analysis with Arabidopsis thaliana
    Isobel A P Parkin
    Department of Agronomy, University of Wisconsin, Madison, 53706, USA
    Genetics 171:765-81. 2005
    ..The comparative map assists in exploiting the Arabidopsis genomic sequence for marker and candidate gene identification within the larger, intractable genomes of the Brassica polyploids...
  44. pmc A genome-wide characterization of microRNA genes in maize
    Lifang Zhang
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
    PLoS Genet 5:e1000716. 2009
    ..As maize is one of the principal models for plant growth and development, this study will serve as a foundation for future research into the functional roles of miRNA genes...
  45. ncbi Ultraconserved regions encoding ncRNAs are altered in human leukemias and carcinomas
    George A Calin
    Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210, USA
    Cancer Cell 12:215-29. 2007
    ..Our findings argue that ncRNAs and interaction between noncoding genes are involved in tumorigenesis to a greater extent than previously thought...
  46. pmc Deep sequencing discovery of novel and conserved microRNAs in trifoliate orange (Citrus trifoliata)
    Changnian Song
    College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
    BMC Genomics 11:431. 2010
    ..Deep sequencing technologies have facilitated identification of species-specific or lowly expressed as well as conserved or highly expressed miRNAs in plants...
  47. ncbi The deep evolution of metazoan microRNAs
    Benjamin M Wheeler
    Department of Computer Science, North Carolina State University, Raleigh, NC 27695, USA
    Evol Dev 11:50-68. 2009
    ..We propose that miRNAs might be excellent phylogenetic markers, and suggest that the advent of morphological complexity might have its roots in miRNA innovation...
  48. pmc Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening
    Simon Moxon
    School of Computing, University of East Anglia, Norwich NR4 7TJ, United Kingdom
    Genome Res 18:1602-9. 2008
    ..This study opens a new avenue in the field of fleshy fruit biology by raising the possibility that fruit development and ripening may be under miRNA regulation...
  49. ncbi Orthologs, paralogs, and evolutionary genomics
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Annu Rev Genet 39:309-38. 2005
    ....
  50. ncbi Evidence that miRNAs are different from other RNAs
    B H Zhang
    The Institute of Environmental and Human Health TIEHH, and Department of Environmental Toxicology, Texas Tech University, Lubbock, Texas 79409 1163, USA
    Cell Mol Life Sci 63:246-54. 2006
    ..001). The MFEI for miRNAs was 0.97, significantly higher than tRNAs (0.64), rRNAs (0.59), or mRNAs (0.65). Our findings should facilitate the prediction and identification of new miRNAs using computational and experimental strategies...
  51. ncbi In vivo enhancer analysis of human conserved non-coding sequences
    Len A Pennacchio
    US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
    Nature 444:499-502. 2006
    ....
  52. pmc Expansion and diversification of the Populus R2R3-MYB family of transcription factors
    Olivia Wilkins
    Department of Cell and Systems Biology and Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada M5S 3B2
    Plant Physiol 149:981-93. 2009
    ....
  53. ncbi Structural basis for double-stranded RNA processing by Dicer
    Ian J Macrae
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    Science 311:195-8. 2006
    ..The 65 angstrom distance between the PAZ and RNase III domains matches the length spanned by 25 base pairs of RNA. Thus, Dicer itself is a molecular ruler that recognizes dsRNA and cleaves a specified distance from the helical end...
  54. pmc Identification of novel and candidate miRNAs in rice by high throughput sequencing
    Ramanjulu Sunkar
    Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
    BMC Plant Biol 8:25. 2008
    ..Deep sequencing of small RNA libraries is an effective approach to uncover rare and lineage- and/or species-specific microRNAs (miRNAs) in any organism...
  55. pmc Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs
    Jasmina Ponjavic
    MRC Functional Genetics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom
    Genome Res 17:556-65. 2007
    ..The proportion of conserved sequence (4.1%-5.5%) in these macroRNAs is comparable to the density of exons within protein-coding transcripts (5...
  56. pmc Most Caenorhabditis elegans microRNAs are individually not essential for development or viability
    Eric A Miska
    Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
    PLoS Genet 3:e215. 2007
    ..This study represents the first comprehensive genetic analysis of miRNA function in any organism and provides a unique, permanent resource for the systematic study of miRNAs...
  57. pmc Discovering motifs in ranked lists of DNA sequences
    Eran Eden
    Computer Science Department, Technion, Haifa, Israel
    PLoS Comput Biol 3:e39. 2007
    ..DRIM is publicly available at http://bioinfo.cs.technion.ac.il/drim...
  58. pmc MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana
    Noah Fahlgren
    Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331, USA
    Plant Cell 22:1074-89. 2010
    ..Additionally, target sites of younger miRNA were lost more frequently than for deeply conserved families. In summary, our systematic analyses emphasize the dynamic nature of the MIRNA complement of plant genomes...
  59. pmc Proteomic analysis of a eukaryotic cilium
    Gregory J Pazour
    Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
    J Cell Biol 170:103-13. 2005
    ..The flagellum also contains many proteins that are conserved in humans but have not been previously characterized in any organism. The results indicate that flagella are far more complex than previously estimated...
  60. pmc Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints
    Manuel Irimia
    Department of Biology, Stanford University, Stanford, California 94305, USA
    Genome Res 22:2356-67. 2012
    ....
  61. ncbi Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function
    Ken C Pang
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane QLD 4072, Australia
    Trends Genet 22:1-5. 2006
    ..Our findings suggest that longer ncRNAs are under the influence of different evolutionary constraints and that the lack of conservation displayed by the thousands of candidate ncRNAs does not necessarily signify an absence of function...
  62. pmc Disruption of an AP-2alpha binding site in an IRF6 enhancer is associated with cleft lip
    Fedik Rahimov
    Department of Pediatrics, University of Iowa, 2182 ML, S Grand Ave, Iowa City, Iowa 52242, USA
    Nat Genet 40:1341-7. 2008
    ..Our findings place IRF6 and AP-2alpha in the same developmental pathway and identify a high-frequency variant in a regulatory element contributing substantially to a common, complex disorder...
  63. pmc Evolution of pathogenicity and sexual reproduction in eight Candida genomes
    Geraldine Butler
    UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
    Nature 459:657-62. 2009
    ..Analysis of the CUG leucine-to-serine genetic-code change reveals that 99% of ancestral CUG codons were erased and new ones arose elsewhere. Lastly, we revise the Candida albicans gene catalogue, identifying many new genes...
  64. ncbi The birth and death of microRNA genes in Drosophila
    Jian Lu
    Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, Illinois 60637, USA
    Nat Genet 40:351-5. 2008
    ..The estimated net gain of long-lived miRNA genes, which is not strongly affected by either the depth or the breadth (number of tissues) of sequencing, is 0.3 genes per Myr in Drosophila...
  65. ncbi GARD: a genetic algorithm for recombination detection
    Sergei L Kosakovsky Pond
    Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
    Bioinformatics 22:3096-8. 2006
    ..The evolution of recombinant sequences can not be properly explained by a single phylogenetic tree, but several phylogenies may be used to correctly model the evolution of non-recombinant fragments...
  66. pmc The role of nucleosome positioning in the evolution of gene regulation
    Alexander M Tsankov
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
    PLoS Biol 8:e1000414. 2010
    ..Our study sheds light on the molecular basis of chromatin organization, and on the role of chromatin organization in the evolution of gene regulation...
  67. pmc Discovery of barley miRNAs through deep sequencing of short reads
    Andreas W Schreiber
    Australian Centre for Plant Functional Genomics, The University of Adelaide, South Australia 5064, Australia
    BMC Genomics 12:129. 2011
    ..However, miRNAs from barley, one of the most important cereal crops, remain unknown...
  68. pmc Protein sectors: evolutionary units of three-dimensional structure
    Najeeb Halabi
    Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390 9050, USA
    Cell 138:774-86. 2009
    ..We propose that sectors represent a structural organization of proteins that reflects their evolutionary histories...
  69. pmc Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa
    Ryan D Morin
    Genome Sciences Centre, BC Cancer Agency, Vancouver V5Z 1L3, Canada
    Genome Res 18:571-84. 2008
    ..Genomic mapping of all sequences to the O. sativa genome can be viewed at http://microrna.bcgsc.ca/cgi-bin/gbrowse/rice_build_3/...
  70. ncbi PISCES: a protein sequence culling server
    Guoli Wang
    Institute for Cancer Research, Fox Chase Cancer Center, 7701 Burholme Avenue, Philadelphia, PA 19111, USA
    Bioinformatics 19:1589-91. 2003
    ..PDB sequences are updated weekly. PISCES can also cull non-PDB sequences provided by the user as a list of GenBank identifiers, a FASTA format file, or BLAST/PSI-BLAST output...
  71. ncbi Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles
    D Gautheret
    Centre d immunologie de Marseille Luminy, CNRS UMR 6102 INSERM U 136, Luminy Case 906, 13288 Marseille Cedex 09, France
    J Mol Biol 313:1003-11. 2001
    ..Furthermore, since the translation of alignments into profiles is straightforward with ERPIN, iterative searches can easily be conducted to enrich collections of homologous RNAs...
  72. ncbi Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype
    Olivier Jaillon
    UMR 8030 Genoscope, CNRS and Université d Evry, 2 rue Gaston Cremieux, 91057 Evry Cedex, France
    Nature 431:946-57. 2004
    ....
  73. ncbi A gene-coexpression network for global discovery of conserved genetic modules
    Joshua M Stuart
    Stanford Medical Informatics, 251 Campus Drive, Medical School Office Building X 215, Stanford, CA 94305 5329, USA
    Science 302:249-55. 2003
    ..By assembling these links into a gene-coexpression network, we found several components that were animal-specific as well as interrelationships between newly evolved and ancient modules...
  74. pmc Confirming the phylogeny of mammals by use of large comparative sequence data sets
    Arjun B Prasad
    Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
    Mol Biol Evol 25:1795-808. 2008
    ..g., in the case of Laurasiatheria), and demonstrate the valuable role that very large comparative sequence data sets can play in refining our understanding of the evolutionary relationships of vertebrates...
  75. pmc Common functions for diverse small RNAs of land plants
    Michael J Axtell
    Department of Biology and Huck Institutes of the Life Sciences, Pensylvania State University, University Park, PA 16802, USA
    Plant Cell 19:1750-69. 2007
    ..Diverse, lineage-specific, small RNAs can therefore perform common biological functions in plants...
  76. pmc Sepsid even-skipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation
    Emily E Hare
    Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America
    PLoS Genet 4:e1000106. 2008
    ..Together, these observations suggest that the local arrangement of binding sites relative to each other is more important than their overall arrangement into larger units of cis-regulatory function...
  77. pmc Identification and characterization of maize microRNAs involved in the very early stage of seed germination
    Liwen Wang
    State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong 271018, PR China
    BMC Genomics 12:154. 2011
    ..However, the number of miRNAs discovered in maize is relatively low and little is known about miRNAs involved in the very early stage during seed germination...
  78. pmc Human developmental enhancers conserved between deuterostomes and protostomes
    Shoa L Clarke
    Department of Genetics, Stanford University, Stanford, California, United States of America
    PLoS Genet 8:e1002852. 2012
    ....
  79. pmc Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response
    Jingyu Zhang
    Key Laboratory of Photosynthesis and Environmental Molecular Physiology, Chinese Academy of Sciences, and National Centre for Plant Gene Research, Beijing 100093, PR China
    BMC Genomics 10:449. 2009
    ..Brachypodium distachyon, with close evolutionary relationship to cool-season cereals, has recently emerged as a novel model plant. There are few reports of Brachypodium miRNAs...
  80. ncbi Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene
    A C Bell
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 0540, USA
    Nature 405:482-5. 2000
    ..Our results reveal that DNA methylation can control gene expression by modulating enhancer access to the gene promoter through regulation of an enhancer boundary...
  81. ncbi A draft sequence of the rice genome (Oryza sativa L. ssp. japonica)
    Stephen A Goff
    Torrey Mesa Research Institute, Syngenta, 3115 Merryfield Row, San Diego, CA 92121, USA
    Science 296:92-100. 2002
    ..Assignment of candidate rice orthologs to Arabidopsis genes is possible in many cases. The rice genome sequence provides a foundation for the improvement of cereals, our most important crops...
  82. ncbi MicroRNAs and their regulatory roles in animals and plants
    Baohong Zhang
    The Institute of Environmental and Human Health, and Department of Environmental Toxicology, Texas Tech University, Lubbock, Texas 79409, USA
    J Cell Physiol 210:279-89. 2007
    ..This review provides a general background and current advance on the discovery, history, biogenesis, genomics, mechanisms, and functions of miRNAs...
  83. ncbi Evolution of the Rab family of small GTP-binding proteins
    J B Pereira-Leal
    Cell and Molecular Biology Section, Division of Biomedical Sciences, Faculty of Medicine, Imperial College, London, SW7 2AZ, UK
    J Mol Biol 313:889-901. 2001
    ..Rab functional groups can help the understanding of the functional evolution of the Rab family in particular and vesicular transport in general, and may be used to predict general functions for novel Rab sequences...
  84. ncbi Modulation of floral development by a gibberellin-regulated microRNA
    Patrick Achard
    Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
    Development 131:3357-65. 2004
    ..We propose that miR159 is a phytohormonally regulated homeostatic modulator of GAMYB activity, and hence of GAMYB-dependent developmental processes...
  85. pmc Essential genes are more evolutionarily conserved than are nonessential genes in bacteria
    I King Jordan
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Res 12:962-8. 2002
    ..In contrast to the results obtained for eukaryotic genes, essential bacterial genes appear to be more conserved than are nonessential genes over both relatively short (microevolutionary) and longer (macroevolutionary) time scales...
  86. pmc Forces shaping the fastest evolving regions in the human genome
    Katherine S Pollard
    Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
    PLoS Genet 2:e168. 2006
    ..A combination of evolutionary forces has contributed to accelerated evolution of the fastest evolving elements in the human genome...
  87. ncbi Molecular evolution of FOXP2, a gene involved in speech and language
    Wolfgang Enard
    Max Planck Institute for Evolutionary Anthropology, Inselstrasse 22, D 04103 Leipzig, Germany
    Nature 418:869-72. 2002
    ..Here we show that human FOXP2 contains changes in amino-acid coding and a pattern of nucleotide polymorphism, which strongly suggest that this gene has been the target of selection during recent human evolution...
  88. ncbi daf-2, an insulin receptor-like gene that regulates longevity and diapause in Caenorhabditis elegans
    K D Kimura
    Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
    Science 277:942-6. 1997
    ..Life-span regulation by insulin-like metabolic control is analogous to mammalian longevity enhancement induced by caloric restriction, suggesting a general link between metabolism, diapause, and longevity...
  89. pmc Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes
    Rebecca A Chodroff
    Department of Physiology, Anatomy, and Genetics, Le Gros Clark Building South Parks Road, University of Oxford, Oxford OX1 3QX, UK
    Genome Biol 11:R72. 2010
    ..This dearth of information is partially attributable to a lack of established non-protein-coding RNA (ncRNA) orthologs among birds and mammals within sequence and expression databases...
  90. ncbi The complete atomic structure of the large ribosomal subunit at 2.4 A resolution
    N Ban
    Department of Molecular Biophysics and Biochemistry and Howard Hughes Medical Institute, New Haven, CT 06520 8114, USA
    Science 289:905-20. 2000
    ..Most of the proteins stabilize the structure by interacting with several RNA domains, often using idiosyncratically folded extensions that reach into the subunit's interior...
  91. pmc Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome
    Tae Hoon Kim
    Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA 92093 0653, USA
    Cell 128:1231-45. 2007
    ..In addition, CTCF localization is largely invariant across different cell types. Our results provide a resource for investigating insulator function and possible other general and evolutionarily conserved activities of CTCF sites...
  92. pmc Chromosomal rearrangement inferred from comparisons of 12 Drosophila genomes
    Arjun Bhutkar
    Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Genetics 179:1657-80. 2008
    ..On the other hand, an analysis of the disruption of syntenic blocks between species allowed the identification of fixed inversion breakpoints and estimates of breakpoint reuse and lineage-specific breakpoint event segregation...
  93. pmc Predicting deleterious amino acid substitutions
    P C Ng
    Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Genome Res 11:863-74. 2001
    ..may be used to identify plausible disease candidates among the SNPs that cause missense substitutions...
  94. ncbi Genome evolution in yeasts
    Bernard Dujon
    Unité de Génétique Moléculaire des Levures, URA 2171 CNRS and UFR 927 Université Pierre et Marie Curie
    Nature 430:35-44. 2004
    ....
  95. ncbi The Trichoplax genome and the nature of placozoans
    Mansi Srivastava
    Center for Integrative Genomics and Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
    Nature 454:955-60. 2008
    ....
  96. pmc Differential recognition of highly divergent downy mildew avirulence gene alleles by RPP1 resistance genes from two Arabidopsis lines
    Anne P Rehmany
    Warwick HRI, University of Warwick, Wellesbourne, Warwick CV35 9EF, United Kingdom
    Plant Cell 17:1839-50. 2005
    ..The presence of the motif in additional secreted proteins from plant pathogenic oomycetes and its similarity to a host-targeting signal from malaria parasites suggest a conserved role in pathogenicity...
  97. pmc InBase: the Intein Database
    Francine B Perler
    New England Biolabs Inc, 32 Tozer Road, Beverly, MA 01915, USA
    Nucleic Acids Res 30:383-4. 2002
    ..It presents general information as well as detailed data for each intein, including tabulated comparisons and a comprehensive bibliography. An intein-specific BLAST server is now available to assist in identifying new inteins...
  98. pmc A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation
    Thomas Geissmann
    Architecture et Reactivite de l ARN, Universite de Strasbourg, CNRS, IBMC, 15 rue Rene Descartes, F 67084 Strasbourg, France
    Nucleic Acids Res 37:7239-57. 2009
    ..This study unexpectedly shows that most of the novel ncRNAs carry the conserved C-rich motif, suggesting that they are members of a class of ncRNAs that target mRNAs by a shared mechanism...
  99. pmc Identification of conserved residues in the E2 envelope glycoprotein of the hepatitis C virus that are critical for CD81 binding
    Ania M Owsianka
    MRC Virology Unit, Institute of Virology, University of Glasgow, UK
    J Virol 80:8695-704. 2006
    ..Specific amino acids conserved across all genotypes that were critical for CD81 binding were W420, Y527, W529, G530, and D535. These data significantly increase our understanding of the CD81 receptor-E2 binding process...
  100. pmc MicroRNAs of Bombyx mori identified by Solexa sequencing
    Shiping Liu
    The Key Sericultural Laboratory of Agricultural Ministry, College of Biotechnology, Southwest University, Tiansheng Road, Beibei, Chongqing 400715, PR China
    BMC Genomics 11:148. 2010
    ....

Research Grants62

  1. SMOOTH MUSCLE MYOSIN PHOSPHATASE SUBUNIT ISOFORMS
    Steven A Fisher; Fiscal Year: 2013
    ..Aim 3: Tra2b as a novel nodal point for the dissection of VSM diversification. An ~500 nt ultra-conserved sequence (UCS) in the first intron of Tra2b will be tested for its ability to drive tissue-specific transcription in ..
  2. Striated Muscle Gene Transcription and Regulatory Gene Cassettes for Gene Therapy
    STEPHEN DENISON HAUSCHKA; Fiscal Year: 2012
    ..control elements &transcription factors associated with four MCK regions containing blocks of highly conserved sequence motifs with unknown functions...
  3. REPAIR OF CARCINOGEN DAMAGED DNA IN HUMAN CHROMATIN
    John J Wyrick; Fiscal Year: 2013
    ..We will also examine BER in human cells with variable CR activity (Aim I). Secondly, we have identified a conserved sequence cassette in yeast histone H2B (named the HBR cassette) that plays a critical role in gene repression, ..
  4. Elucidating the A. baumannii response to calprotectin-mediated zinc starvation
    BRITTANY MORTENSEN; Fiscal Year: 2013
    ..Further in silico analysis of the genomic region upstream of the genes encoding Zur and ZnuABC uncovered a conserved sequence called a zur box, to which Zur binds to repress downstream gene expression...
  5. Regulatory architecture of the Androgen Receptor locus in development & evolution
    Philip L Reno; Fiscal Year: 2010
    ..To rigorously test the functional consequence of the loss of this conserved sequence, I will also use a targeted gene knock-in strategy to delete this element in the mouse and replace it with ..
  6. DGAP: Developmental Genome Anatomy Project
    CYNTHIA CASSON MORTON; Fiscal Year: 2013
    ..Molecular identification and analysis of candidate genes and other conserved sequence elements, as well as mutation studies in affected individuals is the focus of subsequent studies (Project 2)...
  7. Role of miR-8 and Ena in Synaptic Structure and Function
    CARLOS MANUEL LOYA; Fiscal Year: 2010
    ..apparatus at the electron microscopy level;and 3) test a series of Ena mutant transgenes to determine which conserved sequence elements are critical for the localization and function of Ena at the NMJ...
  8. PERMEABILITY OF THE EPIDEMIC TYPHUS RICKETTSIA
    JONATHON PETER AUDIA; Fiscal Year: 2010
    ..prowazekii. Sequence analysis of shuffled fragments within these chimeric proteins will associate conserved sequence motifs with substrate specificity...
  9. Small Molecule Inhibitors of ZAP-70 for the Treatment of Autoimmune Disorders
    Mark Gallop; Fiscal Year: 2013
    ..the ZAP-70 tandem SH2 domains associate with dual tyrosine phosphorylated residues located within conserved sequence motifs (referred to as ITAMs) of the cytoplasmic domains of the CD3 and zeta chains of the TCR...
  10. Selection, Characterization &Application of Paramagnetic Metal-specific DNAzymes
    Yi Lu; Fiscal Year: 2012
    ..Fe3+). Biochemical studies of the selected DNAzymes will provide information about conserved sequence, catalytic parameters, and pH and metal ion dependence of the enzyme activity...
  11. MOLECULAR CONTROL OF CELL PROLIFERATION
    DAVID OWEN MORGAN; Fiscal Year: 2010
    ..biochemical analyses will be used to unveil the functions of three related APC subunits that contain a conserved sequence motif, the tetratricopeptide repeat or TPR, that forms a binding interface involved in substrate recruitment...
  12. Disruption of Reelin biosynthesis by de novo missense mutations found in aut
    DAWN LAMMERT; Fiscal Year: 2013
    ..Objectives: Our research will determine the importance of this conserved sequence and molecular mechanism of Reelin disruption, as well as determine the ability to rescue mutant Reelin ..
  13. MOLECULAR MECHANISM OF PHOTORECEPTOR G PROTEIN SIGNALING
    Nikolai O Artemyev; Fiscal Year: 2013
    ..It remains unknown whether the conserved sequence differences in rod and cone transducin-a (Gat1) subunits translate into the functional differences that ..
  14. Using Sequence and Structure to study post transcriptional regulation
    SEAN WEST; Fiscal Year: 2013
    ..be used with sequence and structural comparisons of the transcriptome from multiple species to determine how conserved sequence and intrinsic RNA structure act to regulate binding by RBPs...
  15. Developmental analysis of SELCT proteins
    ANNE CHURCH HART; Fiscal Year: 2010
    ..Unlike canonical Notch ligands, these proteins lack the conserved DSL domain but they share a conserved sequence motif with classical Notch ligands...
  16. An allosteric inhibitor of ZAP-70 as a novel therapeutic for autoimmune disease
    Arthur Weiss; Fiscal Year: 2010
    ..the tandem SH2 domains of ZAP-70 associate with dual tyrosine phosphorylated residues located within conserved sequence motifs (referred to as ITAMs) of the cytoplasmic domains of the CD3 and zeta chains...
  17. Structural mechanics of MsbA family ABC transporters
    John Hunt; Fiscal Year: 2009
    ..Using combined enzymological and crystallographic studies, we showed that ATP binding to conserved sequence motifs drives the formation an "ATP-sandwich dimer" by the ABC motor domains...
  18. The role of the DOC2.1 protein in Toxoplasma gondii Ca2+- dependent exocytosis
    Marc Jan Gubbels; Fiscal Year: 2013
    ..1. Comparative genomics of TgDOC2.1 identified four conserved sequence block across the Apicomplexa, highlighting a potentially crucial role for these domains (block 2 contains ..
  19. The Role of origin Recognition Complex in the Cell Cycle
    Igor Chesnokov; Fiscal Year: 2009
    ..The function of conserved sequence motifs of Orc6 and Pnut proteins will be defined and the role of Pnut in Orc6 localization will be ..
  20. Characterization of Pseudouridene Synthase TruD
    CLAUDIA CAROLINA RECINOS; Fiscal Year: 2010
    ..The structural role of conserved sequence insertions found in TruD homologs of higher oganisms will be examined in the human homologs by ..
  21. MOLECULAR BIOLOGY OF POLIOVIRUS RNA REPLICATION
    James Bert Flanegan; Fiscal Year: 2010
    ..VPgpUpU, which is synthesized on the cre(2C) hairpin, is used to prime (+) strand synthesis on the highly conserved sequence at the 3'terminus of (-) strand RNA...
  22. LAMININ GENE EXPRESSION IN GLOMERULAR CELLS
    Karol Bomsztyk; Fiscal Year: 2002
    ..In comparing the 5' genomic sequence of human, rat, and mouse laminin gamma1 he discovered a novel and conserved sequence, termed bcn-1...
  23. Modulation of c-MYC Functions in an HTLV-1 Model for Carcinogenesis
    Robert Harrod; Fiscal Year: 2009
    ..A conserved sequence, known as pX, within the 3'region of the HTLV-1 genome encodes five regulatory and accessory proteins, ..
  24. PROPERTIES OF DYNEIN ISOENZYMES
    Ian Gibbons; Fiscal Year: 2003
    ..into families proceeds, the sequence of selected isoforms will be extended in order to look for regions of conserved sequence that are further removed form the hydrolytic ATP-binding site and that show homology to the microtubule-..
  25. Functional Reconstitution of Yeast Exocytosis
    James A McNew; Fiscal Year: 2010
    ..Additionally, we examine the function of the Ssolp polybasic juxtamembrane region, a conserved sequence in all plasma membrane SNAREs...
  26. ISOLATION OF CDNA'S FOR HLA CLASS II TRANSACTING FACTORS
    Benjamin Schwartz; Fiscal Year: 1992
    ..Five motifs of conserved sequence apparently involved in transcriptional regulation have been delineated within the promoter region of the 5' ..
  27. HLA Alleles, Self-Peptides and Microbial Mimicry in SSc
    J Nelson; Fiscal Year: 2005
    ..Finally, HCMV has sequence identity with a conserved sequence of HLA-DRbeta1 (aa 53-57), that extends further (aa 53-58, "LGRPDE") for DRB1 alleles that encode for DR11, ..
  28. MOLECULAR DETERMINANTS OF HUMAN BETA GLOBIN GENE SWITCH
    MARGARET BARON; Fiscal Year: 1999
    ..Binding of a nuclear factor from embryonic erythroid cells to a novel, conserved sequence motif within epsilon-PRE II is required for epsilon-PRE II function, strongly implicating this factor in the ..
  29. GENES, CHROMOSOMAL REGIONS AND DEVELOPMENTAL DISORDERS
    GAIL BRUNS; Fiscal Year: 2000
    ..To determine whether architectural features at WAGR region deletion breakpoints differ depending on the chromosomal domain environments of their initiation and termination points, a number of deletion boundaries will be cloned. ..
  30. RIBOZYMES AND RNA GENE THERAPIES FOR LIVER DISEASES
    Andrea Branch; Fiscal Year: 2003
    ..A derivative targeted against the conserved sequence element at the 3~ end of hepatitis C virus (HCV) RNA will be designed and tested. (B)...
  31. RECA PROTEIN STRUCTURE AND FUNCTION
    KEVIN MCENTEE; Fiscal Year: 1993
    ..In addition, site-directed mutagenesis will be used to alter residues with a conserved sequence in TecA protein that is found in a number of nucleotide binding proteins...
  32. AUTOPROTEOLYSIS OF N-TERMINAL NUCLEOPHILE HYDROLASE
    Hwai Chen Guo; Fiscal Year: 2004
    ..Based on structural geometry and evolutionarily conserved sequence, the residues appearing to be important for autoproteolysis will be selected for site-directed mutagenesis...
  33. TRANSCRIPTIONAL CONTROL OF CHONDROGENIC DIFFERENTIATION
    Thomas Hering; Fiscal Year: 2002
    ..by screening of subtracted cDNA libraries with a degenerate oligonucleotide probe specific to a highly conserved sequence common to zinc-finger proteins...
  34. FUNCTION AND CONSERVATION IN GLOBIN LOCUS CONTROL REGION
    Ross Hardison; Fiscal Year: 2001
    ..This latter region comprises a DNase HS in K562 cells and contains many conserved sequence blocks...
  35. STRUCTURE AND COMPOSITION OF THE GENOME OF IXODID TICKS
    DENSON MCLAIN; Fiscal Year: 1993
    ..a preliminary systematic analysis of 18 tick genera would be conducted using two DNA sequences, a semi-conserved sequence of the 28S rRNA gene and part of the reverse transcriptase gene of a retrovirus- like transposable element...
  36. Imprinted SnoRNA Genes in the PWS deletion Region
    Uta Francke; Fiscal Year: 2005
    ..PWS deletion region (PWCR1 in human and Pwcr1 in mouse) encodes small nucleolar RNAs (snoRNAs) with short conserved sequence elements, called C and D boxes (de Los Santos et al. Amer. J. Hum. Genet. 67:1067, 2000)...
  37. YEAST CENTROMERE STRUCTURE AND FUNCTION
    Molly Fitzgerald Hayes; Fiscal Year: 1993
    ..We will also investigate the in vivo interactions among the conserved sequence elements by selecting for cisacting mutations in CDE I that suppress the functional defects in CDE III ..
  38. Aptamer-based Proteomic Analysis for Cancer Signatures
    Stephen Walton; Fiscal Year: 2007
    ..i) generate molecular barcode-containing, structure-switching aptamers by in vitro selection and identify conserved sequence and structural features; ii) quantify the affinities and association kinetics of aptamertarget protein ..
  39. ANALYSIS OF A MURINE HOMEO BOX LOCUS
    Alexander Awgulewitsch; Fiscal Year: 1993
    ..The fact that this highly conserved sequence has so far been found exclusively in Drosophila genes with developmental control functions, and the ..
  40. Effector roles of T4Dam DNA-methyltransferase subsrates
    Stanley Hattman; Fiscal Year: 2004
    ..by known single amino acid substitutions in the MTase-target recognition domain, as well as in other conserved sequence motifs...
  41. HCV INTERNAL RIBOSOME ENTRY SITE AS TARGET FOR THERAPY
    Hugh Robertson; Fiscal Year: 2003
    ..aims of this proposal are: (i) To map the conserved 5' terminal 400 bases of the HCV genome for regions of conserved sequence, secondary structure, and local tertiary structural elements, emphasizing unique regions combining all three ..
  42. DIRECT SELECTION METHODS
    Michael Lovett; Fiscal Year: 2009
    ..propose to implement improvements to direct genomic selection to more rapidly capture collections of highly conserved sequence elements across diverse genomes and diverse species...
  43. Lysine recognition by lysine-binding regulatory RNAs
    SHARNISE N WILSON; Fiscal Year: 2010
    ..This system uses an RNA to control gene expression by binding lysine. Conserved sequence and structural patters has identified a number of genes within the lysine biosynthetic pathway that contain ..
  44. Region Based Functional Annotation of the Mouse Genome
    TIMOTHY OBRIEN; Fiscal Year: 2006
    ..Computational and comparative genomic analysis to identify genes and additional conserved sequence features will be merged with functional studies...
  45. STRUCTURE AND FUNCTION OF FYVE DOMAINS
    TATIANA KUTATELADZE; Fiscal Year: 2004
    ..are: l: The FYVE domain has a unique 3D structure: The FYVE domain is defined by a unique and highly conserved sequence of 75 residues of unknown structure...
  46. HOXA13 AMINO-TERMINAL FUNCTIONAL DOMAINS
    JEFFREY INNIS; Fiscal Year: 2004
    ..The in vitro system will provide a direct interpretation of the effect of a conserved sequence alteration on normal transcription factor function...
  47. SPECIFICITY OF RNA MATURATION
    Barbara Sollner Webb; Fiscal Year: 2005
    ..By creating targeted mutations in conserved sequence domains and favoring editing complex formation, their roles can be assessed independently of other functions ..
  48. HOW DOES VND INTEGRATE POSITIONAL INFORMATION?
    DERVLA MELLERICK DRESSLER; Fiscal Year: 2003
    ..In addition we will identify conserved sequence islands in the vnd regulatory domain from two related Drosophila species...
  49. POU FACTORS AND NEURONAL DEVELOPMENT
    Wayne Johnson; Fiscal Year: 2000
    ..extracts, transgenic expression of modified Cf1a-lacZ fusion genes and a comparison of evolutionarily conserved sequence elements will be combined to identify sequence elements and corresponding DNA-binding factors which are ..
  50. A Conserved Sequence Approach for MS Association Studies
    Douglas Mortlock; Fiscal Year: 2007
    ..unreadable] [unreadable] [unreadable]..
  51. THE DROSOPHILA CNS: A MODEL FOR PCB NEUROXICITY
    DERVLA MELLERICK DRESSLER; Fiscal Year: 2000
    ..we want to localize the enhancers responsible for vnd expression in transgenic embryos, identify conserved sequence islands in the vnd regulatory domain from two related Drosophila species, perform DNA binding studies with ..
  52. ANTIBODIES AGAINST HIV-1 gp41: TOOLS FOR VACCINE DESIGN
    Michael Zwick; Fiscal Year: 2005
    HIV-1 gp41 contains highly conserved sequence elements that are targets for viral entry inhibitors and broadly neutralizing, monoclonal antibodies (mAbs)...
  53. Identification of a Melonoma Susceptibilty Gene at 1p22
    Kevin Brown; Fiscal Year: 2005
    ..We will construct a custom oligonucleotide microarray with probes representing all evolutionarily conserved sequence at 1p22 and assay expression in melanocytes and melanoma cell lines to identify all expressed genes in the ..
  54. Alpha-synuclein mRNA is a putative microRNA target
    Peter Nelson; Fiscal Year: 2009
    ..On the basis of preliminary evidence, we hypothesize that an evolutionarily conserved sequence element in the 3'-untranslated region of A-SN mRNA is recognized by a specific miRNA (miR-93)...
  55. Sequence and Analyze X. tropicalis developmental genes
    Shizhen Qin; Fiscal Year: 2003
    ..sequence or relevant sequences from other species is available, perform cross-species analyses to identify conserved sequence blocks that might serve as candidates for cis-regulatory elements and modules...
  56. 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. ..
  57. EVOLUTION OF IMMUNE RECOGNITION AND EVASION
    Austin L Hughes; Fiscal Year: 2010
    ..In addition, by increasing our understanding of the population diversity and evolutionary history of human immune system genes, this research will enhance our knowledge of human immune function in health and disease. ..
  58. Predicting common protein mechanisms by the light of evolution
    ANDREW NEUWALD; Fiscal Year: 2009
    ..And (v) propose molecular mechanisms based on these analyses. ..
  59. Advanced Sequence-Based Prediction of Protein Function
    ANDREW NEUWALD; Fiscal Year: 2005
    ..abstract_text> ..
  60. MOLECULAR STRUCTURE OF STEROIDS
    William Duax; Fiscal Year: 2006
    ..Proof of the successful prediction of the structures of 20-30 hypothetical members of the SCOR proteome could provide a model for the prediction of protein folding on the basis of as little as 20% sequence homology. ..
  61. MOLECULAR ANALYSIS OF THE ANTIH INFLUENZAE RESPONSE
    ANN FEENEY; Fiscal Year: 2001
    ..We will also further analyze the diversity in the ani-hib response through the use of combinatorial libraries, correlating affinity with the Vh, Vk and CDR3's which are used. ..
  62. mTOR Signaling Pathways
    Thomas W Sturgill; Fiscal Year: 2010
    ..We will investigate novel candidate mTOR-interacting proteins identified by MS. Finally, to understand better the mechanisms involved in mTORC2, we propose to identify pianissimo-interacting proteins. ..