Experts and Doctors on molecular sequence data in Kyoto, Japan

Summary

Locale: Kyoto, Japan
Topic: molecular sequence data

Top Publications

  1. Moriguchi T, Kuroyanagi N, Yamaguchi K, Gotoh Y, Irie K, Kano T, et al. A novel kinase cascade mediated by mitogen-activated protein kinase kinase 6 and MKK3. J Biol Chem. 1996;271:13675-9 pubmed
    ..In addition, co-expression of TAK1 and p38/MPK2 in cells resulted in activation of p38/MPK2. These results indicate the existence of a novel kinase cascade consisting of TAK1, MAPKK6/MKK3, and p38/MPK2. ..
  2. Yamasaki M, Miyake A, Tagashira S, Itoh N. Structure and expression of the rat mRNA encoding a novel member of the fibroblast growth factor family. J Biol Chem. 1996;271:15918-21 pubmed
    ..The expression profile of the FGF-related mRNA was different from those of other FGF family mRNAs. As this protein is the 10th documented protein related to FGFs, we tentatively term this protein FGF-10. ..
  3. Okamoto Y, Ninomiya H, Tanioka M, Sakamoto A, Miwa S, Masaki T. Palmitoylation of human endothelinB. Its critical role in G protein coupling and a differential requirement for the cytoplasmic tail by G protein subtypes. J Biol Chem. 1997;272:21589-96 pubmed
    ..These results indicated a differential requirement for the carboxyl terminus downstream to the palmitoylation site in the coupling with G protein subtypes, i.e. it is required for the coupling with Gi but not for that with Gq. ..
  4. Tanoue T, Moriguchi T, Nishida E. Molecular cloning and characterization of a novel dual specificity phosphatase, MKP-5. J Biol Chem. 1999;274:19949-56 pubmed
    ..These results suggest that MKP-5 is a novel type of dual specificity phosphatase specific for p38 and SAPK/JNK. ..
  5. Kataoka H, Murayama T, Yokode M, Mori S, Sano H, Ozaki H, et al. A novel snail-related transcription factor Smuc regulates basic helix-loop-helix transcription factor activities via specific E-box motifs. Nucleic Acids Res. 2000;28:626-33 pubmed
    ..Thus, Smuc might regulate bHLH transcription factors by zinc finger domains competing for E-box binding, and non-zinc finger repressor domains might also confer transcriptional repression to control differentiation processes. ..
  6. Danno S, Itoh K, Matsuda T, Fujita J. Decreased expression of mouse Rbm3, a cold-shock protein, in Sertoli cells of cryptorchid testis. Am J Pathol. 2000;156:1685-92 pubmed
    ..Rbm3 may play important roles distinct from those played by Cirp in spermatogenesis and cryptorchidism by regulating the gene expression in Sertoli cells. ..
  7. Matsuda E, Agata Y, Sugai M, Katakai T, Gonda H, Shimizu A. Targeting of Kr├╝ppel-associated box-containing zinc finger proteins to centromeric heterochromatin. Implication for the gene silencing mechanisms. J Biol Chem. 2001;276:14222-9 pubmed
    ..These data strongly suggest that KRAB-ZFPs/KAP-1 silence transcription by dynamic recruitment of the target locus to the specific gene silencing compartment, centromeric heterochromatin, in a histone deacetylase-dependent manner. ..
  8. Yamashita T, Konishi M, Miyake A, Inui K, Itoh N. Fibroblast growth factor (FGF)-23 inhibits renal phosphate reabsorption by activation of the mitogen-activated protein kinase pathway. J Biol Chem. 2002;277:28265-70 pubmed
    ..Inhibitors of the MAPK pathway, PD98059 and SB203580, also blocked the activity of FGF-23. The present findings have revealed a novel MAPK-dependent mechanism of the regulation of phosphate uptake by FGF signaling. ..
  9. Sato T, Fukui T, Atomi H, Imanaka T. Targeted gene disruption by homologous recombination in the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. J Bacteriol. 2003;185:210-20 pubmed

More Information

Publications342 found, 100 shown here

  1. Akiyama Y, Kanehara K, Ito K. RseP (YaeL), an Escherichia coli RIP protease, cleaves transmembrane sequences. EMBO J. 2004;23:4434-42 pubmed
    ..These results show that RseP has potential ability to cut a broad range of membrane protein sequences. Intriguingly, it is nevertheless recruited to the sigma(E) stress-response cascade as a specific player of RIP. ..
  2. Arimatsu Y, Kotani E, Sugimura Y, Furusawa T. Molecular characterization of a cDNA encoding extracellular dsRNase and its expression in the silkworm, Bombyx mori. Insect Biochem Mol Biol. 2007;37:176-83 pubmed publisher
    ..This was supported by the immunohistochemical observation that the mature proteins were localized in the apical side of midgut cells for extracellular secretion...
  3. Ueta R, Fujiwara N, Iwai K, Yamaguchi Iwai Y. Mechanism underlying the iron-dependent nuclear export of the iron-responsive transcription factor Aft1p in Saccharomyces cerevisiae. Mol Biol Cell. 2007;18:2980-90 pubmed
  4. Hosokawa N, Kamiya Y, Kamiya D, Kato K, Nagata K. Human OS-9, a lectin required for glycoprotein endoplasmic reticulum-associated degradation, recognizes mannose-trimmed N-glycans. J Biol Chem. 2009;284:17061-8 pubmed publisher
    ..Thus, we propose a model for mannose trimming and the requirement for hOS-9 lectin activity in glycoprotein ERAD in which N-glycans lacking the terminal mannose from the C branch are recognized by hOS-9 and targeted for degradation. ..
  5. Oishi S, Kodera Y, Nishikawa H, Kamitani H, Watabe T, Ohno H, et al. Design and synthesis of membrane fusion inhibitors against the feline immunodeficiency virus. Bioorg Med Chem. 2009;17:4916-20 pubmed publisher
    ..Comparative analysis of HR2 peptides derived from four FIV strains demonstrated that the interactive surface of the Shizuoka strain-derived HR2 peptides provides the highest affinity of all the FIV strains examined. ..
  6. Sakurai Y, Komatsu K, Agematsu K, Matsuoka M. DNA double strand break repair enzymes function at multiple steps in retroviral infection. Retrovirology. 2009;6:114 pubmed publisher
    ..These results suggest that DSB repair enzymes are involved in multiple steps including integration and pre-integration steps during retroviral replication. ..
  7. Mashimo T, Ohmori I, Ouchida M, Ohno Y, Tsurumi T, Miki T, et al. A missense mutation of the gene encoding voltage-dependent sodium channel (Nav1.1) confers susceptibility to febrile seizures in rats. J Neurosci. 2010;30:5744-53 pubmed publisher
    ..These findings suggest that a missense mutation (N1417H) of the Na(v)1.1 channel confers susceptibility to FS and the impaired biophysical properties of inhibitory GABAergic neurons underlie one of the mechanisms of FS. ..
  8. Iguchi H, Yurimoto H, Sakai Y. Methylovulum miyakonense gen. nov., sp. nov., a type I methanotroph isolated from forest soil. Int J Syst Evol Microbiol. 2011;61:810-5 pubmed publisher
    ..nov., sp. nov. is proposed. The type strain of the type species is HT12(T) (?=?NBRC 106162(T) ?=?DSM 23269(T) ?=?ATCC BAA-2070(T))...
  9. Tsuruyama T, Hiratsuka T, Jin G, Imai Y, Takeuchi H, Maruyama Y, et al. Murine leukemia retrovirus integration induces the formation of transcription factor complexes on palindromic sequences in the signal transducer and activator of transcription factor 5a gene during the development of pre-B lymphomagenesis. Am J Pathol. 2011;178:1374-86 pubmed publisher
  10. Muraki K, Nabetani A, Nishiyama A, Ishikawa F. Essential roles of Xenopus TRF2 in telomere end protection and replication. Genes Cells. 2011;16:728-39 pubmed publisher
    ..We propose that xTRF2 is required for both efficient replication of bulk DNA and protection from the activation of the DNA damage checkpoints pathway, and that those two functions are mechanistically separable. ..
  11. Nakayama Y, Nakamura N, Oki S, Wakabayashi M, Ishihama Y, Miyake A, et al. A putative polypeptide N-acetylgalactosaminyltransferase/Williams-Beuren syndrome chromosome region 17 (WBSCR17) regulates lamellipodium formation and macropinocytosis. J Biol Chem. 2012;287:32222-35 pubmed publisher
  12. Tsushima J, Nishimura K, Tashiro N, Takata K, Ashihara E, Yoshimoto K, et al. Protective effect of planarian DJ-1 against 6-hydroxydopamine-induced neurotoxicity. Neurosci Res. 2012;74:277-83 pubmed publisher
    ..These results suggest that planarians have a DJ-1 ortholog, which has conserved antioxidant and neuroprotective functions. ..
  13. Nagamatsu Y, Takeda K, Kuranaga T, Numoto N, Miki K. Origin of asymmetry at the intersubunit interfaces of V1-ATPase from Thermus thermophilus. J Mol Biol. 2013;425:2699-708 pubmed publisher
    ..Therefore, our result plausibly implies that the essential motion for the torque generation is not the large interdomain movement of the catalytic subunits but the rigid-body rearrangement of subunits. ..
  14. Kishino S, Takeuchi M, Park S, Hirata A, Kitamura N, Kunisawa J, et al. Polyunsaturated fatty acid saturation by gut lactic acid bacteria affecting host lipid composition. Proc Natl Acad Sci U S A. 2013;110:17808-13 pubmed publisher
    ..These findings suggested that lipid metabolism by gastrointestinal microbes affects the health of the host by modifying fatty acid composition. ..
  15. Obara Ishihara T, Okayama H. A B-type cyclin negatively regulates conjugation via interacting with cell cycle 'start' genes in fission yeast. EMBO J. 1994;13:1863-72 pubmed
    ..Thus, in S.pombe, a B-type cyclin, regulated by the newly identified cell cycle 'start' genes, plays a crucial role in the control of sexual development. ..
  16. Reid T, Furuyashiki T, Ishizaki T, Watanabe G, Watanabe N, Fujisawa K, et al. Rhotekin, a new putative target for Rho bearing homology to a serine/threonine kinase, PKN, and rhophilin in the rho-binding domain. J Biol Chem. 1996;271:13556-60 pubmed
    ..To our knowledge, this is the first conserved sequence for Rho effectors, and we have termed this region Rho effector motif class 1. ..
  17. Yabe D, Nakamura T, Kanazawa N, Tashiro K, Honjo T. Calumenin, a Ca2+-binding protein retained in the endoplasmic reticulum with a novel carboxyl-terminal sequence, HDEF. J Biol Chem. 1997;272:18232-9 pubmed
    ..Calumenin is expressed most strongly in heart of adult and 18.5-day embryos. The calumenin gene (Calu) was mapped at the proximal portion of mouse chromosome 7. ..
  18. Akiyama Y, Kihara A, Mori H, Ogura T, Ito K. Roles of the periplasmic domain of Escherichia coli FtsH (HflB) in protein interactions and activity modulation. J Biol Chem. 1998;273:22326-33 pubmed
    ..These results suggest that the periplasmic region of FtsH has crucial roles in the protein-protein interactions of this complex and in the modulation of its proteolytic functions against different substrates. ..
  19. Hoshiyama D, Suga H, Iwabe N, Koyanagi M, Nikoh N, Kuma K, et al. Sponge Pax cDNA related to Pax-2/5/8 and ancient gene duplications in the Pax family. J Mol Evol. 1998;47:640-8 pubmed
    ..Furthermore, the evolutionary rates of the Pax proteins have been shown to decrease with increasing organismal complexity during animal evolution...
  20. Yamane H, Ikeda K, Ushijima K, Sassa H, Tao R. A pollen-expressed gene for a novel protein with an F-box motif that is very tightly linked to a gene for S-RNase in two species of cherry, Prunus cerasus and P. avium. Plant Cell Physiol. 2003;44:764-9 pubmed
    ..We discuss the possibility of the gene for the F-box protein being a candidate for the male determinant of gametophytic self-incompatibility in PRUNUS:..
  21. Irbis C, Ushida K. Detection of methanogens and proteobacteria from a single cell of rumen ciliate protozoa. J Gen Appl Microbiol. 2004;50:203-12 pubmed
    ..multivesiculatum. Some sequences showed similarities to the previously known endosymbiotic proteobacteria. However, there were no proteobacteria that were carried by all the ciliate cells tested. ..
  22. Makino A, Kurosaki K, Ohmae M, Kobayashi S. Chitinase-catalyzed synthesis of alternatingly N-deacetylated chitin: a chitin-chitosan hybrid polysaccharide. Biomacromolecules. 2006;7:950-7 pubmed
    ..Molecular weights of 2 reached 2,020 with using chitinase from Serratia marcescens, which corresponds to 10-12 saccharide units. ..
  23. Tanaka N, Tani Y, Tada T, Lee Y, Kanaori K, Kunugi S. The roles of conserved amino acids on substrate binding and conformational integrity of ClpB N-terminal domain. Biochemistry. 2006;45:8556-61 pubmed
    ..1 degrees C lower than that of wild-type. Our results revealed that conserved amino acids Thr7 and Ser84 both participated in maintaining the conformational integrity of the ClpB N-terminal domain. ..
  24. Gyoja F, Satou Y, Shin I T, Kohara Y, Swalla B, Satoh N. Analysis of large scale expression sequenced tags (ESTs) from the anural ascidian, Molgula tectiformis. Dev Biol. 2007;307:460-82 pubmed
    ..We discuss these remarkable results that allow insight into the molecular mechanism(s) responsible for the anural mode of ascidian development. ..
  25. Hiraga K, Ueno Y, Oda K. Glutamate decarboxylase from Lactobacillus brevis: activation by ammonium sulfate. Biosci Biotechnol Biochem. 2008;72:1299-306 pubmed
    ..Thus the biochemical properties of the GAD from L. brevis IFO12005 were significantly different from those from other sources...
  26. Miyoshi T, Kanoh J, Saito M, Ishikawa F. Fission yeast Pot1-Tpp1 protects telomeres and regulates telomere length. Science. 2008;320:1341-4 pubmed publisher
    ..Such molecular architectures are similar to those of mammalian shelterin, indicating that the overall DNA-protein architecture is conserved across evolution. ..
  27. Ikeda H, Senni K, Fujii N, Setoguchi H. Consistent geographic structure among multiple nuclear sequences and cpDNA polymorphisms of Cardamine nipponica Franch. et Savat. (Brassicaceae). Mol Ecol. 2008;17:3178-88 pubmed publisher
    ..Hence, the consistent history among loci and a more detailed history from several loci indicated that cpDNA can represent the history of vicariance and demonstrated the efficiency of single-copy nuclear genes in phylogeography...
  28. Arizono N, Shedko M, Yamada M, Uchikawa R, Tegoshi T, Takeda K, et al. Mitochondrial DNA divergence in populations of the tapeworm Diphyllobothrium nihonkaiense and its phylogenetic relationship with Diphyllobothrium klebanovskii. Parasitol Int. 2009;58:22-8 pubmed publisher
    ..These results suggest that the two morphologically cryptic lineages have diverged and coexisted over a long period of time...
  29. Tanaka S, Ishihama N, Yoshioka H, Huser A, O Connell R, Tsuji G, et al. The Colletotrichum orbiculare SSD1 mutant enhances Nicotiana benthamiana basal resistance by activating a mitogen-activated protein kinase pathway. Plant Cell. 2009;21:2517-26 pubmed publisher
    ..Therefore, activation of a specific MAP kinase pathway by fungal cell surface components determines the effective level of basal plant resistance. ..
  30. Tsuzuki S, Miyake Y, Inouye K, Fushiki T. The occurrence of matriptase C-terminal fragments on the apical and basolateral sides of Madin-Darby canine kidney epithelial cells. Biosci Biotechnol Biochem. 2009;73:2538-40 pubmed
    ..This suggests that matriptase interacts with various potential substrates when expressed in simple epithelia. ..
  31. Yoshikawa R, Sato E, Igarashi T, Miyazawa T. Characterization of RD-114 virus isolated from a commercial canine vaccine manufactured using CRFK cells. J Clin Microbiol. 2010;48:3366-9 pubmed publisher
    ..Here, we determined the entire nucleotide sequences of RD-114-related viruses isolated from CRFK cells and a vaccine manufactured using CRFK cells. These RD-114-related viruses were nearly identical to the authentic RD-114 virus. ..
  32. Sato Y, Shibata H, Nakatsu T, Nakano H, Kashiwayama Y, Imanaka T, et al. Structural basis for docking of peroxisomal membrane protein carrier Pex19p onto its receptor Pex3p. EMBO J. 2010;29:4083-93 pubmed publisher
    ..The Pex19p peptide contains a characteristic motif, consisting of the leucine triad (Leu18, Leu21, Leu22), and Phe29, which are critical for the Pex3p binding and peroxisome biogenesis. ..
  33. Liu W, Morito D, Takashima S, Mineharu Y, Kobayashi H, Hitomi T, et al. Identification of RNF213 as a susceptibility gene for moyamoya disease and its possible role in vascular development. PLoS ONE. 2011;6:e22542 pubmed publisher
    ..We provide evidence suggesting, for the first time, the involvement of RNF213 in genetic susceptibility to moyamoya disease. ..
  34. Noda T. The maternal genes Ci-p53/p73-a and Ci-p53/p73-b regulate zygotic ZicL expression and notochord differentiation in Ciona intestinalis embryos. Dev Biol. 2011;360:216-29 pubmed publisher
    ..These results suggest that p53 genes are maternal factors that play a crucial role in A-line notochord differentiation in C. intestinalis embryos by regulating Ci-ZicL expression. ..
  35. Sakaguchi S, Qiu Y, Liu Y, Qi X, Kim S, Han J, et al. Climate oscillation during the Quaternary associated with landscape heterogeneity promoted allopatric lineage divergence of a temperate tree Kalopanax septemlobus (Araliaceae) in East Asia. Mol Ecol. 2012;21:3823-38 pubmed publisher
    ..Overall, this study provides evidence that differential impacts of Quaternary climate oscillation associated with landscape heterogeneity have shaped the genetic structure of a wide-ranging temperate tree in East Asia. ..
  36. Mazaki Y, Hashimoto S, Sabe H. Monocyte cells and cancer cells express novel paxillin isoforms with different binding properties to focal adhesion proteins. J Biol Chem. 1997;272:7437-44 pubmed
    ..Therefore, each isoform of paxillin exhibits distinct expression and different biochemical as well as physiological properties and thereby appears to act as a distinct module involved in different functions of integrins. ..
  37. Oyama T, Shimura Y, Okada K. The Arabidopsis HY5 gene encodes a bZIP protein that regulates stimulus-induced development of root and hypocotyl. Genes Dev. 1997;11:2983-95 pubmed
    ..Nuclear localization of the HY5 protein strongly suggests that the HY5 gene modulates the signal transduction pathways under the HY5-related development by controlling expression of genes downstream of these pathways. ..
  38. Moriguchi T, Toyoshima F, Masuyama N, Hanafusa H, Gotoh Y, Nishida E. A novel SAPK/JNK kinase, MKK7, stimulated by TNFalpha and cellular stresses. EMBO J. 1997;16:7045-53 pubmed
    ..Thus, MKK7 is an evolutionarily conserved MAPKK isoform which is specific for SAPK/JNK, is involved in AP-1-dependent transcription and may be a crucial mediator of TNFalpha signalling. ..
  39. Yamamoto S, Mikami T, Ohbayashi N, Ohta M, Itoh N. Structure and expression of a novel isoform of mouse FGF homologous factor (FHF)-4. Biochim Biophys Acta. 1998;1398:38-41 pubmed
  40. Morita M, Tanaka Y, Kodama T, Kyogoku Y, Yanagi H, Yura T. Translational induction of heat shock transcription factor sigma32: evidence for a built-in RNA thermosensor. Genes Dev. 1999;13:655-65 pubmed
  41. Hagiwara K, Matsumoto T. Nucleotide sequences of genome segments 6 and 7 of Bombyx mori cypovirus 1, encoding the viral structural proteins V4 and V5, respectively. J Gen Virol. 2000;81:1143-7 pubmed
    ..34 to 40 kDa (V5). These observations indicate that p50 might be cleaved to V5 during the formation of virus particles. ..
  42. Fujihashi M, Zhang Y, Higuchi Y, Li X, Koyama T, Miki K. Crystal structure of cis-prenyl chain elongating enzyme, undecaprenyl diphosphate synthase. Proc Natl Acad Sci U S A. 2001;98:4337-42 pubmed
    ..The catalytic site is determined on the basis of these structural features, from which a possible reaction mechanism is proposed...
  43. Terakita A, Yamashita T, Nimbari N, Kojima D, Shichida Y. Functional interaction between bovine rhodopsin and G protein transducin. J Biol Chem. 2002;277:40-6 pubmed
    ..These results suggest that the binding of loop 3 of bovine rhodopsin to region A in Galpha(t) is one of the mechanisms of specific G(t) activation by bovine rhodopsin. ..
  44. Yamanaka H, Moriguchi T, Masuyama N, Kusakabe M, Hanafusa H, Takada R, et al. JNK functions in the non-canonical Wnt pathway to regulate convergent extension movements in vertebrates. EMBO Rep. 2002;3:69-75 pubmed
    ..Our results thus demonstrate that the non-canonical Wnt/JNK pathway is conserved in both vertebrate and invertebrate and define that JNK has an activity to regulate morphogenetic cell movements. ..
  45. Nagaoka H, Muramatsu M, Yamamura N, Kinoshita K, Honjo T. Activation-induced deaminase (AID)-directed hypermutation in the immunoglobulin Smu region: implication of AID involvement in a common step of class switch recombination and somatic hypermutation. J Exp Med. 2002;195:529-34 pubmed
    ..These findings strongly suggest that AID itself or a single molecule generated by RNA editing function of AID may mediate a common step of SHM and CSR, which is likely to be involved in DNA cleavage. ..
  46. Nakagawa T, Izumi T, Banba M, Umehara Y, Kouchi H, Izui K, et al. Characterization and expression analysis of genes encoding phosphoenolpyruvate carboxylase and phosphoenolpyruvate carboxylase kinase of Lotus japonicus, a model legume. Mol Plant Microbe Interact. 2003;16:281-8 pubmed publisher
  47. Kanazawa N, Tashiro K, Inaba K, Miyachi Y. Dendritic cell immunoactivating receptor, a novel C-type lectin immunoreceptor, acts as an activating receptor through association with Fc receptor gamma chain. J Biol Chem. 2003;278:32645-52 pubmed
    ..The identification of this activating immunoreceptor provides an example of signaling via a dendritic cell-expressed C-type lectin receptor. ..
  48. Kusakabe M, Nishida E. The polarity-inducing kinase Par-1 controls Xenopus gastrulation in cooperation with 14-3-3 and aPKC. EMBO J. 2004;23:4190-201 pubmed
    ..Thus, our results identify a requirement of Par proteins for Xenopus gastrulation and reveal a novel interrelationship within Par proteins that may provide a general mechanism for spatial control of Par-1. ..
  49. Koyanagi M, Kubokawa K, Tsukamoto H, Shichida Y, Terakita A. Cephalochordate melanopsin: evolutionary linkage between invertebrate visual cells and vertebrate photosensitive retinal ganglion cells. Curr Biol. 2005;15:1065-9 pubmed
    ..The cephalochordate rhabdomeric photoreceptor represents an evolutionary link between the invertebrate visual photoreceptor and the vertebrate circadian photoreceptor. ..
  50. Nishitani Y, Maruyama D, Nonaka T, Kita A, Fukami T, Mio T, et al. Crystal structures of N-acetylglucosamine-phosphate mutase, a member of the alpha-D-phosphohexomutase superfamily, and its substrate and product complexes. J Biol Chem. 2006;281:19740-7 pubmed
    ..By comparing the substrate and product complexes, it is suggested that the substrate rotates about 180 degrees on the axis linking C-4 and the midpoint of the C-5-O-5 bond in the reaction. ..
  51. Begum N, Izumi N, Nishikori M, Nagaoka H, Shinkura R, Honjo T. Requirement of non-canonical activity of uracil DNA glycosylase for class switch recombination. J Biol Chem. 2007;282:731-42 pubmed
    ..These results suggest that UNG is recruited to the CSR machinery through its WXXF motif by a Vpr-like host factor and plays a novel non-canonical role in a CSR step that follows DNA cleavage. ..
  52. Sugihara Mizuno Y, Adachi M, Kobayashi Y, Hamazaki Y, Nishimura M, Imai T, et al. Molecular characterization of angiomotin/JEAP family proteins: interaction with MUPP1/Patj and their endogenous properties. Genes Cells. 2007;12:473-86 pubmed
  53. Gotoh O. Direct mapping and alignment of protein sequences onto genomic sequence. Bioinformatics. 2008;24:2438-44 pubmed publisher
    ..Spaln is accessible online for a few species at http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user. The source code is available for free for academic users from the same site. ..
  54. Matsumura S, Ohmori R, Saito H, Ikawa Y, Inoue T. Coordinated control of a designed trans-acting ligase ribozyme by a loop-receptor interaction. FEBS Lett. 2009;583:2819-26 pubmed publisher
    ..Taken together, the results indicate that a loop-receptor interaction plays a significant role in determining the activity of the trans-acting ribozyme and in its ability to perform multiple turnovers of the reaction. ..
  55. Okuda K, Hammani K, Tanz S, Peng L, Fukao Y, Myouga F, et al. The pentatricopeptide repeat protein OTP82 is required for RNA editing of plastid ndhB and ndhG transcripts. Plant J. 2010;61:339-49 pubmed publisher
    ..OTP82 falls into the DYW subclass containing conserved C-terminal E and DYW motifs. As in CRR22 and CRR28, the DYW motif present in OTP82 is not essential for RNA editing in vivo. ..
  56. Irie K, Kitagawa K, Nagura H, Imai T, Shimomura T, Fujiyoshi Y. Comparative study of the gating motif and C-type inactivation in prokaryotic voltage-gated sodium channels. J Biol Chem. 2010;285:3685-94 pubmed publisher
    ..These results imply that activation gating in prokaryotic Na(V)s does not require gating motifs and that the residues of helix S6 affect C-type inactivation rates in these channels. ..
  57. Sun Q, Hirasawa A, Hara T, Kimura I, Adachi T, Awaji T, et al. Structure-activity relationships of GPR120 agonists based on a docking simulation. Mol Pharmacol. 2010;78:804-10 pubmed publisher
    ..Taken together, our present study showed that a docking simulation using a GPR120 homology model might be useful to predict the agonistic activity of compounds. ..
  58. Sunadome K, Yamamoto T, Ebisuya M, Kondoh K, Sehara Fujisawa A, Nishida E. ERK5 regulates muscle cell fusion through Klf transcription factors. Dev Cell. 2011;20:192-205 pubmed publisher
    ..Therefore, an ERK5/Sp1/Klf module plays a key role in the fusion process during skeletal muscle differentiation. ..
  59. Akagi T, Katayama Ikegami A, Kobayashi S, Sato A, Kono A, Yonemori K. Seasonal abscisic acid signal and a basic leucine zipper transcription factor, DkbZIP5, regulate proanthocyanidin biosynthesis in persimmon fruit. Plant Physiol. 2012;158:1089-102 pubmed publisher
    ..These results suggest that ABA signals may be involved in PA biosynthesis in persimmon fruit via DkMyb4 activation by DkbZIP5. ..
  60. Miura S, Kondo J, Kawakami T, Shukunami C, Aimoto S, Tanaka H, et al. Synthetic disulfide-bridged cyclic peptides mimic the anti-angiogenic actions of chondromodulin-I. Cancer Sci. 2012;103:1311-8 pubmed publisher
  61. Fujita A, Nakamura K, Kato T, Watanabe N, Ishizaki T, Kimura K, et al. Ropporin, a sperm-specific binding protein of rhophilin, that is localized in the fibrous sheath of sperm flagella. J Cell Sci. 2000;113 ( Pt 1):103-12 pubmed
    ..These results suggest that rhophilin and ropporin may form a complex in sperm flagella. ..
  62. Hosaka T, Nakashima Y, Kusuzaki K, Murata H, Nakayama T, Nakamata T, et al. A novel type of EWS-CHOP fusion gene in two cases of myxoid liposarcoma. J Mol Diagn. 2002;4:164-71 pubmed
    ..The association of these clinical and histopathological features suggests a distinct biological property for this rare type of fusion product...
  63. Amo T, Atomi H, Imanaka T. Biochemical properties and regulated gene expression of the superoxide dismutase from the facultatively aerobic hyperthermophile Pyrobaculum calidifontis. J Bacteriol. 2003;185:6340-7 pubmed
    ..We also detected a rapid response in the biosynthesis of these enzymes once the cells were exposed to oxygen...
  64. Ogura K, Yamamoto M. A mariner-like element with a 5' lesion in Drosophila simulans. Genetica. 2003;119:229-35 pubmed
    ..The rate of somatic reversion, estimated by the number of eye-color mosaic flies, was 79.9%, and the reversion frequency in the germline was 0.6%. The change to the 5' ITR contributes to make this transposon precise excision...
  65. Oishi M, Gohma H, Lejukole H, Taniguchi Y, Yamada T, Suzuki K, et al. Generation of a total of 6483 expressed sequence tags from 60 day-old bovine whole fetus and fetal placenta. Anim Biotechnol. 2004;15:1-8 pubmed
    ..The catalog is used to examine expression profile of genes in 60 day-old bovine fetus and placenta. ..
  66. Hatano S, Tada M, Kimura H, Yamaguchi S, Kono T, Nakano T, et al. Pluripotential competence of cells associated with Nanog activity. Mech Dev. 2005;122:67-79 pubmed publisher
    ..Thus, the activity of Nanog is tightly correlated with an undifferentiated state of cells even in nuclear reprogrammed somatic cells. Nanog may function as a key regulator for sustaining pluripotency in a dose-dependent manner...
  67. Yamamoto K, Yoshida H, Kokame K, Kaufman R, Mori K. Differential contributions of ATF6 and XBP1 to the activation of endoplasmic reticulum stress-responsive cis-acting elements ERSE, UPRE and ERSE-II. J Biochem. 2004;136:343-50 pubmed
    ..Accordingly, the induction of Herp mRNA was diminished in the absence of XBP1 whereas that of BiP mRNA was not affected. These results may help in understanding the role of Herp in the quality control system in the ER. ..
  68. Kajikawa M, Yamato K, Fukuzawa H, Sakai Y, Uchida H, Ohyama K. Cloning and characterization of a cDNA encoding beta-amyrin synthase from petroleum plant Euphorbia tirucalli L. Phytochemistry. 2005;66:1759-66 pubmed
    ..This is the first report of a gene involved in the triterpene synthetic pathway from Euphorbiaceae plants...
  69. Eslami B, Kinboshi M, Inoue S, Harada K, Inoue K, Koizumi A. A nonsense polymorphism (Y319X) of the solute carrier family 6 member 18 (SLC6A18) gene is not associated with hypertension and blood pressure in Japanese. Tohoku J Exp Med. 2006;208:25-31 pubmed
    ..The nonsense allele was not a significant predictor for systolic or diastolic blood pressure. This is the first report showing that a single polymorphism in SLC6A18 is not associated with hypertension or blood pressure in Japanese. ..
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    ..Further analysis using an E. coli expression system will reveal substrate specificity of CYP2W1 and why this P450 isoform is universally conserved in vertebrates. ..
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    ..In addition, two of the four CPD recognition residues in the crystal structure of An-photolyase are not found in St-photolyase, which might utilize a different mechanism to recognize the CPD from that of An-photolyase...
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    ..We propose that DsbB is converted by its specific substrate, DsbA, to a superoxidizing enzyme, capable of oxidizing this extremely oxidizing oxidase. ..
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    ..australasiae ecdysone receptor-A, although L. australasiae retinoid X receptor was necessary for the binding of L. australasiae ecdysone receptor-A to ecdysone response elements. ..
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    ..Thus, mDia1 and Daam1 are platelet actin assembly factors having distinct efficiencies, and they are directly regulated by Rho GTPases. ..
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    ..In addition, knockdown of the Mes4 gene in wing imaginal discs using the GAL4-UAS system caused an atrophied wing phenotype, suggesting that Mes4 is required for wing morphogenesis. ..
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    ..This is the first demonstration of functional impairment of the MATE family induced by cSNPs. ..
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    ..VCP modifications including those in this VAR domain may endorse adaptive and multiple functions to VCP in different cell conditions such as in the cell cycle and with abnormal protein accumulation. ..
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    ..The present results indicated that miR-133 regulates the expression of GLUT4 by targeting KLF15 and is involved in metabolic control in cardiomyocytes...
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    ..Moreover, miR-33-deficient mice had significantly higher serum HDL cholesterol levels than WT mice. These data establish a critical role for miR-33 in the regulation of ABCA1 expression and HDL biogenesis in vivo...
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    ..Here, we show that E. coli dihydropyrimidine dehydrogenase is the first member of a novel NADH-dependent subclass of iron-sulfur flavoenzymes catalyzing the conversion of uracil to 5,6-dihydrouracil in vivo. ..
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    ..Our data suggest that Tbx6 and the Wnt pathway cooperatively regulate proper Hes7 expression. Furthermore, proper Hes7 promoter activity and expression is important for the normal pace of oscillation. ..
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    ..This information should be useful for developing a novel immunodeficient strain with superior efficiency for xenogeneic transplantation of human cells. ..
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    ..These results suggest that EP2 gene expression in the macrophage and uterus is under the control of distinct mechanisms involving alternative promoters. ..
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    ..These results reveal that endogenous PGD2 is essential for both PGE2- and bicuculline-induced allodynia. ..
  88. Kita A, Kita S, Fujisawa I, Inaka K, Ishida T, Horiike K, et al. An archetypical extradiol-cleaving catecholic dioxygenase: the crystal structure of catechol 2,3-dioxygenase (metapyrocatechase) from Ppseudomonas putida mt-2. Structure. 1999;7:25-34 pubmed
    ..One of the conserved histidine residues (His199) seems to have important roles in the catalytic cycle...
  89. Komori H, Matsunaga F, Higuchi Y, Ishiai M, Wada C, Miki K. Crystal structure of a prokaryotic replication initiator protein bound to DNA at 2.6 A resolution. EMBO J. 1999;18:4597-607 pubmed publisher
    ..The structure also suggests that superhelical DNA induced at the origin of plasmid F by four RepEs and one HU dimer has an essential role in the initiation of DNA replication...
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    ..Mis6 is likely required for recruiting SpCENP-A to form proper connection of sister centromeres. ..
  91. Ikeda S, Nishikimi A, Ichihara Tanaka K, Muramatsu T, Yamada M. cDNA cloning of bovine midkine and production of the recombinant protein, which affects in vitro maturation of bovine oocytes. Mol Reprod Dev. 2000;57:99-107 pubmed
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    ..MKP-5 and CL100/MKP-1 also bind to p38 alpha and -beta, but not gamma or delta. Finally, we propose a tentative classification of MKPs based on the sequence characteristics of their MAPK-docking site. ..