Experts and Doctors on base sequence in Ithaca, New York, United States


Locale: Ithaca, New York, United States
Topic: base sequence

Top Publications

  1. Giardina C, Pérez Riba M, Lis J. Promoter melting and TFIID complexes on Drosophila genes in vivo. Genes Dev. 1992;6:2190-200 pubmed
    ..This protection appears to be a consequence of TFIID binding, as a similar protection pattern could be produced in vitro with purified protein. ..
  2. Lin H, Wolfner M. The Drosophila maternal-effect gene fs(1)Ya encodes a cell cycle-dependent nuclear envelope component required for embryonic mitosis. Cell. 1991;64:49-62 pubmed
    ..These results suggest that the fs(1)Ya protein is a cell cycle-dependent component of the nuclear envelope that specifically functions in embryonic mitosis. ..
  3. Ren H, Madison J, Thompson J. Identification of an ethanol-soluble protein as beta-amylase and its purification from soybean seeds. Phytochemistry. 1993;33:535-9 pubmed
    ..Therefore, the ethanol-soluble protein was identified as beta-amylase. The enzyme was purified to homogeneity using a two-step purification procedure with a yield of over 50%. ..
  4. Mulero J, Fox T. Alteration of the Saccharomyces cerevisiae COX2 mRNA 5'-untranslated leader by mitochondrial gene replacement and functional interaction with the translational activator protein PET111. Mol Biol Cell. 1993;4:1327-35 pubmed
    ..These results demonstrate an intimate functional interaction between the translational activator protein and the mRNA 5'-UTL and suggest that they may interact directly. ..
  5. Darwin A, Tyson K, Busby S, Stewart V. Differential regulation by the homologous response regulators NarL and NarP of Escherichia coli K-12 depends on DNA binding site arrangement. Mol Microbiol. 1997;25:583-95 pubmed
    ..In conclusion, we propose that 7-2-7 sites are preferred by both NarL and NarP. NarL can also recognize other binding site arrangements, an ability that appears to be lacking in NarP. ..
  6. Wang D, Parrish C. A heterogeneous nuclear ribonucleoprotein A/B-related protein binds to single-stranded DNA near the 5' end or within the genome of feline parvovirus and can modify virus replication. J Virol. 1999;73:7761-8 pubmed
    ..Overexpression of the protein in feline cells from a plasmid vector made them largely resistant to FPV infection. Mutagenesis of the protein binding site within the 5' end viral genome did not affect replication of the virus...
  7. Elble R, Pauli B. Tumor suppression by a proapoptotic calcium-activated chloride channel in mammary epithelium. J Biol Chem. 2001;276:40510-7 pubmed
  8. Lilly J, Havey M. Small, repetitive DNAs contribute significantly to the expanded mitochondrial genome of cucumber. Genetics. 2001;159:317-28 pubmed
    ..Our results demonstrate that the expanded cucumber mitochondrial genome is in part due to extensive duplication of short repetitive sequences, possibly by recombination and/or replication slippage. ..
  9. Hirschberger L, Daval S, Stover P, Stipanuk M. Murine cysteine dioxygenase gene: structural organization, tissue-specific expression and promoter identification. Gene. 2001;277:153-61 pubmed
    ..Western blot analyses indicated that CDO protein levels parallel mRNA levels. These results are consistent with the known function of CDO in whole-body cysteine homeostasis. ..

More Information

Publications146 found, 100 shown here

  1. Bollenbach T, Stern D. Secondary structures common to chloroplast mRNA 3'-untranslated regions direct cleavage by CSP41, an endoribonuclease belonging to the short chain dehydrogenase/reductase superfamily. J Biol Chem. 2003;278:25832-8 pubmed
    ..These results are consistent with a broad role for CSP41 in the degradation of stem-loop-containing mRNAs. ..
  2. De Jong W, Eannetta N, De Jong D, Bodis M. Candidate gene analysis of anthocyanin pigmentation loci in the Solanaceae. Theor Appl Genet. 2004;108:423-32 pubmed
    ..To test the hypothesis that tomato anthocyaninless corresponds to f3'5'h, a portion of the gene was sequenced. A premature stop codon was observed in an anthocyaninless mutant, but not in wild-type...
  3. Kijas J, Zangerl B, Miller B, Nelson J, Kirkness E, Aguirre G, et al. Cloning of the canine ABCA4 gene and evaluation in canine cone-rod dystrophies and progressive retinal atrophies. Mol Vis. 2004;10:223-32 pubmed
    ..To characterize a novel early onset canine retinal disease, and evaluate the ATP-binding cassette transporter gene ABCA4 as a potential candidate gene in this and other canine retinal degenerations...
  4. Hurt D, Widom J, Clardy J. Structure of Plasmodium falciparum dihydroorotate dehydrogenase with a bound inhibitor. Acta Crystallogr D Biol Crystallogr. 2006;62:312-23 pubmed
    ..Because no effective inhibitors have been described for PfDHODH, this structure provides critical insight for the design of potential antimalarials. ..
  5. Wu F, Mueller L, Crouzillat D, P tiard V, Tanksley S. Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes (COSII) for comparative, evolutionary and systematic studies: a test case in the euasterid plant clade. Genetics. 2006;174:1407-20 pubmed publisher
    ..2) No whole-genome duplication event (i.e., polyploidization) occurred immediately prior to or after the radiation of either Solanaceae or Rubiaceae as has been recently suggested...
  6. Szymanski M, Lovette I. High lineage diversity and host sharing of malarial parasites in a local avian assemblage. J Parasitol. 2005;91:768-74 pubmed
    ..These results indicate that some Haemoproteus spp. and Plasmodium spp. lineages exhibit a low degree of host specificity, a phenomenon with implications for ecological and evolutionary interactions among these parasites and their hosts...
  7. Fung J, Morris R, Adrian L, Zinder S. Expression of reductive dehalogenase genes in Dehalococcoides ethenogenes strain 195 growing on tetrachloroethene, trichloroethene, or 2,3-dichlorophenol. Appl Environ Microbiol. 2007;73:4439-45 pubmed
    ..Chlorophenols naturally occur in soils and are good candidates for the original substrates for PceA...
  8. Swingle B, Thete D, Moll M, Myers C, Schneider D, Cartinhour S. Characterization of the PvdS-regulated promoter motif in Pseudomonas syringae pv. tomato DC3000 reveals regulon members and insights regarding PvdS function in other pseudomonads. Mol Microbiol. 2008;68:871-89 pubmed publisher
    ..We conclude that the role of PvdS as a regulator of pyoverdine synthesis is conserved among the fluorescent pseudomonads, but the promoters recognized by PvdS orthologues may differ subtly from species to species...
  9. Cong B, Barrero L, Tanksley S. Regulatory change in YABBY-like transcription factor led to evolution of extreme fruit size during tomato domestication. Nat Genet. 2008;40:800-4 pubmed publisher
    ..Here, we show that the second major step in the evolution of extreme fruit size was the result of a regulatory change of a YABBY-like transcription factor (fasciated) that controls carpel number during flower and/or fruit development...
  10. Eiamphungporn W, Helmann J. Extracytoplasmic function sigma factors regulate expression of the Bacillus subtilis yabE gene via a cis-acting antisense RNA. J Bacteriol. 2009;191:1101-5 pubmed publisher
    ..Here, we demonstrate that yabE is negatively regulated by a cis-acting antisense RNA which, in turn, is regulated by two extracytoplasmic function sigma factors: sigma(X) and sigma(M). ..
  11. Maroja L, Andrés J, Harrison R. Genealogical discordance and patterns of introgression and selection across a cricket hybrid zone. Evolution. 2009;63:2999-3015 pubmed publisher
    ..These are candidate barrier genes with possible reproductive functions. We also use genealogical data to examine the demographic history of the field crickets and the current structure of the hybrid zone...
  12. Havananda T, Brummer E, Doyle J. Complex patterns of autopolyploid evolution in alfalfa and allies (Medicago sativa; Leguminosae). Am J Bot. 2011;98:1633-46 pubmed publisher
  13. Gandhi R, Varak E, Goldberg M. Molecular analysis of a cytochrome P450 gene of family 4 on the Drosophila X chromosome. DNA Cell Biol. 1992;11:397-404 pubmed
    ..This transduced fragment does not rescue any of the lethal mutations that have been identified in this genetically well-characterized region of the Drosophila genome. ..
  14. Ray K, Acland G, Aguirre G. Nonallelism of erd and prcd and exclusion of the canine RDS/peripherin gene as a candidate for both retinal degeneration loci. Invest Ophthalmol Vis Sci. 1996;37:783-94 pubmed
    ..Sequence information of CFRDSP will enable testing this locus as a candidate in other canine hereditary retinal degenerations. ..
  15. Watts J, Morton D, Bestman J, Kemphues K. The C. elegans par-4 gene encodes a putative serine-threonine kinase required for establishing embryonic asymmetry. Development. 2000;127:1467-75 pubmed
    ..We find no asymmetry in the distribution of PAR-4 protein in C. elegans embryos. The distribution of PAR-4 protein in early embryos is unaffected by mutations in the other par genes. ..
  16. Fuangthong M, Atichartpongkul S, Mongkolsuk S, Helmann J. OhrR is a repressor of ohrA, a key organic hydroperoxide resistance determinant in Bacillus subtilis. J Bacteriol. 2001;183:4134-41 pubmed
    ..Thus, B. subtilis contains at least three regulons (sigma(B), PerR, and OhrR) that contribute to peroxide stress responses. ..
  17. Savage A, Zamudio K. MHC genotypes associate with resistance to a frog-killing fungus. Proc Natl Acad Sci U S A. 2011;108:16705-10 pubmed publisher
    ..Our findings demonstrate that immunogenetic variation affects chytridiomycosis survival under controlled experimental conditions, confirming that host genetic polymorphisms contribute to chytridiomycosis resistance. ..
  18. Williams B, Riedy M, Williams E, Gatti M, Goldberg M. The Drosophila kinesin-like protein KLP3A is a midbody component required for central spindle assembly and initiation of cytokinesis. J Cell Biol. 1995;129:709-23 pubmed
    ..Furthermore, these results imply that the central spindle is the source of signals that initiate the cleavage furrow in higher cells. ..
  19. Pohlman R, Genetti H, Winans S. Common ancestry between IncN conjugal transfer genes and macromolecular export systems of plant and animal pathogens. Mol Microbiol. 1994;14:655-68 pubmed
  20. Wang Q, Calvo J. Lrp, a global regulatory protein of Escherichia coli, binds co-operatively to multiple sites and activates transcription of ilvIH. J Mol Biol. 1993;229:306-18 pubmed
    ..We propose a model in which multiple binding sites contribute to the formation of a nucleoprotein complex, but only a particular proximal site positions Lrp properly so that it interacts with RNA polymerase. ..
  21. de la R a Dom nech R, Wiedmann M, Mohammed H, Cummings J, Divers T, Batt C. Equine motor neuron disease is not linked to Cu/Zn superoxide dismutase mutations: sequence analysis of the equine Cu/Zn superoxide dismutase cDNA. Gene. 1996;178:83-8 pubmed
    ..At this time, there is no conclusive evidence for EMND linkage to SOD1 mutations...
  22. Lee G, Thonney M, Richards H. Partial clone and sequence of an ovine glyceraldehyde-3-phosphate dehydrogenase cDNA. J Anim Sci. 1998;76:917 pubmed
  23. Chen S, Iannolo M, Calvo J. Cooperative binding of the leucine-responsive regulatory protein (Lrp) to DNA. J Mol Biol. 2005;345:251-64 pubmed
  24. Lee H, Simon J, Lis J. Structure and expression of ubiquitin genes of Drosophila melanogaster. Mol Cell Biol. 1988;8:4727-35 pubmed
    ..The Drosophila UB3-D gene hybridized to a 0.9-kilobase mRNA that was constitutively expressed, and in contrast to the polyubiquitin gene, it was not inducible by heat shock. ..
  25. Parrish C, Aquadro C, Carmichael L. Canine host range and a specific epitope map along with variant sequences in the capsid protein gene of canine parvovirus and related feline, mink, and raccoon parvoviruses. Virology. 1988;166:293-307 pubmed
    ..A second region between 64 and 73 m.u., which may affect the viability of certain recombinant viruses, contained four nucleotide differences, one of which was a coding change. ..
  26. Boisclair Y, Seto D, Hsieh S, Hurst K, Ooi G. Organization and chromosomal localization of the gene encoding the mouse acid labile subunit of the insulin-like growth factor binding complex. Proc Natl Acad Sci U S A. 1996;93:10028-33 pubmed
    ..Finally, the ALS gene was mapped to mouse chromosome 17 by fluorescence in situ hybridization. ..
  27. Marr M, Roberts J. Function of transcription cleavage factors GreA and GreB at a regulatory pause site. Mol Cell. 2000;6:1275-85 pubmed
    ..Furthermore, GreA and GreB are required to mediate efficient function of the lambda gene Q antiterminator at this site. Thus, cleavage factors are necessary for the natural progression of RNA polymerase in vivo. ..
  28. Cao M, Helmann J. Regulation of the Bacillus subtilis bcrC bacitracin resistance gene by two extracytoplasmic function sigma factors. J Bacteriol. 2002;184:6123-9 pubmed
    ..A sigX sigM double mutant was similar to a bcrC mutant in sensitivity. These results support the suggestion that one function of B. subtilis ECF sigma factors is to coordinate antibiotic stress responses. ..
  29. Barr S, Pannabecker T, Gilmour R, Chandler J. Upregulation of cardiac cell plasma membrane calcium pump in a canine model of Chagas disease. J Parasitol. 2003;89:381-4 pubmed
  30. Xiao Y, Luo M, Hayes R, Kim J, Ng S, Ding F, et al. Structure Basis for Directional R-loop Formation and Substrate Handover Mechanisms in Type I CRISPR-Cas System. Cell. 2017;170:48-60.e11 pubmed publisher
    ..The combination of both negative and positive checkpoints ensures stringent yet efficient target degradation in type I CRISPR-Cas systems. ..
  31. Normark B, McCune A, Harrison R. Phylogenetic relationships of neopterygian fishes, inferred from mitochondrial DNA sequences. Mol Biol Evol. 1991;8:819-34 pubmed publisher
    ..Where molecules and morphology disagree, provisional morphology-based constraints on the analysis of molecular data offer a practical means of integrating the two types of data...
  32. Holzer K, Liu W, Hammes G. Molecular cloning and sequencing of chicken liver fatty acid synthase cDNA. Proc Natl Acad Sci U S A. 1989;86:4387-91 pubmed
    ..The molecular weight of the complete polypeptide chain is 267,288. A linear functional map of the chicken fatty acid synthase derived from its primary sequence is presented. ..
  33. Yuan Z, Liu W, Hammes G. Molecular cloning and sequencing of DNA complementary to chicken liver fatty acid synthase mRNA. Proc Natl Acad Sci U S A. 1988;85:6328-31 pubmed
    ..The partial amino acid sequence of the chicken liver fatty acid synthase shows greater than 70% similarity with the rat mammary gland enzyme. ..
  34. Kaelber J, Demogines A, Harbison C, Allison A, Goodman L, Ortega A, et al. Evolutionary reconstructions of the transferrin receptor of Caniforms supports canine parvovirus being a re-emerged and not a novel pathogen in dogs. PLoS Pathog. 2012;8:e1002666 pubmed publisher
    ..This alters our understanding of this well-known example of viral emergence by indicating that canine parvovirus emergence likely resulted from the re-adaptation of a parvovirus to the resistant receptor of a former host. ..
  35. Condon B, Leng Y, Wu D, Bushley K, Ohm R, Otillar R, et al. Comparative genome structure, secondary metabolite, and effector coding capacity across Cochliobolus pathogens. PLoS Genet. 2013;9:e1003233 pubmed publisher
    ..Functional analysis of several strain-unique PKSs and NRPSs reveal a strong correlation with a role in virulence. ..
  36. Sleat D, Palukaitis P. Site-directed mutagenesis of a plant viral satellite RNA changes its phenotype from ameliorative to necrogenic. Proc Natl Acad Sci U S A. 1990;87:2946-50 pubmed
    ..This necrosis was similar to that induced by a naturally necrogenic satellite RNA. The various mutations did not modify the effect of WL1-sat RNA on the symptoms induced by CMV on tobacco or squash. ..
  37. Fredrick K, Helmann J. Dual chemotaxis signaling pathways in Bacillus subtilis: a sigma D-dependent gene encodes a novel protein with both CheW and CheY homologous domains. J Bacteriol. 1994;176:2727-35 pubmed
    ..W. Hanlon, L. Márques-Magaña, P. B. Carpenter, M. J. Chamberlin, and G. W. Ordal, J. Biol. Chem. 267:12055-12060, 1992). ..
  38. Reijo R, Cho D, Huffaker T. Deletion of a single-copy tRNA affects microtubule function in Saccharomyces cerevisiae. Genetics. 1993;135:955-62 pubmed
    ..It also does not suppress by interfering with the protein arginylation that targets certain proteins for degradation. These results leave open the prospect that this tRNA(Arg)AGG plays a novel role in the cell. ..
  39. van Der Hoeven R, Monforte A, Breeden D, Tanksley S, Steffens J. Genetic control and evolution of sesquiterpene biosynthesis in Lycopersicon esculentum and L. hirsutum. Plant Cell. 2000;12:2283-94 pubmed
  40. Priestnall S, Wiinberg B, Spohr A, Neuhaus B, Kuffer M, Wiedmann M, et al. Evaluation of "Helicobacter heilmannii" subtypes in the gastric mucosas of cats and dogs. J Clin Microbiol. 2004;42:2144-51 pubmed
    ..heilmannii" bacteria that are distinct from type 1 and from "H. suis." As "H. heilmannii" type 1 predominates in people, the zoonotic risk posed by dogs and cats is likely small...
  41. Moll S, Schneider D, Stodghill P, Myers C, Cartinhour S, Filiatrault M. Construction of an rsmX co-variance model and identification of five rsmX non-coding RNAs in Pseudomonas syringae pv. tomato DC3000. RNA Biol. 2010;7:508-16 pubmed
    ..We also found that these rsmX ncRNA genes share a conserved upstream region suggesting that their expression is dependent upon the global response regulator, GacA. ..
  42. Newman S, Tantasawat P, Steffens J. Tomato polyphenol oxidase B is spatially and temporally regulated during development and in response to ethylene. Molecules. 2011;16:493-517 pubmed publisher
    ..It was shown that PPO B expression was tissue specific, developmentally regulated, ethylene induced, and localized predominantly to mitotic or apoptotic tissues. ..
  43. Burge C, Douglas N, Conti Jerpe I, Weil E, Roberts S, Friedman C, et al. Friend or foe: the association of Labyrinthulomycetes with the Caribbean sea fan Gorgonia ventalina. Dis Aquat Organ. 2012;101:1-12 pubmed publisher
    ..Further studies are needed to understand the pathogenesis of this microorganism in sea fans and its relationship with MFPS. ..
  44. Dean D, Maroja L, Cottrill S, Bomkamp B, Westervelt K, Deitcher D. The wavy Mutation Maps to the Inositol 1,4,5-Trisphosphate 3-Kinase 2 (IP3K2) Gene of Drosophila and Interacts with IP3R to Affect Wing Development. G3 (Bethesda). 2015;6:299-310 pubmed publisher
    ..In proof of concept, a dominant modifier screen revealed that mutations in IP3R strongly suppress the wy phenotype, suggesting that the wy phenotype results from reduced IP4 levels, and/or excessive IP3R signaling. ..
  45. McMullin T, Fox T. COX3 mRNA-specific translational activator proteins are associated with the inner mitochondrial membrane in Saccharomyces cerevisiae. J Biol Chem. 1993;268:11737-41 pubmed
    ..Amino-terminal sequencing of proteins isolated from mitochondria revealed that PET54 is not processed during import to mitochondria while the PET122 precursor is cleaved between the 8th and 9th residues...
  46. Hamblin M, Aquadro C. Contrasting patterns of nucleotide sequence variation at the glucose dehydrogenase (Gld) locus in different populations of Drosophila melanogaster. Genetics. 1997;145:1053-62 pubmed
    ..The difference in patterns of variation across these population samples suggests that selection on Gld (or the Gld region) has been different in the Chinese population than in the other three. ..
  47. Sheehan M, Farmer P, Brutnell T. Structure and expression of maize phytochrome family homeologs. Genetics. 2004;167:1395-405 pubmed
    ..These results are discussed in relation to phytochrome gene regulation in model eudicots and monocots and in light of current genome sequencing efforts in maize. ..
  48. Zeiss C, Trepanier L, Aguirre G, Ray K. A highly conserved microsatellite in the dystrophin gene of diverse mammalian species. Anim Genet. 1998;29:224-7 pubmed
  49. Wagner B, Miller D, Lear T, Antczak D. The complete map of the Ig heavy chain constant gene region reveals evidence for seven IgG isotypes and for IgD in the horse. J Immunol. 2004;173:3230-42 pubmed
    ..Fluorescence in situ hybridization was used to localize the IGHC region to Equus caballus (ECA) 24qter, the horse chromosome corresponding to human chromosome 14, where the human IGH locus is found. ..
  50. Sooksa nguan T, Yakubov B, Kozlovskyy V, Barkume C, Howe K, Thannhauser T, et al. Drosophila ABC transporter, DmHMT-1, confers tolerance to cadmium. DmHMT-1 and its yeast homolog, SpHMT-1, are not essential for vacuolar phytochelatin sequestration. J Biol Chem. 2009;284:354-62 pubmed publisher
    ..These findings significantly change our current understanding of the function of HMT-1 proteins and invoke a PC-independent role for these transporters in Cd2+ detoxification...
  51. Hah N, Murakami S, Nagari A, Danko C, Kraus W. Enhancer transcripts mark active estrogen receptor binding sites. Genome Res. 2013;23:1210-23 pubmed publisher
    ..Together, our studies shed new light on the activity of ESR1 at its enhancer sites and provide new insights about enhancer function. ..
  52. Sleat D, Palukaitis P. A single nucleotide change within a plant virus satellite RNA alters the host specificity of disease induction. Plant J. 1992;2:43-9 pubmed
    ..Thus, two single nucleotides have been identified which play central roles in those interactions between the virus, its satellite RNA and the host plant, and together result in a specific disease state. ..
  53. Grandoni J, Zahler S, Calvo J. Transcriptional regulation of the ilv-leu operon of Bacillus subtilis. J Bacteriol. 1992;174:3212-9 pubmed
    ..Measurement of mRNA degradation rates showed that the half-life of ilv-leu mRNA was the same when the cells were grown with or without leucine. These data demonstrate that the ilv-leu operon is regulated by transcription attenuation. ..
  54. Bartnikas T, Tosques I, Laratta W, Shi J, Shapleigh J. Characterization of the nitric oxide reductase-encoding region in Rhodobacter sphaeroides 2.4.3. J Bacteriol. 1997;179:3534-40 pubmed
    ..Regulatory studies demonstrated that the first four genes, norCBQD, are expressed only when the oxygen concentration is low and nitrate is present but that the two distal genes, nnrTU, are expressed constitutively...
  55. Giardina C, Lis J. Polymerase processivity and termination on Drosophila heat shock genes. J Biol Chem. 1993;268:23806-11 pubmed
    ..The data obtained are consistent with polymerases terminating at multiple sites downstream of the polyadenylation site. ..
  56. Stover P, Chen L, Suh J, Stover D, Keyomarsi K, Shane B. Molecular cloning, characterization, and regulation of the human mitochondrial serine hydroxymethyltransferase gene. J Biol Chem. 1997;272:1842-8 pubmed
    ..Mitochondrial SHMT mRNA levels in MCF-7 cells did not vary during the cell cycle and were not affected by the absence of glycine, serine, folate, thymidylate, or purines from the media. ..
  57. Spiridonov N, Wilson D. Characterization and cloning of celR, a transcriptional regulator of cellulase genes from Thermomonospora fusca. J Biol Chem. 1999;274:13127-32 pubmed
    ..The results suggest that CelR may act as a repressor, and that the mechanism of induction involves a direct interaction of CelR with cellobiose. ..
  58. Anderson D, Stover P. SHMT1 and SHMT2 are functionally redundant in nuclear de novo thymidylate biosynthesis. PLoS ONE. 2009;4:e5839 pubmed publisher
  59. Liao P, Choi Y, Lee K. FSscan: a mechanism-based program to identify +1 ribosomal frameshift hotspots. Nucleic Acids Res. 2009;37:7302-11 pubmed publisher
    ..coli. The results have implications for bioinformatic identification of novel frameshift proteins, ribosomal frameshifting, coding sequence detection and the application of mass spectrometry on studying frameshift proteins. ..
  60. den Bakker H, Cummings C, Ferreira V, Vatta P, Orsi R, Degoricija L, et al. Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss. BMC Genomics. 2010;11:688 pubmed publisher
    ..This information will allow for the development of genetic and genomic criteria for pathogenic strains, including development of assays that specifically detect pathogenic Listeria strains. ..
  61. Renna M, Najimudin N, Winik L, Zahler S. Regulation of the Bacillus subtilis alsS, alsD, and alsR genes involved in post-exponential-phase production of acetoin. J Bacteriol. 1993;175:3863-75 pubmed
    ..Two mutations that cause increased expression of the alsSD operon have been isolated, cloned, and sequenced. They each change an amino acid in the AlsR protein. ..
  62. Renshaw R, Glaser A, Van Campen H, Weiland F, Dubovi E. Identification and phylogenetic comparison of Salem virus, a novel paramyxovirus of horses. Virology. 2000;270:417-29 pubmed publisher
    ..Sequencing of P gene cDNA clones confirmed the use of a cotranscriptional editing mechanism for the regulation of P/V expression. Based on the location of its origin it has been named Salem virus (SalV)...
  63. Beckley J, Pauli B, Elble R. Re-expression of detachment-inducible chloride channel mCLCA5 suppresses growth of metastatic breast cancer cells. J Biol Chem. 2004;279:41634-41 pubmed
    ..Together, these results establish mCLCA5 as the mouse ortholog of hCLCA2, demonstrate that mCLCA5 is a detachment-sensitive growth inhibitor, and suggest a mechanism whereby these channels may antagonize mammary tumor progression. ..
  64. Stewart V, Parales J, Merkel S. Structure of genes narL and narX of the nar (nitrate reductase) locus in Escherichia coli K-12. J Bacteriol. 1989;171:2229-34 pubmed
    ..We report here the nucleotide sequences of narL and narX. The deduced protein sequences aid in defining distinct subclasses of regulators and sensors in the family of two-component regulatory proteins. ..
  65. Cui Y, Midkiff M, Wang Q, Calvo J. The leucine-responsive regulatory protein (Lrp) from Escherichia coli. Stoichiometry and minimal requirements for binding to DNA. J Biol Chem. 1996;271:6611-7 pubmed
    ..The extent of the contribution to binding is dependent upon whether the single strand is on the left or right of the double-stranded region and whether the polarity of the single-stranded DNA is 5' to 3' or 3' to 5'. ..
  66. Wang J, Yen A. A novel retinoic acid-responsive element regulates retinoic acid-induced BLR1 expression. Mol Cell Biol. 2004;24:2423-43 pubmed
  67. Jiao J, Kim H, Liu R, Hogan C, Sun K, Tam L, et al. Transgenic analysis of the physiological functions of Mahogunin Ring Finger-1 isoforms. Genesis. 2009;47:524-34 pubmed publisher
    ..Our data show that different Mgrn1 isoforms are not functionally equivalent in vivo and that the presence of only isoform I or III is sufficient for normal development, pigmentation, and neuronal integrity. ..
  68. Mohammed J, Flynt A, Siepel A, Lai E. The impact of age, biogenesis, and genomic clustering on Drosophila microRNA evolution. RNA. 2013;19:1295-308 pubmed publisher
    ..These studies highlight the previously unappreciated impact of biogenesis strategy and genomic location on the evolutionary dynamics of miRNAs, and affirm that miRNAs do not evolve as a unitary class...
  69. Vander Horn P, Zahler S. Cloning and nucleotide sequence of the leucyl-tRNA synthetase gene of Bacillus subtilis. J Bacteriol. 1992;174:3928-35 pubmed
    ..subtilis ilv-leu operon. The DNA of the B. subtilis leuS open reading frame is 48% identical to the leuS gene of Escherichia coli and is predicted to encode a polypeptide with 46% identity to the leucyl-tRNA synthetase of E. coli. ..
  70. Dibenedetto A, Harada H, Wolfner M. Structure, cell-specific expression, and mating-induced regulation of a Drosophila melanogaster male accessory gland gene. Dev Biol. 1990;139:134-48 pubmed
    ..The mating-stimulated synthesis of the mst 316-lacZ fusion protein, and by inference of the native gene product, appears to be due at least in part to increased transcript levels. ..
  71. Kim S, Batt C. Cloning and sequencing of the Lactococcus lactis subsp. lactis groESL operon. Gene. 1993;127:121-6 pubmed
    ..lactis subsp. lactis and other Gram+ bacterial promoters. Northern analysis demonstrated that the groESL operon is under tight regulation and a dramatic induction of mRNA synthesis occurs within 15 min after heat shock. ..
  72. Kim S, Shi H, Lee D, Lis J. Specific SR protein-dependent splicing substrates identified through genomic SELEX. Nucleic Acids Res. 2003;31:1955-61 pubmed
    ..These results indicate that B52 has unique functions in the removal of some introns during development, and plays a critical role in cellular regulatory networks. ..
  73. Chen K, Cong B, Wing R, Vrebalov J, Tanksley S. Changes in regulation of a transcription factor lead to autogamy in cultivated tomatoes. Science. 2007;318:643-5 pubmed
    ..1 protein, but rather by a mutation in the Style2.1 promoter that results in a down-regulation of Style2.1 expression during flower development. ..
  74. Miller M, Jarosinski K, Schat K. Negative modulation of the chicken infectious anemia virus promoter by COUP-TF1 and an E box-like element at the transcription start site binding deltaEF1. J Gen Virol. 2008;89:2998-3003 pubmed publisher
    ..Electromobility shift assays showed that the transcription regulator delta-EF1 (deltaEF1) binds to this E box region. These findings indicate that the CAV promoter activity can be affected directly or indirectly by COUP-TF1 and deltaEF1...
  75. Ramsey J, MacDonald S, Jander G, Nakabachi A, Thomas G, Douglas A. Genomic evidence for complementary purine metabolism in the pea aphid, Acyrthosiphon pisum, and its symbiotic bacterium Buchnera aphidicola. Insect Mol Biol. 2010;19 Suppl 2:241-8 pubmed publisher
    ..Further, the coupled purine metabolism of aphid and Buchnera could contribute to the dependence of the pea aphid on this symbiosis...
  76. Williams B, Karr T, Montgomery J, Goldberg M. The Drosophila l(1)zw10 gene product, required for accurate mitotic chromosome segregation, is redistributed at anaphase onset. J Cell Biol. 1992;118:759-73 pubmed
    ..Upon anaphase onset, there is an extremely rapid redistribution of the zw10 protein to a location at or near the kinetochores of the separating chromosomes. ..
  77. McCallum S, Wu W, Cerione R. Identification of a putative effector for Cdc42Hs with high sequence similarity to the RasGAP-related protein IQGAP1 and a Cdc42Hs binding partner with similarity to IQGAP2. J Biol Chem. 1996;271:21732-7 pubmed
    ..These findings identify IQGAP1 and IQGAP2 as a new class of target/effectors that utilize both regions of the switch I domain and an insert region distinct to Rho proteins for binding to Cdc42. ..
  78. Kachroo P, Shanklin J, Shah J, Whittle E, Klessig D. A fatty acid desaturase modulates the activation of defense signaling pathways in plants. Proc Natl Acad Sci U S A. 2001;98:9448-53 pubmed
    ..Because reduced S-ACP DES activity leads to the induction of certain defense responses and the inhibition of others, we propose that a FA-derived signal modulates crosstalk between different defense signaling pathways. ..
  79. Yang J, Lin R, Sullivan J, Hoecker U, Liu B, Xu L, et al. Light regulates COP1-mediated degradation of HFR1, a transcription factor essential for light signaling in Arabidopsis. Plant Cell. 2005;17:804-21 pubmed
    ..Additionally, our results substantiate the E3 ligase activity of COP1 and its critical role in desensitizing light signaling. ..
  80. Roberts J, Shankar S, Filter J. RNA polymerase elongation factors. Annu Rev Microbiol. 2008;62:211-33 pubmed publisher
  81. den Bakker H, Bundrant B, Fortes E, Orsi R, Wiedmann M. A population genetics-based and phylogenetic approach to understanding the evolution of virulence in the genus Listeria. Appl Environ Microbiol. 2010;76:6085-100 pubmed publisher
    ..Overall, our data suggest that, for some pathogens, loss of virulence genes may represent a selective advantage, possibly by facilitating adaptation to a specific ecological niche. ..
  82. Begun D, Aquadro C. Molecular variation at the vermilion locus in geographically diverse populations of Drosophila melanogaster and D. simulans. Genetics. 1995;140:1019-32 pubmed
    ..simulans populations, the vermilion data raise the possibility that both mtDNA and allozymes have been influenced by selection...
  83. Chien Y, Zinder S. Cloning, functional organization, transcript studies, and phylogenetic analysis of the complete nitrogenase structural genes (nifHDK2) and associated genes in the archaeon Methanosarcina barkeri 227. J Bacteriol. 1996;178:143-8 pubmed
    ..These results support a model in which the nitrogenase structural genes in M. barkeri are cotranscribed in a single NH4(+)-repressed operon...
  84. Kelleher N, Taylor S, Grannis D, Kinsland C, Chiu H, Begley T, et al. Efficient sequence analysis of the six gene products (7-74 kDa) from the Escherichia coli thiamin biosynthetic operon by tandem high-resolution mass spectrometry. Protein Sci. 1998;7:1796-801 pubmed
    ..74 (ThiS) and 26,896.5 Da (ThiG); MS/MS uncovered three reading frame errors and a stop codon for the first protein. MS/MS ions are consistent with 68 fragments predicted by the corrected ThiS/ThiG DNA sequences. ..
  85. Komine Y, Kikis E, Schuster G, Stern D. Evidence for in vivo modulation of chloroplast RNA stability by 3'-UTR homopolymeric tails in Chlamydomonas reinhardtii. Proc Natl Acad Sci U S A. 2002;99:4085-90 pubmed
    ..This suggests that the poly(A) tail is only recognized as an instability determinant when exposed at the 3' end of a message. ..
  86. Cassidy Hanley D, Bisharyan Y, Fridman V, Gerber J, Lin C, Orias E, et al. Genome-wide characterization of Tetrahymena thermophila chromosome breakage sites. II. Physical and genetic mapping. Genetics. 2005;170:1623-31 pubmed
    ..By providing unique sequence from natural ends of macronuclear chromosomes, Cbs junctions will provide useful sequence tags for relating macro- and micronuclear genetic, physical, and whole-genome sequence maps...
  87. Jarosinski K, Osterrieder N, Nair V, Schat K. Attenuation of Marek's disease virus by deletion of open reading frame RLORF4 but not RLORF5a. J Virol. 2005;79:11647-59 pubmed
    ..i.; however, two chickens had tumors at the termination of the experiment. The data indicate that RLORF4 is involved in attenuation of MDV, although the function of RLORF4 is still unknown...
  88. Hagarman J, O Brien T. An essential gene mutagenesis screen across the highly conserved piebald deletion region of mouse chromosome 14. Genesis. 2009;47:392-403 pubmed publisher
  89. Brahamsha B, Greenberg E. Cloning and sequence analysis of flaA, a gene encoding a Spirochaeta aurantia flagellar filament surface antigen. J Bacteriol. 1989;171:1692-7 pubmed
    ..W. Charon, R. G. Cook, M. D. Fuentes, and R. J. Limberger, J. Bacteriol. 170:4072-4082, 1988). The region of identity in the deduced S. aurantia polypeptide was preceded by a possible signal sequence and signal peptidase cleavage site...
  90. Gunsalus K, Bonaccorsi S, Williams E, Verni F, Gatti M, Goldberg M. Mutations in twinstar, a Drosophila gene encoding a cofilin/ADF homologue, result in defects in centrosome migration and cytokinesis. J Cell Biol. 1995;131:1243-59 pubmed
    ..We discuss these results in terms of possible roles of the actin-based cytoskeleton in centrosome movement and in cytokinesis. ..
  91. Kalogeraki V, Winans S. Wound-released chemical signals may elicit multiple responses from an Agrobacterium tumefaciens strain containing an octopine-type Ti plasmid. J Bacteriol. 1998;180:5660-7 pubmed
    ..Disruptions of virH, virK, virL, or virM did not affect tumorigenesis of Kalanchöe diagramontiana leaves or carrot disks, suggesting that they may play an entirely different role during pathogenesis...
  92. Hashimoto Y, Zhang S, Zhang S, Chen Y, Blissard G. Correction: BTI-Tnao38, a new cell line derived from Trichoplusia ni, is permissive for AcMNPV infection and produces high levels of recombinant proteins. BMC Biotechnol. 2012;12:12 pubmed publisher