Nobuyoshi Shimizu

Summary

Affiliation: Keio University
Country: Japan

Publications

  1. ncbi Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence
    Stefan Taudien
    Genomanalyse, Institut fur Molekulare Biotechnologie, Jena, Germany
    BMC Genomics 5:92. 2004
  2. ncbi Overexpression of the human MNB/DYRK1A gene induces formation of multinucleate cells through overduplication of the centrosome
    Eishi Funakoshi
    Department of Biochemistry, Faculty of Pharmaceutical Sciences, Setsunan University, Osaka 573 0101, Japan
    BMC Cell Biol 4:12. 2003
  3. ncbi MutationView/KMcancerDB: a database for cancer gene mutations
    Nobuyoshi Shimizu
    Department of Molecular Biology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku ku, Tokyo, Japan
    Cancer Sci 98:259-67. 2007
  4. ncbi A novel giant gene CSMD3 encoding a protein with CUB and sushi multiple domains: a candidate gene for benign adult familial myoclonic epilepsy on human chromosome 8q23.3-q24.1
    Atsushi Shimizu
    Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan
    Biochem Biophys Res Commun 309:143-54. 2003
  5. ncbi Myocyte enhancer factor 2 regulates expression of medaka Oryzias latipes fast skeletal myosin heavy chain genes in a temperature-dependent manner
    Chun Shi Liang
    Laboratory of Aquatic Molecular Biology and Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo ku, Tokyo, Japan
    Gene 407:42-53. 2008
  6. ncbi Initial characterization of an uromodulin-like 1 gene on human chromosome 21q22.3
    Kazunori Shibuya
    Department of Molecular Biology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku ku, Tokyo 160 8582, Japan
    Biochem Biophys Res Commun 319:1181-9. 2004
  7. ncbi Nucleolar localization of DGCR8 and identification of eleven DGCR8-associated proteins
    Aiko Shiohama
    Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan GSP Center, The Leading Institute of Keio University, Ibaraki, Japan
    Exp Cell Res 313:4196-207. 2007
  8. ncbi Evolutionary conservation of a unique amino acid sequence in human DICER protein essential for binding to Argonaute family proteins
    Takashi Sasaki
    Department of Molecular Biology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku ku, Tokyo, 160 8582, Japan
    Gene 396:312-20. 2007
  9. ncbi Identification of a novel zinc finger protein gene (ZNF298) in the GAP2 of human chromosome 21q
    Kazunori Shibuya
    Department of Molecular Biology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku ku, Tokyo 160 8582, Japan
    Biochem Biophys Res Commun 332:557-68. 2005
  10. ncbi Fast skeletal muscle myosin heavy chain gene cluster of medaka Oryzias latipes enrolled in temperature adaptation
    Chun Shi Liang
    Laboratory of Aquatic Molecular Biology and Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo ku, Tokyo, Japan
    Physiol Genomics 29:201-14. 2007

Detail Information

Publications87

  1. ncbi Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence
    Stefan Taudien
    Genomanalyse, Institut fur Molekulare Biotechnologie, Jena, Germany
    BMC Genomics 5:92. 2004
    ..1. This DEF locus, however, represents one of the regions in the euchromatic part of the final human genome sequence which contains segmental duplications, and recalcitrant gaps indicating high structural dynamics...
  2. ncbi Overexpression of the human MNB/DYRK1A gene induces formation of multinucleate cells through overduplication of the centrosome
    Eishi Funakoshi
    Department of Biochemistry, Faculty of Pharmaceutical Sciences, Setsunan University, Osaka 573 0101, Japan
    BMC Cell Biol 4:12. 2003
    ..This gene encodes a dual specificity protein kinase that catalyzes its autophosphorylation on serine/threonine and tyrosine residues. But, the functions of the MNB/DYRK1A gene in cellular processes are unknown...
  3. ncbi MutationView/KMcancerDB: a database for cancer gene mutations
    Nobuyoshi Shimizu
    Department of Molecular Biology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku ku, Tokyo, Japan
    Cancer Sci 98:259-67. 2007
    ..In the present paper, we briefly review various useful databases for cancer-related genes, and describe MutationView/KMcancerDB in more detail...
  4. ncbi A novel giant gene CSMD3 encoding a protein with CUB and sushi multiple domains: a candidate gene for benign adult familial myoclonic epilepsy on human chromosome 8q23.3-q24.1
    Atsushi Shimizu
    Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan
    Biochem Biophys Res Commun 309:143-54. 2003
    ..Comparative genomic analysis revealed a conserved family of CSMD genes in the mouse and fugu genomes. Possible functions of the CSMD gene family are discussed...
  5. ncbi Myocyte enhancer factor 2 regulates expression of medaka Oryzias latipes fast skeletal myosin heavy chain genes in a temperature-dependent manner
    Chun Shi Liang
    Laboratory of Aquatic Molecular Biology and Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo ku, Tokyo, Japan
    Gene 407:42-53. 2008
    ..Thus, these transient transfection assays demonstrated that the MEF2 binding site is crucial for a temperature-dependent expression of mMYHs...
  6. ncbi Initial characterization of an uromodulin-like 1 gene on human chromosome 21q22.3
    Kazunori Shibuya
    Department of Molecular Biology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku ku, Tokyo 160 8582, Japan
    Biochem Biophys Res Commun 319:1181-9. 2004
    ..Both proteins seemed to localize in cytoplasm, but UMODL1 is likely to be ubiquitinated and rapidly degraded in HEK293 cells. This gene may be a potent candidate for Down syndrome or bipolar affective disorder...
  7. ncbi Nucleolar localization of DGCR8 and identification of eleven DGCR8-associated proteins
    Aiko Shiohama
    Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan GSP Center, The Leading Institute of Keio University, Ibaraki, Japan
    Exp Cell Res 313:4196-207. 2007
    ..Thus, our studies provided additional new evidence for the involvement of various protein complexes in the molecular mechanisms of apparently complex innate RNA interference machinery...
  8. ncbi Evolutionary conservation of a unique amino acid sequence in human DICER protein essential for binding to Argonaute family proteins
    Takashi Sasaki
    Department of Molecular Biology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku ku, Tokyo, 160 8582, Japan
    Gene 396:312-20. 2007
    ..Significant difference in the RIBOc-A domain of DICER protein between vertebrate and non-vertebrate species may help exploring the functional complexity in the RNA-mediated gene silencing mechanism...
  9. ncbi Identification of a novel zinc finger protein gene (ZNF298) in the GAP2 of human chromosome 21q
    Kazunori Shibuya
    Department of Molecular Biology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku ku, Tokyo 160 8582, Japan
    Biochem Biophys Res Commun 332:557-68. 2005
    ..Interestingly, this gene crosses over a clone gap (GAP2) remaining in the band 21q22.3. We obtained the DNA fragments corresponding to GAP2 using ZNF298 cDNA sequence as anchor primers for PCR and determined its genomic DNA sequence...
  10. ncbi Fast skeletal muscle myosin heavy chain gene cluster of medaka Oryzias latipes enrolled in temperature adaptation
    Chun Shi Liang
    Laboratory of Aquatic Molecular Biology and Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo ku, Tokyo, Japan
    Physiol Genomics 29:201-14. 2007
    ....
  11. ncbi A cluster of 21 keratin-associated protein genes within introns of another gene on human chromosome 21q22.3
    Kazunori Shibuya
    Department of Molecular Biology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo 160 8582, Japan
    Genomics 83:679-93. 2004
    ..This finding suggests a novel transcription mechanism in which C21orf29/TSPEAR gene transcription passes over the multiple transcriptional termination sites of the KAP genes...
  12. ncbi Identification and characterization of a novel gene family YPEL in a wide spectrum of eukaryotic species
    Katsuhiro Hosono
    Department of Molecular Biology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo 160 8582, Japan
    Gene 340:31-43. 2004
    ..The subcellular localization of YPEL proteins in association with centrosome or mitotic spindle suggests a novel function involved in the cell division...
  13. ncbi Sequence analysis of filaggrin gene by novel shotgun method in Japanese atopic dermatitis
    Takashi Sasaki
    Department of Molecular Biology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku ku, Tokyo 160 8582, Japan
    J Dermatol Sci 51:113-20. 2008
    ..This unique gene structure has hampered the precise DNA sequence determination...
  14. ncbi Parkin interacts with LIM Kinase 1 and reduces its cofilin-phosphorylation activity via ubiquitination
    Meng K Lim
    Department of Molecular Biology, Keio University School of Medicine, 35 Shinanomachi, Tokyo, Japan
    Exp Cell Res 313:2858-74. 2007
    ..These findings demonstrate a cell-type dependent functional interaction between parkin and LIMK1 and provide new evidence that links parkin and LIMK1 in the pathogenesis of familial PD...
  15. ncbi Integrative annotation of 21,037 human genes validated by full-length cDNA clones
    Tadashi Imanishi
    Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
    PLoS Biol 2:e162. 2004
    ..The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology...
  16. ncbi Identification of two novel clusters of ultrahigh-sulfur keratin-associated protein genes on human chromosome 11
    Shoichi Yahagi
    Department of Molecular Biology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku ku, Tokyo 160 8582, Japan
    Biochem Biophys Res Commun 318:655-64. 2004
    ..We postulated a mechanism by which these two KAP gene clusters are generated via genomic duplication of a primordial gene cluster followed by genetic modification during evolution...
  17. ncbi Analysis of porcine optineurin and myocilin expression in trabecular meshwork cells and astrocytes from optic nerve head
    Minoru Obazawa
    National Institute of Sensory Organs, National Tokyo Medical Center, Tokyo, Japan
    Invest Ophthalmol Vis Sci 45:2652-9. 2004
    ..To determine the cDNA sequences and analyze the expression of porcine optineurin and myocilin in trabecular meshwork cells (TMCs) and astrocytes from the optic nerve head under normal and experimental conditions...
  18. ncbi Analysis of eighteen deletion breakpoints in the parkin gene
    Shuichi Asakawa
    Department of Molecular Biology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku ku, Tokyo 160 8582, Japan
    Biochem Biophys Res Commun 389:181-6. 2009
    ..Here, we discuss the possible mechanisms for deletion hot spot formation and its effects on human genomes...
  19. ncbi Novel human BTB/POZ domain-containing zinc finger protein ZNF295 is directly associated with ZFP161
    Jun Wang
    Department of Molecular Biology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku ku, Tokyo 160 8582, Japan
    Biochem Biophys Res Commun 327:615-27. 2005
    ..We postulated that ZNF295 may be involved in the bi-directional control of gene expression in concert with ZFP161...
  20. ncbi Multiple gene organization of pufferfish Fugu rubripes tropomyosin isoforms and tissue distribution of their transcripts
    Takuya Toramoto
    Laboratory of Aquatic Molecular Biology and Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, 113 8657, Japan
    Gene 331:41-51. 2004
    ..This indicated that the Fugu TPM1 and TPM4 genes had resulted from a gene duplication in the fish evolutionary lineage...
  21. ncbi KMeyeDB: a graphical database of mutations in genes that cause eye diseases
    Takashi Kawamura
    Department of Molecular Biology, Keio University School of Medicine, Shinjuku ku, Tokyo, Japan
    Hum Mutat 31:667-74. 2010
    ..Some genes are involved in multiple types of eye diseases, whereas several eye diseases are caused by different mutations in one gene...
  22. ncbi Identification of three novel proteins (SGSM1, 2, 3) which modulate small G protein (RAP and RAB)-mediated signaling pathway
    Hao Yang
    Department of Molecular Biology, Keio University School of Medicine, Tokyo 160 8582, Japan
    Genomics 90:249-60. 2007
    ..Based on these results, we postulated that the SGSM family members function as modulators of the small G protein RAP and RAB-mediated neuronal signal transduction and vesicular transportation pathways...
  23. ncbi Hyper-expansion of large DNA segments in the genome of kuruma shrimp, Marsupenaeus japonicus
    Takashi Koyama
    Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4 5 7 Konan, Minato ku, Tokyo, 108 8477, Japan
    BMC Genomics 11:141. 2010
    ..We examined the BAC clone that includes the redundant sequence to further analyze its length, copy number and location in the kuruma shrimp genome...
  24. ncbi Complete nucleotide sequences of mitochondrial genomes of two solitary entoprocts, Loxocorone allax and Loxosomella aloxiata: implications for lophotrochozoan phylogeny
    Shin ichi Yokobori
    Laboratory for Cellular Biochemistry, Department of Molecular Biology, School of Life Science, Tokyo University of Pharmacy and Life Sciences, 1432 1 Horinouchi, Hachioji, Tokyo 192 0392, Japan
    Mol Phylogenet Evol 47:612-28. 2008
    ..Molecular phylogenetic analyses based on the sequences of mt protein-coding genes suggested a possible close relationship between Entoprocta and Phoronida, and a close relationship among Brachiopoda, Annelida, and Echiura...
  25. ncbi Transcription factor single-minded 2 (SIM2) is ubiquitinated by the RING-IBR-RING-type E3 ubiquitin ligases
    Michiyo Okui
    Department of Molecular Biology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku ku, Tokyo 160 8582, Japan
    Exp Cell Res 309:220-8. 2005
    ..We postulated that transcription factor SIM2 and E3 ubiquitin ligase Parkin may interact each other to play an important physiological role in the brain development which is controlled by ubiquitination...
  26. ncbi Characterization of human and mouse TRPM2 genes: identification of a novel N-terminal truncated protein specifically expressed in human striatum
    Takuji Uemura
    Department of Molecular Biology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku ku, Tokyo 160 8582, Japan
    Biochem Biophys Res Commun 328:1232-43. 2005
    ..These new findings are invaluable to further study the regulation of TRPM2 gene expression and to examine the possible involvement of the TRPM2 gene in the pathophysiology of bipolar disorder...
  27. ncbi Gene analysis and evaluation of the single founder effect in Japanese patients with Oguchi disease
    Masamichi Saga
    Department of Ophthalmology, Keio University School of Medicine, Tokyo, Japan
    Jpn J Ophthalmol 48:350-2. 2004
    ..To analyze mutations of the arrestin/S-antigen (SAG) gene in nine newly identified Oguchi disease patients, and to examine whether the 926delA (formerly called 1147delA) mutation in the SAG gene is inherited from a single founder...
  28. ncbi The DNA sequence of medaka chromosome LG22
    Takashi Sasaki
    Department of Molecular Biology, Keio University School of Medicine, 35 Shinanomachi, Tokyo 160 8582, Japan
    Genomics 89:124-33. 2007
    ..These precise comparative genomics allowed us to identify the pieces of ancient chromosomes of the common vertebrate ancestor and estimate chromosomal evolution in the vertebrate lineage...
  29. ncbi Two patients with atypical interstitial deletions of 8p23.1: mapping of phenotypical traits
    Marco T Paez
    International Research and Educational Institute for Integrated Medical Sciences IREIIMS, Tokyo Women s Medical University, Tokyo, Japan
    Am J Med Genet A 146:1158-65. 2008
    ....
  30. ncbi Comparative genomics of the keratin-associated protein (KAP) gene clusters in human, chimpanzee, and baboon
    Kazunori Shibuya
    Department of Molecular Biology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
    Mamm Genome 15:179-92. 2004
    ..These findings suggest that the ancestral KAP gene cluster was composed of 17 genes before the divergence of Old World monkeys (baboon) to the anthropoid (human and chimpanzee)...
  31. ncbi CancerProView: a graphical image database of cancer-related genes and proteins
    Susumu Mitsuyama
    Laboratory of Gene Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku ku, Tokyo, 160 8582, Japan
    Genomics 100:81-92. 2012
    ..The CancerProView database can be operated via Internet with any Web browser, and the system is freely available to interested users without ID and password...
  32. ncbi Identification of eight members of the Argonaute family in the human genome small star, filled
    Takashi Sasaki
    Department of Molecular Biology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku ku, Tokyo, 160 8582, Japan
    Genomics 82:323-30. 2003
    ..We postulate that at least some members of the human Argonaute family may be involved in the development and maintenance of stem cells through the RNA-mediated gene-quelling mechanisms associated with DICER...
  33. ncbi Simple PCR-based DNA microarray system to identify human pathogenic fungi in skin
    Tomotaka Sato
    Department of Dermatology, Keio University School of Medicine, Tokyo, Japan
    J Clin Microbiol 48:2357-64. 2010
    ....
  34. ncbi Molecular cloning and expression analysis of a novel gene DGCR8 located in the DiGeorge syndrome chromosomal region
    Aiko Shiohama
    Department of Molecular Biology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku ku, 160 8582, Tokyo, Japan
    Biochem Biophys Res Commun 304:184-90. 2003
    ..2...
  35. ncbi [The integrated database for mutations in disease-causing genes: Mutation View/KMDB]
    Masafumi Ohtsubo
    Department of Molecular Biology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
    Seikagaku 75:311-8. 2003
  36. ncbi Increased nuclear factor-kappa B activation is related to the tumor development of renal cell carcinoma
    Mototsugu Oya
    Department of Urology and Department of Molecular Biology, Keio University School of Medicine, Shinjuku ku, Tokyo 160 8582, Japan
    Carcinogenesis 24:377-84. 2003
    ..The NF-kappa B activity may therefore be a late event in carcinogenesis related to tumor development, thereby representing a possible molecular target in the treatment of RCC...
  37. ncbi Aire-dependent thymic expression of desmoglein 3, the autoantigen in pemphigus vulgaris, and its role in T-cell tolerance
    Naoko Wada
    Department of Dermatology, Keio University School of Medicine, Tokyo, Japan
    J Invest Dermatol 131:410-7. 2011
    ..These findings indicate that Aire has an important role in Dsg3 expression as well as in selection of T cells that help B cells to produce anti-Dsg3 IgG in thymus...
  38. ncbi Retinoic acid signaling positively regulates liver specification by inducing wnt2bb gene expression in medaka
    Takahiro Negishi
    Department of Developmental and Regenerative Biology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
    Hepatology 51:1037-45. 2010
    ..These results suggest that a common molecular mechanism may underlie liver and pectoral fin specification during piscine embryogenesis...
  39. ncbi Role of TBX1 in human del22q11.2 syndrome
    Hisato Yagi
    Division of Genomic Medicine, Institute of Advanced Biomedical Engineering and Science, Graduate School of Medicine, Tokyo Women s Medical University, Tokyo, Japan
    Lancet 362:1366-73. 2003
    ..At least 30 genes have been mapped to the deleted region. However, the association of these genes with the cause of this syndrome is not clearly understood...
  40. ncbi Renal cancer cells lacking hypoxia inducible factor (HIF)-1alpha expression maintain vascular endothelial growth factor expression through HIF-2alpha
    Toshiaki Shinojima
    Department of Urology, Keio University School of Medicine, Shinjuku ku, Tokyo 160 8582, Japan
    Carcinogenesis 28:529-36. 2007
    ..HIF-1alpha may therefore represent an important target molecule for RCC therapy; however, HIF-2alpha should be targeted in HIF-1alpha defective renal cancer cells...
  41. ncbi Variants in optineurin gene and their association with tumor necrosis factor-alpha polymorphisms in Japanese patients with glaucoma
    Tomoyo Funayama
    Department of Ophthalmology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku ku, Tokyo 160 8582, Japan
    Invest Ophthalmol Vis Sci 45:4359-67. 2004
    ..To investigate sequence variations in the optineurin (OPTN) gene and their association with TNF-alpha polymorphisms in Japanese patients with glaucoma...
  42. ncbi Suppressive effects of interleukin-18 on liver function in rat liver allografts
    Shigeshi Ono
    Department of Surgery, Keio University School of Medicine, Tokyo, Japan
    J Surg Res 176:293-300. 2012
    ..It is also a crucial regulator of lymphocyte production of interferon-γ (IFN-γ), which can promote acute cellular rejection of transplanted solid organs...
  43. ncbi Construction of BAC library for the amphibian Xenopus tropicalis
    Yasuyuki Ishii
    Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan
    Genes Genet Syst 79:49-51. 2004
    ..This result suggests the presence of at least two clusters for the Pcdh gamma gene in the genome of X. tropicalis...
  44. ncbi Dual promoter expression system with insulator ensures a stringent tissue-specific regulation of two reporter genes in the transgenic fish
    Atsushi Shimizu
    Department of Molecular Biology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku ku, Tokyo, 160 8582, Japan
    Transgenic Res 22:435-44. 2013
    ..Thus, our dual promoter expression system with insulator is compatible to the conventional IRES and fused reporter gene systems and will be an alternative method to produce the transgenic fishes...
  45. ncbi Rapid quantification of the heteroplasmy of mutant mitochondrial DNAs in Leber's hereditary optic neuropathy using the Invader technology
    Yukihiko Mashima
    Department of Ophthalmology, Keio University School of Medicine, Shinjuku, Tokyo 160 8582, Japan
    Clin Biochem 37:268-76. 2004
    ..To quantify the degree of heteroplasmy of a mitochondrial DNA (mtDNA) mutation in Leber's hereditary optic neuropathy (LHON) a biplex Invader assay was applied...
  46. ncbi NF-kappaB-dependent increase in intrarenal angiotensin II induced by proteinuria
    Osamu Takase
    Department of Internal Medicine, and Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan
    Kidney Int 68:464-73. 2005
    ..Induction of angiotensinogen and decrease in ACE2 levels may be involved in this NF-kappaB-dependent increase in angiotensin II...
  47. ncbi [Drug discovery based on the human genome sciences]
    Nobuyoshi Shimizu
    Department of Molecular Biology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
    Gan To Kagaku Ryoho 29:1-6. 2002
  48. ncbi Gene transfer of truncated IkappaBalpha prevents tubulointerstitial injury
    Osamu Takase
    Department of Internal Medicine, Keio University Medical School, Tokyo, Japan
    Kidney Int 63:501-13. 2003
    ..We investigated the role of nuclear factor-kappaB (NF-kappaB) in tubular epithelial cells in the development of proteinuria-induced TI injury...
  49. ncbi AIRE functions as an E3 ubiquitin ligase
    Daisuke Uchida
    Division of Molecular Immunology, Institute for Enzyme Research, University of Tokushima, 3 18 15 Kuramoto, Tokushima 770 8503, Japan
    J Exp Med 199:167-72. 2004
    ..These results add a novel enzymatic function for AIRE and suggest an indispensable role of the Ub proteasome pathway in the establishment of self-tolerance, in which AIRE is involved...
  50. ncbi Mutation analysis of the BRAF codon 599 in malignant pleural mesothelioma by enriched PCR-RFLP
    Hideaki Dote
    Department of Cancer and Thoracic Surgery, Graduate School of Medicine and Dentistry, Okayama University, 2 5 1 Shikata cho, Okayama 700 8558, Japan
    Oncol Rep 11:361-3. 2004
    ..However, it may be a rare type of mutation in MPMs. Our new assay is useful and can be applied for screening of BRAF codon 599 mutation in various kinds of clinical samples...
  51. ncbi A novel nuclear localization signal in the human single-minded proteins SIM1 and SIM2
    Akiko Yamaki
    Department of Medical Genetics, Kyorin University School of Health Sciences, 146 Miyashita cho, Hachioji, Tokyo 192 8508, Japan
    Biochem Biophys Res Commun 313:482-8. 2004
    ..Thus, the NLS consisting of a cluster of basic amino acids with Pro and Tyr at the C-terminal end is novel and well conserved in the SIM proteins during evolution...
  52. ncbi Characterization of AOC2 gene encoding a copper-binding amine oxidase expressed specifically in retina
    Qiang Zhang
    National Institute of Sensory Organs, National Tokyo Medical Center, 2 5 1 Higashigaoka, Meguro, Tokyo 152 8902, Japan
    Gene 318:45-53. 2003
    ....
  53. ncbi Three novel mutations of the PAX6 gene in Japanese aniridia patients
    Toshio Kawano
    Department of Ophthalmology, Hamamatsu University School of Medicine, Hamamatsu, Japan
    J Hum Genet 52:571-4. 2007
    ..The database for PAX6 gene mutation has been made using a graphical data display system MutationView ( http://mutview.dmb.med.keio.ac.jp/ )...
  54. ncbi A novel third gonadotropin-releasing hormone receptor in the medaka Oryzias latipes: evolutionary and functional implications
    Kataaki Okubo
    Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113 8657, Bunkyo, Japan
    Gene 314:121-31. 2003
    ..These data identify GnRH-R3 as a new member of GnRH-R that arose in a recent genome duplication but has distinctive genomic structure and functional characteristic...
  55. ncbi Detection of codon 61 point mutations of the K-ras gene in lung and colorectal cancers by enriched PCR
    Shinichi Toyooka
    Department of Cancer and Thoracic Surgery, Graduate School of Medicine and Dentistry, Okayama University, Okayama 700-8558, Japan
    Oncol Rep 10:1455-9. 2003
    ....
  56. ncbi DMY is a Y-specific DM-domain gene required for male development in the medaka fish
    Masaru Matsuda
    Laboratory of Reproductive Biology, National Institute for Basic Biology, Okazaki 444 8585, Japan
    Nature 417:559-63. 2002
    ..These findings strongly suggest that the sex-specific DMY is required for testicular development and is a prime candidate for the medaka sex-determining gene...
  57. ncbi Genomic analysis of Hox clusters in the sea lamprey Petromyzon marinus
    Steven Q Irvine
    Yale University, Department of Molecular, Cellular and Developmental Biology, New Haven, Connecticut 06520-8103, USA
    J Exp Zool 294:47-62. 2002
    ..marinus has a total of either three or four Hox clusters. We also identify four highly conserved non-coding sequence motifs shared with higher vertebrates in a genomic comparison of Hox 10 genes...
  58. ncbi The transmembrane serine protease (TMPRSS3) mutated in deafness DFNB8/10 activates the epithelial sodium channel (ENaC) in vitro
    Michel Guipponi
    Division of Medical Genetics, University of Geneva Medical School, and Geneva University Hospitals, Switzerland
    Hum Mol Genet 11:2829-36. 2002
    ....
  59. ncbi Construction and initial analysis of bacterial artificial chromosome (BAC) contigs from the sex-determining region of the platyfish Xiphophorus maculatus
    Alexander Froschauer
    Lehrstuhl Physiologische Chemie I, Biozentrum, , Am Hubland, D-97074, , Germany
    Gene 295:247-54. 2002
    ....
  60. ncbi Molecular cloning and characterization of DMRT genes from the medaka Oryzias latipes and the platyfish Xiphophorus maculatus
    Mariko Kondo
    Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
    Gene 295:213-22. 2002
    ..Surprisingly it is also not the same as its putative tilapia ortholog (DMO). These differences in expression suggest that DMRT4 might fulfill divergent functions in different species...
  61. ncbi Distinct clinical phenotype and immunoreactivity in Japanese siblings with autoimmune polyglandular syndrome type 1 (APS-1) associated with compound heterozygous novel AIRE gene mutations
    Kazuhiko Kogawa
    Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Japan
    Clin Immunol 103:277-83. 2002
    ..The same AIRE gene mutations can thus be associated with characteristic and noncharacteristic phenotypes of APS-1, and HLA may possibly influence the phenotype of APS-1...
  62. ncbi Structural characterization of GnRH loci in the medaka genome
    Kataaki Okubo
    Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113 8657, Japan
    Gene 293:181-9. 2002
    ....
  63. ncbi Mutant analyses reveal different functions of fgfr1 in medaka and zebrafish despite conserved ligand-receptor relationships
    Hayato Yokoi
    Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    Dev Biol 304:326-37. 2007
    ..Comparative analysis using different fish is thus invaluable for shedding light on evolutionary diversification of gene function...
  64. ncbi Aberrant promoter methylation of insulin-like growth factor binding protein-3 gene in human cancers
    Kunitoshi Tomii
    Department of Cancer and Thoracic Surgery, Shikata Laboratory, Advanced Science Research Center, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
    Int J Cancer 120:566-73. 2007
    ..079). In summary, our results showed that IGFBP-3 methylation played an important role in the silencing of its expression, suggesting that IGFBP-3 may act as a tumor suppressor gene in several human cancers examined...
  65. ncbi Distinct genomic sequence of the CNR/Pcdhalpha genes in chicken
    Hidehiko Sugino
    Genome Information Research Center, Osaka University, 3 1, Yamadaoka Suita, Osaka 565 0871, Japan
    Biochem Biophys Res Commun 316:437-45. 2004
    ..Due to the high CG content, chicken variable exons (from v1 to v12) encode 3 to 4 frame-shifted open reading frames, which span 1.5-3.0kb, in both the sense and anti-sense orientations...
  66. ncbi Molecular cloning and characterization of gene for Golgi-localized syntaphilin-related protein on human chromosome 8q23
    Eishi Funakoshi
    Department of Biochemistry, Faculty of Pharmaceutical Sciences, Setsunan University, 45 1 Nagaotoge cho, Hirakata, Osaka 573 0101, Japan
    Gene 344:259-71. 2005
    ..These results indicate that KIAA1472 gene products may play an important role in vesicular traffic in various tissues including the brain...
  67. ncbi Genomic organization and transcripts of the zebrafish Protocadherin genes
    Motoki N Tada
    KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
    Gene 340:197-211. 2004
    ..Thus, although the Pcdhalpha families were common to diverse vertebrates, their gene number, structure, and transcripts were different between teleosts and mammals...
  68. ncbi MEPD: a resource for medaka gene expression patterns
    Thorsten Henrich
    EMBL Heidelberg Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Bioinformatics 21:3195-7. 2005
    ..Presently, MEPD has 19,757 entries, for 1024 of them the expression pattern has been determined...
  69. ncbi The minimal eukaryotic ribosomal DNA units in the primitive red alga Cyanidioschyzon merolae
    Shinichiro Maruyama
    Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7 3 1 Hongo, Bunkyo, Tokyo 113 0033, Japan
    DNA Res 11:83-91. 2004
    ..They consist of only 3 single units of rRNA genes distributed on separate chromosomal loci, representing an implication for concerted evolution. Based on these results, the origin and evolution of the nucleolus are discussed...
  70. ncbi Unprecedented intraspecific diversity of the MHC class I region of a teleost medaka, Oryzias latipes
    Kentaro Tsukamoto
    Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Japan
    Immunogenetics 57:420-31. 2005
    ....
  71. ncbi XAGE-1 expression in non-small cell lung cancer and antibody response in patients
    Kazuhiko Nakagawa
    Department of Immunology, Okayama University Graduate School of Medicine and Dentistry, Okayama, Japan
    Clin Cancer Res 11:5496-503. 2005
    ..We here investigated the mRNA expression of four XAGE-1 variants and XAGE-1 protein expression in non-small cell lung cancer (NSCLC). Humoral immune response to XAGE-1b was also evaluated in patients...
  72. ncbi Single nucleotide polymorphisms in the EXO1 gene and risk of colorectal cancer in a Japanese population
    Hiromasa Yamamoto
    Department of Cancer and Thoracic Surgery, Graduate School of Medicine and Dentistry, Okayama University, 2 5 1 Shikata cho, Okayama 700 8558, Japan
    Carcinogenesis 26:411-6. 2005
    ..This is the first report to provide evidence for an association of EXO1 gene polymorphisms with colorectal cancer risk. The EXO1 genotypes were not associated with any clinicopathological characteristics in colorectal cancer patients...
  73. ncbi Detection of EGFR gene mutation in lung cancer by mutant-enriched polymerase chain reaction assay
    Hiroaki Asano
    Department of Cancer and Thoracic Surgery, Graduate School of Medicine and Dentistry, Okayama University, Okayama, Japan
    Clin Cancer Res 12:43-8. 2006
    ..Thus, mutant-enriched PCR may provide a valuable method of potentially detecting a small fraction of mutant genes in heterogeneous specimens, indicating its possible use in clinical application for NSCLC...
  74. ncbi Organization and structure of hox gene loci in medaka genome and comparison with those of pufferfish and zebrafish genomes
    Gene Kurosawa
    Division of Biological Sciences, Graduate School of Science, Nagoya University, Nagoya, Aichi 460 8602, Japan
    Gene 370:75-82. 2006
    ..Thus, the hox gene sets should have been well conserved once they had been established in respective species...
  75. ncbi Genomic structure and expression of the soluble guanylyl cyclase alpha2 subunit gene in the medaka fish Oryzias latipes
    Yuko Yao
    Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo, Japan
    Zoolog Sci 20:1293-304. 2003
    ..Linkage analysis on the medaka fish chromosome demonstrated that the OlGCS-alpha2 gene was mapped to LG13; this mapping position was different from those for the OlGCS-alpha1 and OlGCS-beta1 genes (LG1)...
  76. ncbi Molecular cloning of the m-Golsyn gene and its expression in the mouse brain
    Eishi Funakoshi
    Department of Biochemistry, Faculty of Pharmaceutical Sciences, Setsunan University, 45 1 Nagaotoge cho, Hirakata, Osaka 573 0101, Japan
    Gene Expr 13:27-40. 2006
    ..These results indicate that the m-Golsyn protein may play an important role in intracellular protein transport in neuronal cells of the brain...
  77. ncbi Double mutation and gene copy number of EGFR in gefitinib refractory non-small-cell lung cancer
    Masaki Tokumo
    Department of Cancer and Thoracic Surgery, Graduate School of Medicine and Dentistry, Okayama University, 2-5-1 Shikata-cho, Okayama 700-8558, Japan
    Lung Cancer 53:117-21. 2006
    ..Our findings encourage further molecular analysis to elucidate the relationship between the EGFR status, including mutations and amplifications, and the responsiveness of NSCLC to gefitinib...
  78. ncbi Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D
    Motomichi Matsuzaki
    Department of Biomedical Chemistry, Graduate School of Medicine, University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    Nature 428:653-7. 2004
    ..These results indicate that the C. merolae genome provides a model system with a simple gene composition for studying the origin, evolution and fundamental mechanisms of eukaryotic cells...
  79. ncbi Clinical and biological features associated with epidermal growth factor receptor gene mutations in lung cancers
    Hisayuki Shigematsu
    Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX 75390 8593, USA
    J Natl Cancer Inst 97:339-46. 2005
    ..However, the role of such mutations in the pathogenesis of lung cancers is unclear...
  80. ncbi Genomic sequences encoding two types of medaka hemopexin-like protein Wap65, and their gene expression profiles in embryos
    Makiko Nakaniwa
    Laboratory of Aquatic Molecular Biology and Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113 8657, Japan
    J Exp Biol 208:1915-25. 2005
    ..The differences between mWap65-1 and mWap65-2 in their expression profiles indicate their distinct roles during ontogeny...
  81. ncbi The genome size evolution of medaka (Oryzias latipes) and fugu (Takifugu rubripes)
    Shuichiro Imai
    Division of Biological Science, Graduate School of Science, Nagoya University, Japan
    Genes Genet Syst 82:135-44. 2007
    ..These results strongly indicated that amplification of repetitive elements and compilation of indels are major driving forces to facilitate changes in the genome size...
  82. ncbi Dose effect of smoking on aberrant methylation in non-small cell lung cancers
    Shinichi Toyooka
    Int J Cancer 110:462-4. 2004
  83. ncbi [Integrated database for mutations in disease genes: MutationView/KMDB]
    Masafumi Ohtsubo
    Tanpakushitsu Kakusan Koso 48:762-9. 2003
  84. ncbi Single nucleotide polymorphism of the AXIN2 gene is preferentially associated with human lung cancer risk in a Japanese population
    Hirotaka Kanzaki
    Department of Molecular Genetics, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700 8558, Japan
    Int J Mol Med 18:279-84. 2006
    ..This is the first report to show an association between the AXIN2 SNP and lung cancer risk...
  85. ncbi The medaka draft genome and insights into vertebrate genome evolution
    Masahiro Kasahara
    Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277 0882, Japan
    Nature 447:714-9. 2007
    ....
  86. ncbi Interleukin-17 augments tumor necrosis factor-alpha-induced granulocyte and granulocyte/macrophage colony-stimulating factor release from human colonic myofibroblasts
    Akira Andoh
    Department of Internal Medicine, Shiga University of Medical Science, Seta Tukinowa, Otsu, 520-2192, Japan
    J Gastroenterol 40:802-10. 2005
    ..CONCLUSIONS: IL-17 augments TNF-alpha-induced G- and GM-CSF release via transcriptional and posttranscriptional mechanisms...
  87. ncbi Identification of novel tropomyosin 1 genes of pufferfish (Fugu rubripes) on genomic sequences and tissue distribution of their transcripts
    Daisuke Ikeda
    Laboratory of Aquatic Molecular Biology and Biotechnology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
    Mol Biol Rep 30:83-90. 2003
    ....