reading frames

Summary

Summary: The three possible sequences of CODONS by which GENETIC TRANSLATION may occur from one nucleotide sequence. A segment of mRNA 5'AUCCGA3' could be translated as 5'AUC.. or 5'UCC.. or 5'CCG.., depending on the location of the START CODON.

Top Publications

  1. pmc P-site tRNA is a crucial initiator of ribosomal frameshifting
    Pavel V Baranov
    Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112 5330, USA
    RNA 10:221-30. 2004
  2. pmc Genetic analysis of the E site during RF2 programmed frameshifting
    Christina L Sanders
    Department of Biology, Wake Forest University, Winston Salem, NC 27106, USA
    RNA 13:1483-91. 2007
  3. ncbi Antisense oligo-mediated multiple exon skipping in a dog model of duchenne muscular dystrophy
    Toshifumi Yokota
    Research Center for Genetic Medicine, Children s National Medical Center, 111 Michigan Avenue, NW, Washington, DC, USA
    Methods Mol Biol 709:299-312. 2011
  4. pmc Dual coding in alternative reading frames correlates with intrinsic protein disorder
    Erika Kovacs
    Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Karolina ut 29, H 1113 Budapest, Hungary
    Proc Natl Acad Sci U S A 107:5429-34. 2010
  5. ncbi Entries in the Leiden Duchenne muscular dystrophy mutation database: an overview of mutation types and paradoxical cases that confirm the reading-frame rule
    Annemieke Aartsma-Rus
    Leiden University Medical Center, Department of Human Genetics, P O Box 9600, 2300 RC Leiden, The Netherlands
    Muscle Nerve 34:135-44. 2006
  6. ncbi The ribosomal grip of the peptidyl-tRNA is critical for reading frame maintenance
    S Joakim Nasvall
    Department of Molecular Biology, Umea University, S 901 87 Umea, Sweden
    J Mol Biol 385:350-67. 2009
  7. ncbi Potential evolutionary influences on overlapping reading frames in the bovine leukemia virus pXBL region
    Xiangrong Zhao
    Graduate Program in Endocrinology, University of California at Berkeley, 3060 Valley Life Science Building, Berkeley, CA 94720 3140, USA
    Genomics 89:502-11. 2007
  8. ncbi Cytolytic CD8+ T cells directed against a cryptic epitope derived from a retroviral alternative reading frame confer disease protection
    On Ho
    Department of Microbiology and Immunology, Dartmouth Medical School, Lebanon, NH 03756, USA
    J Immunol 176:2470-5. 2006
  9. ncbi Endonucleases: tools to correct the dystrophin gene
    Joel Rousseau
    Unité de recherche de recherche en Génétique Humaine, Centre de recherche de CHUL, CHUQ, Faculte de Medecine, Universite Laval, Quebec, Canada
    J Gene Med 13:522-37. 2011
  10. ncbi Immunology. Hide and seek in the peptidome
    Jonathan W Yewdell
    Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892 0440, USA
    Science 301:1334-5. 2003

Detail Information

Publications229 found, 100 shown here

  1. pmc P-site tRNA is a crucial initiator of ribosomal frameshifting
    Pavel V Baranov
    Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112 5330, USA
    RNA 10:221-30. 2004
    ..This model offers an alternative explanation to previously published mechanisms of programmed frameshifting, such as out-of-frame tRNA binding, and a different perspective on simultaneous tandem tRNA slippage...
  2. pmc Genetic analysis of the E site during RF2 programmed frameshifting
    Christina L Sanders
    Department of Biology, Wake Forest University, Winston Salem, NC 27106, USA
    RNA 13:1483-91. 2007
    ..These findings indicate that pairing between the deacyl-tRNA and the E-site codon opposes frameshifting. We discuss the implications of these findings on frame maintenance and on the RF2 programmed frameshift mechanism...
  3. ncbi Antisense oligo-mediated multiple exon skipping in a dog model of duchenne muscular dystrophy
    Toshifumi Yokota
    Research Center for Genetic Medicine, Children s National Medical Center, 111 Michigan Avenue, NW, Washington, DC, USA
    Methods Mol Biol 709:299-312. 2011
    ....
  4. pmc Dual coding in alternative reading frames correlates with intrinsic protein disorder
    Erika Kovacs
    Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Karolina ut 29, H 1113 Budapest, Hungary
    Proc Natl Acad Sci U S A 107:5429-34. 2010
    ..By discussing several examples, we demonstrate that dual coding may be an effective mechanism for the evolutionary appearance of novel intrinsically disordered regions with new functions...
  5. ncbi Entries in the Leiden Duchenne muscular dystrophy mutation database: an overview of mutation types and paradoxical cases that confirm the reading-frame rule
    Annemieke Aartsma-Rus
    Leiden University Medical Center, Department of Human Genetics, P O Box 9600, 2300 RC Leiden, The Netherlands
    Muscle Nerve 34:135-44. 2006
    ..In this study we provide an update of the mutational variability in the DMD gene, particularly focusing on genotype-phenotype correlations and mutations that appear to be exceptions to the reading-frame rule...
  6. ncbi The ribosomal grip of the peptidyl-tRNA is critical for reading frame maintenance
    S Joakim Nasvall
    Department of Molecular Biology, Umea University, S 901 87 Umea, Sweden
    J Mol Biol 385:350-67. 2009
    ..We suggest that the "ribosomal grip" of the peptidyl-tRNA is pivotal for maintaining the reading frame...
  7. ncbi Potential evolutionary influences on overlapping reading frames in the bovine leukemia virus pXBL region
    Xiangrong Zhao
    Graduate Program in Endocrinology, University of California at Berkeley, 3060 Valley Life Science Building, Berkeley, CA 94720 3140, USA
    Genomics 89:502-11. 2007
    ..contains a pXBL region encoding the 3' parts of four regulatory proteins (Tax, Rex, G4, R3) in overlapping reading frames. Here we report the pXBL polymorphisms of 30 isolates from four countries...
  8. ncbi Cytolytic CD8+ T cells directed against a cryptic epitope derived from a retroviral alternative reading frame confer disease protection
    On Ho
    Department of Microbiology and Immunology, Dartmouth Medical School, Lebanon, NH 03756, USA
    J Immunol 176:2470-5. 2006
    ..epitopes," defined by their nontraditional methods of generation, including derivation from alternative reading frames (ARFs)...
  9. ncbi Endonucleases: tools to correct the dystrophin gene
    Joel Rousseau
    Unité de recherche de recherche en Génétique Humaine, Centre de recherche de CHUL, CHUQ, Faculte de Medecine, Universite Laval, Quebec, Canada
    J Gene Med 13:522-37. 2011
    ..The experiments were performed in human cells (i.e. 293 T cells, myoblasts and myotubes)...
  10. ncbi Immunology. Hide and seek in the peptidome
    Jonathan W Yewdell
    Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892 0440, USA
    Science 301:1334-5. 2003
  11. ncbi The ambush hypothesis at the whole-organism level: Off frame, 'hidden' stops in vertebrate mitochondrial genes increase developmental stability
    Hervé Seligmann
    Center for Ecological and Evolutionary Synthesis, Department of Biological Sciences, University of Oslo, Blindern, N 0316 Oslo, Norway
    Comput Biol Chem 34:80-5. 2010
    ..Results suggest adaptive rather than neutralist interpretations of the ambush hypothesis...
  12. ncbi Meganucleases can restore the reading frame of a mutated dystrophin
    P Chapdelaine
    CHUL, Centre de recherche du CHUQ, Quebec, Canada
    Gene Ther 17:846-58. 2010
    ..New MGNs engineered to target a sequence including or near nonsense mutation could also be used to delete it...
  13. ncbi Improving gene recognition accuracy by combining predictions from two gene-finding programs
    Sanja Rogic
    Computer Science Department, The University of California at Santa Cruz, Baskin Engineering, 95064, USA
    Bioinformatics 18:1034-45. 2002
    ..The current programs can identify up to 75% of exons correctly and less than 50% of predicted gene structures correspond to actual genes. New approaches to computational gene-finding are clearly needed...
  14. ncbi Nonsense-associated altered splicing: a frame-dependent response distinct from nonsense-mediated decay
    Jun Wang
    Department of Immunology, The University of Texas, M D Anderson Cancer Center, Houston, TX 77030, USA
    Mol Cell 10:951-7. 2002
    ..Our results suggest that NAS and NMD are distinct mechanisms despite being triggered by the same signal...
  15. ncbi An "integrated model" of programmed ribosomal frameshifting
    Jason W Harger
    Graduate School of Biomedical Sciences, Rutgers University, Piscataway, NJ 08854, USA
    Trends Biochem Sci 27:448-54. 2002
    ....
  16. ncbi Exon skipping-mediated dystrophin reading frame restoration for small mutations
    Pietro Spitali
    Department of Experimental and Diagnostic Medicine, Section of Medical Genetics, University of Ferrara, Italy
    Hum Mutat 30:1527-34. 2009
    ..This behavior may be related to the effect of the mutations on exon skipping propensity, and highlights the complexity of identifying optimal AONs for skipping exons with small mutations...
  17. pmc Robust, vaccine-induced CD8(+) T lymphocyte response against an out-of-frame epitope
    Nicholas J Maness
    Department of Pathology and Laboratory Medicine, University of Wisconsin Madison, Madison, WI 53706, USA
    J Immunol 184:67-72. 2010
    ..Our data demonstrate both that the pathway from vaccination to immune response is not well understood and that products of alternate reading frames may be rich and untapped sources of T cell epitopes.
  18. ncbi Alternative reading frames of the INK4a tumor suppressor gene encode two unrelated proteins capable of inducing cell cycle arrest
    D E Quelle
    Howard Hughes Medical Institute, St Jude Children s Research Hospital, Memphis, Tennessee 38101, USA
    Cell 83:993-1000. 1995
    ..Economical reutilization of coding sequences in this manner is practically without precedent in mammalian genomes, and the unitary inheritance of p16INK4a and p19ARF may underlie their dual requirement in cell cycle control...
  19. ncbi Codon-optimized reading frames facilitate high-level expression of the HIV-1 minor proteins
    D S Anson
    Department of Genetic Medicine, Children, Youth, and Women s Health Service, 72 King William Road, North Adelaide, Australia
    Mol Biotechnol 31:85-8. 2005
    We have constructed reading frames for the HIV-1 YU-2 minor proteins Vpr, Vpu, Vif and Nef that are codon-optimized for high-level expression in mammalian cells...
  20. pmc Selecting open reading frames from DNA
    Paola Zacchi
    SISSA, Trieste, Italy
    Genome Res 13:980-90. 2003
    We describe a method to select DNA encoding functional open reading frames (ORFs) from noncoding DNA within the context of a specific vector...
  21. ncbi Efficiencies of translation in three reading frames of unusual non-ORF sequences isolated from phage display
    E Goldman
    Department of Microbiology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey 07103, USA
    FASEB J 14:603-11. 2000
    ..These sequences have been cloned in all three reading frames relative to the reporter...
  22. ncbi Tumor immunotherapy with alternative reading frame peptide antigens
    Thomas J Graddis
    Dendreon Corporation, 3005 1st Avenue, Seattle, WA 98121, USA
    Immunobiology 209:535-44. 2004
    ..The strategy described here has potential for designing highly efficient novel vaccines for Ag-specific immunotherapy of human malignancies...
  23. pmc Identification of endogenous retroviral reading frames in the human genome
    Palle Villesen
    Bioinformatics Research Center, University of Aarhus, Høegh Guldbergs Gade 10, Bldg 090, DK 8000 Aarhus, Denmark
    Retrovirology 1:32. 2004
    ..encoded genes are degenerate due to mutational decay and only a few non-HERV-K loci are known to retain intact reading frames. Additional intact HERV genes may exist, since retroviral reading frames have not been systematically ..
  24. pmc Identification of cryptic MHC I-restricted epitopes encoded by HIV-1 alternative reading frames
    Sylvain Cardinaud
    Unité Cellulaire Antivirale, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
    J Exp Med 199:1053-63. 2004
    ..MHC) I-restricted epitopes are widely believed to be derived from viral proteins encoded by primary open reading frames. However, the HIV-1 genome contains alternative reading frames (ARFs) potentially encoding small polypeptides...
  25. pmc Evidence for a subpopulation of conserved alternative splicing events under selection pressure for protein reading frame preservation
    Alissa Resch
    Molecular Biology Institute, Institute for Genomics and Proteomics, and Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095 1570, USA
    Nucleic Acids Res 32:1261-9. 2004
    ..These data indicate that a subpopulation of modern alternative splicing events was present in the common ancestors of these genomes, and was under functional selection pressure to preserve the protein reading frame...
  26. pmc Mutations of LRTOMT, a fusion gene with alternative reading frames, cause nonsyndromic deafness in humans
    Zubair M Ahmed
    Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, Rockville, Maryland 20850, USA
    Nat Genet 40:1335-40. 2008
    ..3-q13.4. LRTOMT has two alternative reading frames and encodes two different proteins, LRTOMT1 and LRTOMT2, detected by protein blot analyses...
  27. ncbi Translation from cryptic reading frames of DNA vaccines generates an extended repertoire of immunogenic, MHC class I-restricted epitopes
    Reinhold Schirmbeck
    Institute of Medical Microbiology and Immunology, University of Ulm, Ulm, Germany
    J Immunol 174:4647-56. 2005
    ..Human CMV promoter-driven Pol constructs encoding different Pol fragments in primary or alternative reading frames elicited comparable levels of Pol3-specific T cell responses...
  28. pmc A peptide-loaded dendritic cell based cytotoxic T-lymphocyte (CTL) vaccination strategy using peptides that span SIV Tat, Rev, and Env overlapping reading frames
    Zachary Klase
    Department of Infectious Diseases, Saint Michael s Medical Center, Newark, New Jersey, USA
    Retrovirology 3:1. 2006
    ..if the immunizing CTL epitope falls within a region of the virus that has a high density of overlapping reading frames which encode several viral proteins...
  29. ncbi Maintaining the ribosomal reading frame: the influence of the E site during translational regulation of release factor 2
    Viter Marquez
    Max Planck Institut fur Molekulare Genetik, AG Ribosomen, Ihnestrasse 73, D 14195 Berlin, Germany
    Cell 118:45-55. 2004
    ..Consistently, in a minimal system, the presence of the E site tRNA prevents the +1 frameshift event, illustrating the importance of the E site for reading-frame maintenance...
  30. pmc Human molybdopterin synthase gene: identification of a bicistronic transcript with overlapping reading frames
    B Stallmeyer
    Botanisches Institut der Technischen Universität, Braunschweig, Humboldtstr 1, D 38106 Braunschweig, Germany
    Am J Hum Genet 64:698-705. 1999
    ..shows a bicistronic structure, encoding the small and large subunits of the MPT-synthase in two different open reading frames (ORFs) that overlap by 77 nucleotides...
  31. pmc Unanticipated antigens: translation initiation at CUG with leucine
    Susan R Schwab
    Division of Immunology, Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
    PLoS Biol 2:e366. 2004
    ..These peptides are derived from not only conventional but also cryptic translational reading frames, including some without conventional AUG codons...
  32. pmc Multiple exon skipping and RNA circularisation contribute to the severe phenotypic expression of exon 5 dystrophin deletion
    F Gualandi
    Sezione di Genetica Medica, Dipartimento di Medicina Sperimentale e Diagnostica, Universita di Ferrara, Italy
    J Med Genet 40:e100. 2003
  33. ncbi Translational bypassing: a new reading alternative of the genetic code
    I Groisman
    Department of Molecular Biology, Hebrew University Hadassah Medical School, Jerusalem 91220, Israel
    Biochem Cell Biol 73:1055-9. 1995
    ..The understanding of this mechanism and its associated signals may be considered a paradigm for the expression of other genes by this alternative reading of the genetic code...
  34. pmc The role of upstream sequences in selecting the reading frame on tmRNA
    Mickey R Miller
    Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
    BMC Biol 6:29. 2008
    ..The -1 triplet hypothesis is important because it is the most credible model in which direct binding and recognition by the ribosome sets the reading frame on tmRNA...
  35. ncbi Removal of an intron with unique 3' branch site creates an amino-terminal protein sequence directing the scERV1 gene product to mitochondria
    T Lisowsky
    Botanisches Institut I, Universitat Dusseldorf, Germany
    Yeast 12:1501-10. 1996
    ..an additional intron in the 5' region of the mouse gene and possible amino-terminal extensions of the reading frames. In this work, reinvestigation of the 5' region of the yeast gene identifies a putative intron with an unusual ..
  36. pmc Comparative sequence of human and mouse BAC clones from the mnd2 region of chromosome 2p13
    W Jang
    Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109 0618, USA
    Genome Res 9:53-61. 1999
    ....
  37. ncbi The three dominant female-sterile mutations of the Drosophila ovo gene are point mutations that create new translation-initiator AUG codons
    M Mevel-Ninio
    Centre de Génétique Moléculaire du CNRS, Gif sur Yvette, France
    Development 122:4131-8. 1996
    ..We propose that premature expression of long Ovo protein isoforms occurs in ovoD mutants and interferes with wild-type Ovo function in controlling female germline differentiation...
  38. ncbi Multiple isoforms of DNA methyltransferase are encoded by the vertebrate cytosine DNA methyltransferase gene
    J Deng
    Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec H3G 1Y6, Canada
    J Biol Chem 273:22869-72. 1998
    ..The data presented here point toward a new mechanism for generating diversity of DNA MeTases and possibly diverse DNA methylation patterns...
  39. ncbi Sequence variants in the sulfonylurea receptor (SUR) gene are associated with NIDDM in Caucasians
    H Inoue
    Division of Metabolism, Diabetes and Endocrinology, Washington University School of Medicine, St Louis, Missouri 63110, USA
    Diabetes 45:825-31. 1996
    ..9% of patients and 0.5% of control subjects (P < 0.0001, OR 21.5, 95% CI 2.91-159.6). These results suggest that defects at the SUR locus may be a major contributor to the inherited basis of NIDDM in Northern European Caucasians...
  40. pmc Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes
    Michael F Lin
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
    Genome Res 17:1823-36. 2007
    ..These results affect >10% of annotated fly genes and demonstrate the power of comparative genomics to enhance our understanding of genome organization, even in a model organism as intensively studied as Drosophila melanogaster...
  41. pmc The importance of being divisible by three in alternative splicing
    Alon Magen
    Department of Human Genetics and Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Nucleic Acids Res 33:5574-82. 2005
    ..These findings suggest that alternative splicing of symmetrical and non-symmetrical exons is governed by different selective pressures and serves different purposes...
  42. pmc Translation of the F protein of hepatitis C virus is initiated at a non-AUG codon in a +1 reading frame relative to the polyprotein
    Martin Baril
    Departement de Biochimie, Université de Montréal 2900 Blvd Edouard Monpetit, Montreal, Quebec, Canada H3T 1J4
    Nucleic Acids Res 33:1474-86. 2005
    ..These observations are consistent with a Met-tRNA(i)-dependent initiation of translation at a non-AUG codon for the synthesis of the F protein...
  43. ncbi Decoding errors and the involvement of the E-site
    Knud H Nierhaus
    Max Planck Institut fur Molekulare Genetik, Ihnestrasse 73, AG Ribosomen, D 14195 Berlin, Germany
    Biochimie 88:1013-9. 2006
    ..A cognate tRNA at the E-site is an essential prerequisite for this high precision...
  44. ncbi Regulated readthrough: a new method for the alternative tagging and targeting of recombinant proteins
    Thomas Bouquin
    Maxygen ApS, Agern Alle 1, DK 2970 Hoersholm, Denmark
    J Biotechnol 125:516-28. 2006
    ....
  45. ncbi Fusion of FIG to the receptor tyrosine kinase ROS in a glioblastoma with an interstitial del(6)(q21q21)
    Alain Charest
    Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Genes Chromosomes Cancer 37:58-71. 2003
    ..This is the first example of a fusion RTK protein that results from an intra-chromosomal deletion, and it represents the first fusion RTK protein isolated from a human astrocytoma...
  46. ncbi Growth at low temperature suppresses readthrough of the UGA stop codon during the expression of Bacillus subtilis flgM gene in Escherichia coli
    Beatriz Gonzalez
    Laboratory of Bioreactors, Plant Division, Genetic Engineering and Biotechnology Center, PO Box 6162, CP 10600, La Habana, Cuba
    J Biotechnol 101:173-80. 2003
    ..The possible causes that contribute to reduce the proportion of readthrough protein species against the correct terminated product are discussed...
  47. ncbi Translocation of a tRNA with an extended anticodon through the ribosome
    Steven S Phelps
    Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Dr, La Jolla, CA 92093 0314, USA
    J Mol Biol 360:610-22. 2006
    ..Flexibility within the loop may allow conformational adjustment upon A site binding and for interacting with the four nucleotide codon in order to shift the mRNA reading frame...
  48. ncbi An extended RNA code and its relationship to the standard genetic code: an algebraic and geometrical approach
    Marco V José
    Theoretical Biology Group, Instituto de Investigaciones Biomedicas, Universidad Nacional Autonoma de Mexico, Mexico D F 04510, Mexico
    Bull Math Biol 69:215-43. 2007
    ..RNY plus codons obtained by considering the RNA code but in the second (NYR type), and the third, (YRN type) reading frames. In each of these reading frames, there are 16 triplets that altogether complete a set of 48 triplets, which ..
  49. pmc Identification of the functional initiation codons of a phase-variable gene of Haemophilus influenzae, lic2A, with the potential for differential expression
    Kevin Dixon
    University of Oxford, John Radcliffe Hospital, UK
    J Bacteriol 189:511-21. 2007
    Simple sequence repeats located within reading frames mediate phase-variable ON/OFF switches in gene expression by generating frameshifts...
  50. ncbi Alternatively spliced TCR mRNA induced by disruption of reading frame
    Jun Wang
    Department of Immunology, The University of Texas M D Anderson Cancer Center, Box 180, 1515 Holcombe Boulevard, Houston, TX 77030, USA
    Science 297:108-10. 2002
    ..The finding that translation signals regulate the levels of alternatively spliced mRNAs generated in the nucleus may alter the current view of how gene expression is controlled in eukaryotic cells...
  51. ncbi Codon reading by tRNAAla with modified uridine in the wobble position
    Ute Kothe
    Institute of Physical Biochemistry, University of Witten Herdecke, 58448 Witten, Germany
    Mol Cell 25:167-74. 2007
    ..g., the GCC codon. The ribosome accepts the C-cmo(5)U pair as an almost-correct base pair, unlike third-position mismatches, which lead to the incorporation of incorrect amino acids and are efficiently rejected...
  52. ncbi Accurate translocation of mRNA by the ribosome requires a peptidyl group or its analog on the tRNA moving into the 30S P site
    Kurt Fredrick
    Center for Molecular Biology of RNA, Sinsheimer Laboraties, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
    Mol Cell 9:1125-31. 2002
    ..If aminoacyl-tRNA is translocated, an intermediate level of translocational accuracy is observed. Thus, translocational accuracy depends on the acylation state of the tRNA entering the 30S P site...
  53. pmc Improvement of reading frame maintenance is a common function for several tRNA modifications
    J Urbonavicius
    Department of Microbiology, Umea University, S 90 187 Umeå, Sweden
    EMBO J 20:4863-73. 2001
    ..We propose that the improvement of reading frame maintenance has been and is the major selective factor for the emergence of new modified nucleosides...
  54. ncbi Cloning and characterization of the mouse and human enamelin genes
    J C Hu
    University of Texas Health Science Center at San Antonio, School of Dentistry, Department of Pediatric Dentistry, 78229 3900, USA
    J Dent Res 80:898-902. 2001
    ....
  55. ncbi A novel HLA-B*39 allele (HLA-B*3916) due to a rare mutation causing cryptic splice site activation
    R Tamouza
    Laboratoire d Immunologie et d Histocompatibilité, Hôpital Saint Louis and INSERM U396, Paris, France
    Hum Immunol 61:467-73. 2000
    ....
  56. ncbi In vivo studies on putative Shine-Dalgarno sequences of the halophilic archaeon Halobacterium salinarum
    Simone Sartorius-Neef
    Institut fur Mikrobiologie und Genetik, Technische Universitat Darmstadt, Schnittspahnstr 10, D 64287 Darmstadt, Germany
    Mol Microbiol 51:579-88. 2004
    ..With the exception of gvpA and gvpO, all reading frames of the p-gvpDEFGHIJKLM and p-gvpACNO mRNAs contained upstream of the AUG start codon a putative Shine-Dalgarno ..
  57. pmc FGF3 from Xenopus laevis
    P Kiefer
    Imperial Cancer Research Fund, London, UK
    EMBO J 12:4159-68. 1993
    ..Increasing the contribution from mouse FGF3 led to a more restricted host range for the chimeric ligand...
  58. ncbi The major genetic defect responsible for the polymorphism of S-mephenytoin metabolism in humans
    S M de Morais
    NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
    J Biol Chem 269:15419-22. 1994
    ..Finally, the familial inheritance of the deficient allele was found to be concordant with that of the phenotypic trait...
  59. ncbi Rat gastric H,K-ATPase beta-subunit gene: intron/exon organization, identification of multiple transcription initiation sites, and analysis of the 5'-flanking region
    P R Newman
    Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati College of Medicine, Ohio 45267 0524
    Genomics 11:252-62. 1991
    ..These include a sequence that may form a triple helix and an adjacent sequence with the potential to form Z-DNA...
  60. ncbi Autoregulatory frameshifting in decoding mammalian ornithine decarboxylase antizyme
    S Matsufuji
    Howard Hughes Medical Institute, University of Utah, Salt Lake City 84112
    Cell 80:51-60. 1995
    ..The shift site sequence, UCC-UGA-U, is not similar to other known frameshift sites. The mechanism does not seem to involve re-pairing of peptidyl-tRNA in the new frame but rather reading or occlusion of a fourth base...
  61. pmc A reassessment of the relationship between aroK- and aroL-encoded shikimate kinase enzymes of Escherichia coli
    M J Whipp
    Department of Microbiology, University of Melbourne, Parkville, Victoria, Australia
    J Bacteriol 177:1627-9. 1995
    ..The corrected sequence alters the length of the aroK coding region such that the AroK and AroL proteins are now of comparable length and the homology between them extends the entire length of the two enzymes...
  62. ncbi Characterization of the memory gene dunce of Drosophila melanogaster
    Y H Qiu
    Department of Cell Biology, Baylor College of Medicine, Houston, TX 77030
    J Mol Biol 222:553-65. 1991
    ..The results suggest that the remarkable structural complexity of dnc may reflect an intricate control of the spatial and/or temporal expression of various isoforms of cAMP PDEase...
  63. pmc DNA sequences of the tail fiber genes of bacteriophage P2: evidence for horizontal transfer of tail fiber genes among unrelated bacteriophages
    E Haggard-Ljungquist
    Department of Microbial Genetics, Karolinska Institutet, Stockholm, Sweden
    J Bacteriol 174:1462-77. 1992
    ....
  64. pmc Cloning, sequence analysis, and expression of the structural gene encoding glucose-fructose oxidoreductase from Zymomonas mobilis
    V Kanagasundaram
    Centre for Protein and Enzyme Technology, LaTrobe University, Bundoora, Victoria, Australia
    J Bacteriol 174:1439-47. 1992
    ..coli clone. However, the gfo gene cloned into a shuttle vector was shown to overexpress glucose-fructose oxidoreductase to levels of up to 6% of the soluble protein in Z. mobilis...
  65. pmc Nucleotide sequence of the jaagsiekte retrovirus, an exogenous and endogenous type D and B retrovirus of sheep and goats
    D F York
    Laboratoire de Virologie, Faculte de Medecine Nord, Marseille, France
    J Virol 66:4930-9. 1992
    ..Southern blot studies show that closely related sequences are present in sheep and goat normal genomic DNA, indicating that JSRV could be endogenous in ovine and caprine species...
  66. ncbi Liddle's syndrome: heritable human hypertension caused by mutations in the beta subunit of the epithelial sodium channel
    R A Shimkets
    Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06510
    Cell 79:407-14. 1994
    ..These findings demonstrate that Liddle's syndrome is caused by mutations in the beta subunit of the epithelial sodium channel and have implications for the regulation of this epithelial ion channel as well as blood pressure homeostasis...
  67. ncbi Genomic organization of Drosophila choline acetyltransferase
    H Sugihara
    Division of Neurosciences, Beckman Research Institute of the City of Hope, Duarte, California 91010
    J Neurochem 57:1636-42. 1991
    ..An exon I probe detected two bands of RNA whereas an exon VIII probe hybridized with only the smaller band, previously identified as ChAT mRNA. These results indicate a complex transcription pattern for the ChAT locus in Drosophila...
  68. ncbi Frame shift by insertion of 2 basepairs in codon 394 of CYP11B1 causes congenital adrenal hyperplasia due to steroid 11 beta-hydroxylase deficiency
    A Helmberg
    Department for Molecular Biology, University of Innsbruck Medical School, Austria
    J Clin Endocrinol Metab 75:1278-81. 1992
    ..Due to parental consanguinity, this defect was homozygous and, therefore, provides a full molecular explanation for this disease...
  69. ncbi A structurally novel staphylococcal protein A from the V8 strain
    V Finck-Barbançon
    Laboratoire de Toxicologie, Institut de Bactériologie, Faculté de Médecine de l Université Louis Pasteur, Strasbourg, France
    FEMS Microbiol Lett 70:1-8. 1992
    ..Contrary to what had been proposed previously, the first translated amino acid is probably not a leucine, but very likely a methionine located 12 residues upstream...
  70. ncbi Shorter variants of the D3 dopamine receptor produced through various patterns of alternative splicing
    B Giros
    Unité de Neurobiologie et Pharmacologie U 109 de I INSERM, Centre Paul Broca, Paris, France
    Biochem Biophys Res Commun 176:1584-92. 1991
    ..The functional significance and possible role of these shorter variants of the dopamine D3 receptor in cell signalling remain to be established...
  71. ncbi Molecular cloning, structure, promoters and regulatory elements for transcription of the Bacillus licheniformis encoded regulon for xylose utilization
    A Scheler
    Lehrstuhl fur Mikrobiologie, Friedrich Alexander Universitat Erlangen Nurnberg, Erlangen, Federal Republic of Germany
    Arch Microbiol 155:526-34. 1991
    ..The next greater differences are found to the S. xylosus and the greatest to the E. coli encoded genes. These results are discussed with respect to the taxonomic relations of these bacteria...
  72. ncbi Multiple mRNA species code for two non-allelic forms of ovine alpha s2-casein
    M Boisnard
    Unité d Endocrinologie Moléculaire, Institut National de la Recherche Agronomique, Jouy en Josas, France
    Eur J Biochem 201:633-41. 1991
    ..If so, the overall organization of the alpha s2-casein gene in the different species might be more similar than expected from structural comparisons of the cognate mRNA or caseins...
  73. pmc Glanzmann thrombasthenia secondary to a Gly273-->Asp mutation adjacent to the first calcium-binding domain of platelet glycoprotein IIb
    M Poncz
    Department of Medicine, School of Medicine, University of Pennsylvania, Philadelphia 19104
    J Clin Invest 93:172-9. 1994
    ..The impaired GPIIb-IIIa transport is responsible for the thrombasthenia in this patient...
  74. pmc Molecular study of pyruvate kinase deficient patients with hereditary nonspherocytic hemolytic anemia
    L Baronciani
    Department of Molecular and Experimental Medicine, Scripps Research Institute, La Jolla, California 92037, USA
    J Clin Invest 95:1702-9. 1995
    ..e., found with 1705C and 14 repeats in the microsatellite. This finding is consistent with a single origin of this common mutation. Other mutations occurring more than once were of much lower frequency than the 1529A mutation...
  75. ncbi Aberrant splicing of phenylalanine hydroxylase mRNA: the major cause for phenylketonuria in parts of southern Europe
    B Dworniczak
    Institute of Human Genetics, WWU, Munster, Germany
    Genomics 11:242-6. 1991
    ..This loss of enzyme activity is probably caused by conformational changes resulting from the insertion of three additional amino acids (Gly-Leu-Gln) between the normal sequences encoded by exon 10 and exon 11...
  76. ncbi Sequence and linkage analysis of the Coxiella burnetii citrate synthase-encoding gene
    R A Heinzen
    Department of Microbiology, Washington State University, Pullman 99164 4340
    Gene 109:63-9. 1991
    ..coli succinate dehydrogenase. This report represents the first nt sequence analysis of a gene of known function from the obligate intracellular parasite, C. burnetii...
  77. ncbi Novel testis germ cell-specific transcript of the CREB gene contains an alternatively spliced exon with multiple in-frame stop codons
    G Waeber
    Laboratory of Molecular Endocrinology, Massachusetts General Hospital, Howard Hughes Medical Institute, Harvard Medical School, Boston 02114
    Endocrinology 131:2010-5. 1992
    ....
  78. ncbi Homology between the HrpO protein of Pseudomonas solanacearum and bacterial proteins implicated in a signal peptide-independent secretion mechanism
    C L Gough
    Laboratoire de Biologie Moleculaire des relations Plantes Microorganismes, INRA CNRS, Castanet Tolosan, France
    Mol Gen Genet 239:378-92. 1993
    ..Three complete open reading frames (ORFs) are predicted within this region...
  79. ncbi Myxoma virus expresses a secreted protein with homology to the tumor necrosis factor receptor gene family that contributes to viral virulence
    C Upton
    Department of Biochemistry, University of Alberta, Edmonton, Canada
    Virology 184:370-82. 1991
    Poxviruses are known to contain a large number of open reading frames, particularly near the termini of the viral genome, that are not required for growth in tissue culture...
  80. pmc Sequence and organization of genes encoding enzymes involved in pyruvate metabolism in Mycoplasma capricolum
    P P Zhu
    Laboratory of Biochemical Genetics, National Heart, Lung and Blood Institute, Bethesda, Maryland 20892, USA
    Protein Sci 5:1719-36. 1996
    ..Examination of the sequence revealed open reading frames corresponding to numerous genes involved with the oxidation of pyruvate...
  81. ncbi Identification and properties of the genes encoding the poly(A) polymerase and a small (22 kDa) and the largest subunit (147 kDa) of the DNA-dependent RNA polymerase of molluscum contagiosum virus
    K C Sonntag
    Institut fur Medizinische Virologie, Universitat Heidelberg, Federal Republic of Germany
    Virology 210:471-8. 1995
    ..The oligonucleotide primers were designed according to the coding usage statistics of known open reading frames of the viral genome...
  82. ncbi Molecular characterization of IRF3 and IRF7 in rainbow trout, Oncorhynchus mykiss: functional analysis and transcriptional modulation
    J W Holland
    Scottish Fish Immunology Research Centre, Aberdeen University, Aberdeen AB24 2TZ, Scotland, United Kingdom
    Mol Immunol 46:269-85. 2008
    ..RtIRF7 was found to be 2055 bp, with a 102 bp 5'-UTR and a 705 bp 3'-UTR. The open reading frames (ORFs) translate into 464 amino acid and 415 amino acid proteins, respectively, each possessing a putative DNA-..
  83. pmc Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics
    D R Smith
    Genome Therapeutics Corporation, Collaborative Research Division, Waltham, Massachusetts 02154, USA
    J Bacteriol 179:7135-55. 1997
    ..A total of 1,855 open reading frames (ORFs) have been identified that appear to encode polypeptides, 844 (46%) of which have been assigned putative ..
  84. ncbi Mutational analysis of mau genes involved in methylamine metabolism in Paracoccus denitrificans
    C J van der Palen
    Department of Molecular and Cellular Biology, BioCentrum Amsterdam, Vrije Universiteit, The Netherlands
    Eur J Biochem 230:860-71. 1995
    ..Sequence analysis of this fragment revealed the presence of four open reading frames, all transcribed in the same direction...
  85. pmc Heat shock response of murine Chlamydia trachomatis
    J N Engel
    Department of Microbiology and Immunology, University of California Medical Center, San Francisco 94143
    J Bacteriol 172:6959-72. 1990
    ..The second locus encoded three potential nonoverlapping open reading frames. One of the open reading frames was 52% homologous to the ribosomal protein S18 of Escherichia coli and thus ..
  86. pmc Convergent peripheral pathways catalyze initial glucose catabolism in Pseudomonas putida: genomic and flux analysis
    Teresa del Castillo
    Department of Environmental Protection, Estacion Experimental del Zaidin, Consejo Superior de Investigaciones Cientificas, C Prof Albareda, 1, E 18008 Granada, Spain
    J Bacteriol 189:5142-52. 2007
    ..Glucose is transported to the cytoplasm in a process mediated by an ABC uptake system encoded by open reading frames PP1015 to PP1018 and is then phosphorylated by glucokinase (encoded by the glk gene) and converted by glucose-..
  87. ncbi DNA sequence and transcriptional analyses of the region of the equine herpesvirus type 1 Kentucky A strain genome encoding glycoprotein C
    T Matsumura
    Department of Microbiology and Immunology, Louisiana State University Medical Center, Shreveport 71130
    Virology 193:910-23. 1993
    ..129 to 0.152) encoding open reading frames (ORFs) 15 and 16...
  88. ncbi A 4.6 kb DNA region of Rhizobium meliloti involved in determining urease and hydrogenase activities carries the structural genes for urease (ureA, ureB, ureC) interrupted by other open reading frames
    G Miksch
    Lehrstuhl fur Genetik, Fakultat fur Biologie, Universitat Bielefeld, Germany
    Mol Gen Genet 242:539-50. 1994
    A 4.6 kb DNA region of the Rhizobium meliloti strain AK631 was found to contain seven open reading frames (ORFs), all oriented in the same direction...
  89. pmc Cloning, sequencing, and expression of clustered genes encoding beta-hydroxybutyryl-coenzyme A (CoA) dehydrogenase, crotonase, and butyryl-CoA dehydrogenase from Clostridium acetobutylicum ATCC 824
    Z L Boynton
    Department of Biochemistry and Cell Biology, The Institute of Biosciences and Bioengineering, Rice University, Houston, Texas 77005 1892, USA
    J Bacteriol 178:3015-24. 1996
    ..2 kDa; the hbd gene encodes BHBD, with 282 residues and a molecular mass of 30.5 kDa. Three open reading frames (bcd, etfB, and etfA) are located between crt and hbd...
  90. pmc RS1 element of Vibrio cholerae can propagate horizontally as a filamentous phage exploiting the morphogenesis genes of CTXphi
    Shah M Faruque
    Molecular Genetics Laboratory, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka 1212, Bangladesh
    Infect Immun 70:163-70. 2002
    ..Integrated CTXPhi is often flanked by another genetic element known as RS1 which carries all open reading frames (ORFs) found in RS2 and an additional ORF designated rstC...
  91. pmc Nucleotide sequence of the Serratia marcescens threonine operon and analysis of the threonine operon mutations which alter feedback inhibition of both aspartokinase I and homoserine dehydrogenase I
    K Omori
    Research Laboratory of Applied Biochemistry, Tanabe Seiyaku Co, Ltd, Osaka, Japan
    J Bacteriol 175:785-94. 1993
    The nucleotide sequence of the Serratia marcescens threonine operon (thrA1A2BC) was determined. Three long open reading frames were identified; these open reading frames code for aspartokinase I (AKI)-homoserine dehydrogenase I (HDI), ..
  92. ncbi Myxoma virus and Shope fibroma virus encode dual-specificity tyrosine/serine phosphatases which are essential for virus viability
    K Mossman
    Department of Biochemistry, University of Alberta, Edmonton, Canada
    Virology 206:572-82. 1995
    ..of the genomes of the Leporipoxviruses myxoma virus and Shope fibroma virus (SFV) led to the discovery of open reading frames homologous to the vaccinia H1L gene encoding a soluble protein phosphatase with dual tyrosine/serine ..
  93. ncbi Mutations in the C, D, and V open reading frames of human parainfluenza virus type 3 attenuate replication in rodents and primates
    A P Durbin
    National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
    Virology 261:319-30. 1999
    ..These results indicate that the C, D, and V proteins of HPIV3 each has a role in virus replication in vitro, in vivo, or both, and define mutations that might be useful for the development of a vaccine against HPIV3...
  94. pmc Isolation of a new broad-host-range IncQ-like plasmid, pTC-F14, from the acidophilic bacterium Acidithiobacillus caldus and analysis of the plasmid replicon
    M N Gardner
    Department of Microbiology, University of Stellenbosch, Matieland 7602, South Africa
    J Bacteriol 183:3303-9. 2001
    ..Sequence analysis of the pTC-F14 replicon region revealed five open reading frames and a replicon organization like that of the broad-host-range IncQ plasmids...
  95. ncbi Characterization of a 45-kDa flavoprotein and evidence for a rubredoxin, two proteins that could participate in electron transport from H2 to CO2 in methanogenesis in Methanobacterium thermoautotrophicum
    J NOLLING
    Department of Microbiology, Ohio State University, Columbus, USA
    Eur J Biochem 231:628-38. 1995
    ..of the flavoprotein-A-encoding gene (fpaA) and the co-transcription of fpaA with two downstream open reading frames, one of which (rdxA) appears to encode a rubredoxin...
  96. ncbi The genome of bacteriophage phiKZ of Pseudomonas aeruginosa
    Vadim V Mesyanzhinov
    Laboratory of Gene Technology, Katholieke Universiteit Leuven, Kardinaal Mercierlaan 92, B 3001 Leuven, Belgium
    J Mol Biol 317:1-19. 2002
    ..The genome has 306 open reading frames (ORFs) varying in size from 50 to 2237 amino acid residues...
  97. pmc Synthesis of catalytically active form III ribulose 1,5-bisphosphate carboxylase/oxygenase in archaea
    Michael W Finn
    Department of Microbiology, The Ohio State University, Columbus, Ohio 43210 1292, USA
    J Bacteriol 185:3049-59. 2003
    ..However, the recent completion of several genome-sequencing projects uncovered open reading frames resembling RubisCO in the third domain of life, the archaea...
  98. ncbi Identification, characterization and genetic mapping of TLR7, TLR8a1 and TLR8a2 genes in rainbow trout (Oncorhynchus mykiss)
    Yniv Palti
    United States Department of Agriculture, Agriculture Research Service, National Center for Cool and Cold Water Aquaculture, Kearneysville, WV 25430, USA
    Dev Comp Immunol 34:219-33. 2010
    ..Direct sequencing of two representative BACs revealed intact omTLR7 and omTLR8a1 open reading frames (ORFs) located on chromosome 3 and a second locus on chromosome 22 that contains an omTLR8a2 ORF and a ..
  99. ncbi Characterization of a (2R,3R)-2,3-butanediol dehydrogenase as the Saccharomyces cerevisiae YAL060W gene product. Disruption and induction of the gene
    E Gonzalez
    Department of Biochemistry and Molecular Biology, Faculty of Sciences, Universitat Autonoma de Barcelona, E 08193 Bellaterra Barcelona, and Spain
    J Biol Chem 275:35876-85. 2000
    ..completion of the Saccharomyces cerevisiae genome project in 1996 showed that almost 60% of the potential open reading frames of the genome had no experimentally determined function...
  100. ncbi Nucleotide sequence and genome organization of biologically active proviruses of the bovine immunodeficiency-like virus
    K J Garvey
    Laboratory of Cell and Molecular Structure, NCl Frederick Cancer Research Facility, Maryland 21701
    Virology 175:391-409. 1990
    The complete nucleotide sequences and translations of major open reading frames (ORF) of two distinct, infectious, proviral molecular clones (106 and 127) of the bovine immunodeficiency-like virus (BIV), obtained from a single virus ..
  101. ncbi Nociceptin/orphanin FQ and the opioid receptor-like ORL1 receptor
    J C Meunier
    Unité de Neuropharmacologie Moléculaire, Institut de Pharmacologie et de Biologie Structurale, C N R S UPR 9062, Toulouse, France
    Eur J Pharmacol 340:1-15. 1997
    Homology cloning and, more recently, the sequencing of whole genomes, have identified many open reading frames encoding proteins of unknown function, in particular putative G protein-coupled membrane receptors...

Research Grants70

  1. Defining the functions of uncharacterized genes in priority pathogens
    Sean Crosson; Fiscal Year: 2013
    ..immediate goal of this project is to define the cellular and biochemical functions of 57 uncharacterized open reading frames (ORFs), hypothetical proteins, and small non-coding RNAs in B. abortus...
  2. The Roles of Conserved outer-membrane proteins in SFG rickettsia pathogenesis
    Juan J Martinez; Fiscal Year: 2013
    ..degenerate or split, at least 4 genes, sca0 (rompA), sca1, sca2, and sca5 (rompB) are present as complete open reading frames in R. conorii and many other SFG rickettsia...
  3. Function of mRNA Editing in Trypanosomes
    Stephen L Hajduk; Fiscal Year: 2010
    ..Alternatively edited mRNAs, creating novel open reading frames, were found for each of these genes...
  4. Development of a novel vaccine for protection against gammaherpesvirus infection
    Blossom A Damania; Fiscal Year: 2010
    ..RRV was originally isolated from rhesus macaques, is very closely related to KSHV and most of the eighty open reading frames (ORFs) of RRV share high homology with the corresponding ORFs of KSHV...
  5. Varicella-Zoster Virus: T Cell/Skin Tropism &Immunity
    Ann Arvin; Fiscal Year: 2013
    ..The VZV genome has at least 71 known or predicted open reading frames (ORFs) but understanding how these gene products function in virulence is difficult because VZV is highly ..
  6. DNA-Binding Protein Discovery by the Combinatorial Method REPSA
    Michael van Dyke; Fiscal Year: 2013
    ..For example, while the bacteria Escherichia coli strain K12 has 4364 open reading frames, only about half of these genes have been well characterized by genetic, biochemical or molecular biological ..
  7. The Viral Life Cycle of Human Endogenous Retrovirus Type K
    Derek Dube; Fiscal Year: 2013
    ..Due to their recent integration, while most HERV genomes have been mutated and deleted to render their open reading frames non-functional, many of the more than 91 HERV-K genomes present maintain intact open reading frames for their ..
  8. Pathogenic mechanisms of non-01/non-0139 V. cholerae
    Michelle Dziejman; Fiscal Year: 2012
    ..genome sequencing of a clinically isolated non-O1/non-O139 strain, AM-19226, has revealed the presence of open reading frames (ORFs) having significant similarity to genes encoding a Type Three Secretion System (TTSS)...
  9. Effect of chromatin remodelers/modifiers on HIV-1 Tat activated transcription
    Fatah Kashanchi; Fiscal Year: 2010
    ..and Tat-p/CAF complexes in chromatin marking and transcription elongation on the HIV-1 promoter and open reading frames in cell lines and PBMC infected cells? (II) What is the role of the Tat- SWI/SNF (Tat-PBAF) complex in ..
  10. Molecular bssis of mef-mediated antibiotic resistance in Streptococcus pneumoniae
    David S Stephens; Fiscal Year: 2010
    ..At least four sites of insertion of mega have been identified. In addition to mefE, four other open reading frames (ORFs) organized into two convergent clusters are found in mega...
  11. Molecular mechanism of omega-3 response
    JAMES T BRENNA; Fiscal Year: 2013
    ..a) Determine the promoters and full length open reading frames (ORFs) of FADS CS and AT with RNA-Seq using human liver...
  12. Generation and validation of a comprehensive human disease mutant ORF resource
    Luke J Whitesell; Fiscal Year: 2010
    ..Open Reading Frames (ORFs) encoding ~10,000 different disease causing alleles will be generated using a recombinational cloning ..
  13. DNA REPAIR AND ANTITOPOISOMERASE DRUG EFFECTS
    John L Nitiss; Fiscal Year: 2010
    ..Successful utilization of these tools, notably a set of strains deleting all non-essential open reading frames has required us to develop new approaches to efficiently enhance the sensitivity of yeast cells to drugs ..
  14. The Significance of Polymorphic Endogenous Retroviruses to Human Mental Health
    JULIA HALO WILDSCHUTTE; Fiscal Year: 2010
    ..Although most are defective, HML-2 proviruses with intact open reading frames in some or all genes exist...
  15. ERV3 Control of Human Placentation
    NEAL STEWART ROTE; Fiscal Year: 2013
    ..small number of endogenous retrovirus (ERV) integration sites retained isolated transcriptionally active open reading frames so that a variety of gag (matrix and capsid), pol (polymerase and other enzymes), and env (envelope) proteins ..
  16. REGULATION OF CHOLESTEROL HOMEOSTASIS BY NONCODING RNAS
    Daniel S Ory; Fiscal Year: 2013
    ..The goal of this proposal is to study how these genes modulate the distribution and level of cholesterol in cells. The proposed studies may identify new targets for drug development for lowering cholesterol in disease states. ..
  17. Ribosome Profiling in Plasmodium falciparum
    Marilyn Parsons; Fiscal Year: 2013
    ..genome annotation by determining whether proteins are translated from mRNAs corresponding to individual open reading frames, particularly those annotated as hypothetical proteins and those encoded by non-canonical protein-coding open ..
  18. Guide RNA Binding Complex
    RUSLAN AFASIZHEV; Fiscal Year: 2013
    ..an extensive post-transcriptional uridine insertion/deletion RNA editing is required to produce open reading frames. The cascade of editing reactions is catalyzed by enzymes embedded into the ~15-subunit RNA editing core ..
  19. Rhesus HHV-8 homologue in AIDS-related malignancies
    Scott W Wong; Fiscal Year: 2013
    ..needed to identify viral determinants of pathogenesis and how these specific determinants, either viral open reading frames (ORFs) or other viral-encoded macromolecules are involved in HHV8-mediated pathogenesis...
  20. The Drosophila Gene Tagging Project: Transgenes with Swappable Protein Tags
    ROGER ALLEN HOSKINS; Fiscal Year: 2013
    ..One of the most useful applications of P[acman] is to incorporate tags within open reading frames of genes to express fusion proteins...
  21. Analysis of an orchestrated cell death mediated by Vibrio parahaemolytics T3SS1
    Kim Orth; Fiscal Year: 2013
    ..The effectors on the first pathogenicity island have been identified as open reading frames with no obvious homology to any known protein. Recently, we have demonstrated that the V...
  22. Evaluating the efficiency and specificity of stop codon suppression therapy
    Michael T Howard; Fiscal Year: 2013
    ..These include cellular transcripts with regulatory short 5'UTR open reading frames or long 3'UTRs, selenoprotein mRNAs, and transcripts encoded by transposable elements or non-functional ..
  23. Creating Platforms for the Proteomics and Membrane Proteins
    PAUL CREMER; Fiscal Year: 2012
    ..PUBLIC HEALTH RELEVANCE: It is generally believed that 15 to 30% of open reading frames in the genomes of most organisms encode membrane proteins...
  24. CTL and HIV Polymorphisms in Heterosexual Transmission
    Jianming Tang; Fiscal Year: 2013
    ..kinetics of CTL escape and reversion of both conventional and cryptic epitopes (epitopes encoded by alternate reading frames) across the viral proteome...
  25. Universal Clone Resources for Drosophila Proteomics
    Susan E Celniker; Fiscal Year: 2013
    ..these collections are and will continue to be the primary source of high quality Drosophila melanogaster open reading frames (ORFs) that are easily transferred into a number of different expression vectors...
  26. The mechanisms of eukaryotic translation termination and ribosomal recycling
    Tatyana V Pestova; Fiscal Year: 2013
    ..This mostly occurs after translation of short open reading frames (ORFs), whereas reinitiation after long ORFs is rare and appears to be limited to several virus families...
  27. Ribosome profiling of Trypanosoma brucei
    Marilyn Parsons; Fiscal Year: 2012
    ..the current debate over the function of the numerous recently identified RNAs that contain only short open-reading frames, and has the potential to identify non-canonical protein-coding open-reading frames, thus significantly ..
  28. Comprehensive transcriptome analysis for Porphyromonas gingivalis
    Tsute Chen; Fiscal Year: 2009
    ..invaluable to the research communities, these microarrays were designed based on computer-predicted open reading frames (ORFs) only, and are limited to gene expression studies only in the protein-coding regions...
  29. Ribosomal scanning and initiation codon selection
    Tatyana V Pestova; Fiscal Year: 2013
    ..40S subunits back to the 5'-end of the same mRNA, and reinitiation after translation of short open reading frames. PUBLIC HEALTH RELEVANCE: Protein synthesis is of central importance in cell metabolism, and its complex ..
  30. Chlamydia trachomatis proteomics
    Guangming Zhong; Fiscal Year: 2013
    ..Zhong's lab expressed all C. trachomatis open reading frames (ORFs) as soluble fusion proteins and developed a high quality whole genome scale proteome array in the past 5 ..
  31. How Genetic Variation in Protein Kinases Affects Drug Response
    EDWARD E HARLOW; Fiscal Year: 2010
    ..Our first goal will be to generate a resource of ~3000 open reading frames capturing variants of 535 human protein kinases...
  32. Protein and Peptide Derived Cofactors
    Judith P Klinman; Fiscal Year: 2013
    ..least well understood among the pathways that lead to enzymatic cofactors, and each of the five conserved open reading frames that encode for essential proteins in PQQ production is being studied...
  33. Viral Modulation of Genetic Stability
    Matthew D Weitzman; Fiscal Year: 2013
    ..that result in Ad genomes being joined into concatemers during infection with viruses deleted of the E4 open reading frames. Concatemerization requires host DNA repair proteins, including the Mre11/Rad50/Nbs1 complex (MRN)...
  34. MHC-BOUND, SIV-DERIVED, CTL AND HTL EPITOPES
    David I Watkins; Fiscal Year: 2013
    ..Finally, we recently discovered that there are several MHC class l-restricted epitopes in SIV cryptic Open Reading Frames (cORFs)...
  35. MHC-BOUND, SIV-DERIVED, CTL AND HTL EPITOPES
    David I Watkins; Fiscal Year: 2011
    ..Finally, we recently discovered that there are several MHC class l-restricted epitopes in SIV cryptic Open Reading Frames (cORFs)...
  36. Disabling of the Anaphase Promoting Complex by Human Cytomegalovirus
    DEBORAH HYE SPECTOR; Fiscal Year: 2010
    ..The first utilizes a library of cDNA constructs corresponding to all of the HCMV open reading frames (ORFs), and the second utilizes a library of HCMV Bacterial Artificial Chromosomes (BACs) that have mutations ..
  37. Identification of Pathways Affected by Essential Proteins of Unknown Function
    SEAN DAVID MOORE; Fiscal Year: 2012
    ..coli that have not yet been assigned a function. Of the ~4,300 E. coli open reading frames, roughly a third have not had their encoded protein functions experimentally verified...
  38. Large-Scale High-Confidence Binary Protein Interaction Network for Drosophila
    Norbert Perrimon; Fiscal Year: 2013
    ..screen for high-confidence identification of binary protein interactions among 10,000 Drosophila open reading frames (ORFs)...
  39. COMMON AND RARE SEQUENCE VARIANTS IN BREAST CANCER RISK
    SEAN VAHRAM TAVTIGIAN; Fiscal Year: 2011
    ..In the second arm, we will mutation screen the open reading frames of strong candidate susceptibility genes in both the cases and the controls...
  40. Generating and Managing Large Scale Proteogenomic Data for ENCODE Cell Lines
    MORGAN CORINNE contact GIDDINGS; Fiscal Year: 2010
    ..has been used to reveal new genes, new alternative splice variants, new start sites, and upstream open reading frames (ORFs)...
  41. The Discovery of Human Peptide Encoding Genes
    Alan Saghatelian; Fiscal Year: 2013
    ..Since SEPs are produced from short open reading frames (sORFs) in the genome this discovery also represents the characterization of 32 new human genes...
  42. Vpr as a Mediator Proteasomal Degradation
    CARLOS M DE NORONHA; Fiscal Year: 2010
    ..by the observation that several of these viruses, including HIV2, have duplicated vpr to generate two open reading frames, vpr and vpx. This duplication has permitted divergence and presumably, further optimization of Vpr functions...
  43. Bridging KSHV capsids to the nuclear egress complex
    Prashant Desai; Fiscal Year: 2013
    ..will test capsid-associated proteins, for example, the capsid vertex-specific component (CVSC) encoded by open reading frames (ORF) 19 and 32 for the ability to bridge capsids with nuclear membranes...
  44. Pathogenesis of Persistent Chlamydial STDs
    Deborah Dean; Fiscal Year: 2007
    ..However, the discovery of open reading frames predicted to encode a nine-member polymorphic membrane protein (Prop) gene (pmp) family in the recently ..
  45. Creation and validation of a lux-positive Candida strain
    Yue Fu; Fiscal Year: 2007
    ..albicans. Internal ribosomal entry sequences (IRES) will allow translation of multiple open reading frames from single messenger RNA (mRNA) strands. Candidal promoters will be used in lieu of S...
  46. TYPE III COLLAGEN GENE EXPRESSION IN CARTILAGE
    SHERRILL ADAMS; Fiscal Year: 1993
    ..They will also define any open reading frames in the RNA, thus indicating whether the RNA is likely to encode a protein (either a non- collagen protein or ..
  47. ANTIGENIC DETERMINANTS OF VARICELLA VIRUS
    Charles Grose; Fiscal Year: 2006
    ..The VZV genome encodes about 70 open reading frames. The predominant VZV glycoprotein complex, in contrast to other alphaherpesviruses, is gE:gI...
  48. HIV-1 Cryptic Epitopes: Implications for Vaccine Design
    Paul A Goepfert; Fiscal Year: 2013
    ..Cryptic epitopes (CE) are translated from alternate reading frames (ARF) and not the main reading frame used to synthesize the functional proteins...
  49. Southern California Primary Infection Program
    Douglas D Richman; Fiscal Year: 2010
    ..Ongoing and proposed studies include the characterization of CD4 and CD8 responses to full length HIV reading frames, the relative contributions of immune responses to consensus and autologous sequences of HIV, the generation ..
  50. Single molecule translational profiling
    Joseph D Puglisi; Fiscal Year: 2013
    ..for single-molecule translational profiling (2) use these reagents to characterize translational start sites, reading frames, termination sites and drug effects in three organisms: E...
  51. Global Identification of transcribed elements in the C. elegans genome
    Robert H Waterston; Fiscal Year: 2011
    ..spectrometry to distinguish protein coding transcripts from noncoding transcripts for small potential open reading frames. The result will be a set of transcripts that will approach completion for protein coding genes and their UTRs ..
  52. Nanoliter Lab-on-a-chip for Protein Crystallization
    Vamsee Pamula; Fiscal Year: 2007
    unreadable] DESCRIPTION (provided by applicant): The human genome contains at least 30,000 unique open reading frames that may yield >100,000 polypeptide products...
  53. Francisella tularensis Pathogenesis
    Thomas H Kawula; Fiscal Year: 2013
    ..This situation is due, in part, to the fact that most open reading frames in Francisella have no known orthologs...
  54. MITOCHONDRIAL RNA EDITING IN TRYPANOSOMA BRUCEI
    DONNA KOSLOWSKY; Fiscal Year: 1999
    ..It allows the generation of translatable messages by creating the open reading frames as well as proper initiation and termination signals...
  55. STRUCTURE OF VIRAL RNA IN RIBOSOMAL FRAMESHIFTING
    Alexander Rich; Fiscal Year: 2004
    ..The - 1 shift in reading frames causes stop codon readthrough, and results in production of a single fusion protein...
  56. Scope and mechanism of eptide translation from short open reading frames in the h
    SARAH ANN SLAVOFF; Fiscal Year: 2013
    ..provided by applicant): Peptides of fewer than 100 amino acids that are directly translated from short open reading frames (sORFs) encoded in the genomes of widely divergent species, including human, have recently been discovered to ..
  57. Drug abuse: Discovering ligands for pertinent GPCRs
    Marc G Caron; Fiscal Year: 2013
    ..With NIDA support over the past three years we have established a cDNA collection containing the open reading frames for almost all human addiction associated GPCRs, and more importantly an expanding repository of off-the shelf ..
  58. SITE SPECIFIC RECOMBINATION IN STAPHYLOCOCCUS AUREUS
    Ellen Murphy; Fiscal Year: 1990
    ..The nucleotide sequence of Tn554 contains six open reading frames; two are the antibiotic resistance markers ermA and spc; three, tnpA, tnpB and tnpC, are required for ..
  59. MOLECULAR ANALYSIS OF A POTENTIAL TRANSPORT OPERON IN AA
    Karen Novak; Fiscal Year: 2001
    ..We have identified seven open reading frames (ORFs) encoding putative proteins homologous with those predicted by the ptl and virB transport operons on the ..
  60. ANIMAL MODELS OF MOLECULAR PATHOGENSIS OF HTLV-1
    Michael Lairmore; Fiscal Year: 2003
    ..Regulatory and accessory genes of HTLV-1 are encoded in four open reading frames (ORF I-IV) of the pX region of the virus...
  61. Mechanisms of Protein Structure Evolution
    John Moult; Fiscal Year: 2010
    ..number of protein folds and apparently young proteins: that these (1) are the result of generation of new open reading frames or frame shifted older ones;(2) are the outcome of extensive recombination of portions of older proteins;(3) ..
  62. 'RECODING: DYNAMIC REPROGRAMMING OF GENETIC READOUT'
    John Atkins; Fiscal Year: 2004
    ..Reprogramming of the readout of certain mRNAs can cause a different meaning for a code word or alternative reading frames to be accessed...
  63. Mucosal Helper-dependent Adenovirus Vaccines Against HIV
    Michael Barry; Fiscal Year: 2009
    ..Current first generation adenoviral (FG-Ad) vaccines encode 17 adenoviral open reading frames that can be targeted by anti-vector T cells...
  64. Immunoevasive Mucosal Vaccines Against HIV-1
    Michael A Barry; Fiscal Year: 2013
    ..Current first generation adenoviral (FG-Ad) vaccines encode 17 adenoviral open reading frames that can be targeted by anti-vector T cells...
  65. HEPATIC DRUG ELIMINATION IN PREGNANCY
    Mary Vore; Fiscal Year: 2007
    ..pump (BSEP) from the canalicular membrane and decreased bile flow, and 3) identification of upstream open reading frames (uORF) in the 5' leader sequences of rat, human and mouse MRP2...
  66. HEPATIC DRUG ELIMINATION IN PREGNANCY
    Mary Vore; Fiscal Year: 2010
    ..pump (BSEP) from the canalicular membrane and decreased bile flow, and 3) identification of upstream open reading frames (uORF) in the 5'leader sequences of rat,human and mouse MRP2...
  67. Integrated genomic approaches to identify and validate cancer targets
    William C Hahn; Fiscal Year: 2010
    ..to develop and implement genome scale RNA interference libraries, complete collections of human open reading frames (ORFs) and comprehensive protein-protein interaction maps...
  68. HIV Frameshift Site RNA Structure, Function and Ligand Interactions
    Samuel E Butcher; Fiscal Year: 2013
    ..The HIV-1 FS site is a highly conserved genomic RNA structure located between the gag and pol reading frames. Its purpose is to stimulate a -1 FS that is required for expression of the Pol genes, which are in the -1 ..
  69. IN VIVO INDUCED ANTIGEN TECHNOLOGY OF AA IN LJP
    Martin Handfield; Fiscal Year: 2003
    ..cloned DNA inserts in reactive clones will be analyzed for IPTG inducibility and sequenced to determine open reading frames likely to be responsible for expression of the in vivo-induced antigens...
  70. PHOSPHORYLATION IN RENAL CELL INJURY
    Goutam Ghosh Choudhury; Fiscal Year: 2004
    ..Open reading frames of interacting proteins will be determined by nucleotide sequencing...