109 results on '"Kusuda J"'
Search Results
2. Positive and negative regulation of adenovirus infection by CAR-like soluble protein, CLSP
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Kawabata, K, Tashiro, K, Sakurai, F, Osada, N, Kusuda, J, Hayakawa, T, Yamanishi, K, and Mizuguchi, H
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- 2007
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3. An enhanced promoter trap protocol
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Toyoda, A., Kusuda, J., Maeda, H., and Hashimoto, K.
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- 1995
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4. The complete nucleotide sequence of the tobacco chloroplast genome
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Shinozaki, K., Ohme, M., Tanaka, M., Wakasugi, T., Hayshida, N., Matsubayasha, T., Zaita, N., Chunwongse, J., Obokata, J., Yamaguchi-Shinozaki, K., Ohto, C., Torazawa, K., Meng, B. Y., Sugita, M., Deno, H., Kamogashira, T., Yamada, K., Kusuda, J., Takaiwa, F., Kata, A., Tohdoh, N., Shimada, H., and Sugiura, M.
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- 1986
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5. Molecular cloning and characterization of Bombyx densovirus genomic DNA
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Bando, H., Kusuda, J., and Kawase, S.
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- 1987
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6. Sequence analysis, gene expression, and chromosomal assignment of mouse Borg4 gene and its human orthologue
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Osada, N., primary, Kusuda, J., additional, Suzuki, Y., additional, Sugano, S., additional, and Hashimoto, K., additional
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- 2000
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7. Cloning, expression analysis and chromosome mapping of human casein kinase 1 γ1 (CSNK1G1): Identification of two types of cDNA encoding the kinase protein associated with heterologous carboxy-terminal sequences
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Kusuda, J., primary, Hirai, M., additional, Tanuma, R., additional, and Hashimoto, K., additional
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- 2000
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8. Genomic structure and chromosome location of RPL27A/Rpl27a, the genes encoding human and mouse ribosomal protein L27A
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Kusuda,, J., primary, Hirai, M., additional, Tanuma, R., additional, Hirata, M., additional, and Hashimoto, K., additional
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- 1999
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9. cDNA cloning and chromosome mapping of the mouse casein kinase I epsilon gene (Csnk1e)
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Kusuda, J., primary, Hirai, M., additional, Tanuma, R., additional, and Hashimoto, K., additional
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- 1999
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10. The Human CC Chemokine TECK (SCYA25) Maps to Chromosome 19p13.2
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Nomiyama, H., primary, Amano, K., additional, Kusuda, J., additional, Imai, T., additional, Miura, R., additional, Yoshie, O., additional, and Matsuda, Y., additional
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- 1998
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11. Assignment of the Human CC Chemokine MPIF-2/Eotaxin-2 (SCYA24) to Chromosome 7q11.23
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Nomiyama, H., primary, Osborne, L.R., additional, Imai, T., additional, Kusuda, J., additional, Miura, R., additional, Tsui, L.-C., additional, and Yoshie, O., additional
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- 1998
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12. Cloning and chromosome mapping of the human casein kinase I γ3 gene (CSNK1G3)
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Kusuda, J., primary, Hirai, M., additional, Toyoda, A., additional, Tanuma, R., additional, and Hashimoto, K., additional
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- 1998
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13. Human chemokines fractalkine (SCYD1), MDC (SCYA22) and TARC (SCYA17) are clustered on chromosome 16q131
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Nomiyama, H., primary, Imai, T., additional, Kusuda, J., additional, Miura, R., additional, Callen, D.F., additional, and Yoshie, O., additional
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- 1998
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14. Erratum to: "Identification of the gene-richest bands in human chromosomes" [Gene 174 (1996) 85–94]
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Saccone, S., primary, Cacciò, S., additional, Kusuda, J., additional, Andreozzi, L., additional, and Bernardi, G., additional
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- 1997
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15. Cloning, expression analysis and chromosome mapping of human casein kinase 1 Á 1 (CSNK1G1): Identification of two types of cDNA encoding the kinase protein associated with heterologous carboxy-terminal sequences.
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Kusuda, J., Hirai, M., Tanuma, R., and ashimotoa, K.
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HUMAN cloning , *EUKARYOTIC cells , *PROTISTA , *GROWTH factors , *DNA , *AMINO acids - Abstract
Casein kinase 1 γ1(CK1 γ1) is known to be involved in the growth and morphogenesis of eukaryotic cells. We have isolated two types of cDNA for human casein kinase 1 γ1 (hCK1 γ1). One of them (hCK1 γ1S) was found to encode a polypeptide consisting of 393 amino acids, which is highly homologous with already reported rat CK1 γ1 (rCK1 γ1). The other type of cDNA (hCK1 γ1L) encodes a polypeptide consisting of 422 amino acids, which is quite identical in the kinase domain, but different in the C-terminal sequence from hCK1 γ1S. Namely, hCK1 γ1L has a characteristic sequence of 50 amino acids at the C-terminal end and this motif was shown to be shared by the casein kinase γ2 and γ3 from rat and human, suggesting that it is a signature sequence of the γ-isoforms. In this sense, newly isolated hCK1 γ1L might be the original form of CK1 γ1 subspecies rather than rCK1 γ1 and hCK1 γ1S. RTPCR analysis revealed that hCK1 γ1S mRNA is predominantly present in the testis, whereas the abundance of hCK1 γ1L mRNA was nearly the same in the twelve tissues examined. These results suggest that novel hCK1 γ1L may have a unique functional role different from that of hCK1 γ1S and rCK1 γ1. The human hCK1 γ1 gene (CSNK1G1) was mapped to chromosome 15q22.1→q22.31 by fluorescence in situ hybridization. [ABSTRACT FROM AUTHOR]
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- 2000
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16. Genomic structure and chromosome location of RPL27A/ Rpl27a, the genes encoding human and mouse ribosomal protein L27A.
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Kusuda, J., Hirai, M., Tanuma, R., Hirata, M., and Hashimoto, K.
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GENE mapping , *MOLECULAR cloning , *RIBOSOMES , *INTRONS , *AMINO acid sequence , *FLUORESCENCE in situ hybridization - Abstract
The intron-containing genes encoding human and mouse ribosomal protein (r-protein) L27A were cloned and sequenced. The human r-protein L27A gene (RPL27A) shared an identical exon/intron structure with the mouse r-protein 27A gene (Rpl27a). The translational start codon ATG was separated from the main reading frame by the first intron sequence in both genes. An approximately 200-bp sequence upstream of the translational start site of both genes displayed remarkable similarity, and contained the putative promoters lacking canonical TATA, but harbored Sp1 binding sites and a short stretch of pyrimidine cluster, similar to other r-protein genes. Transcriptional regulatory elements, Box-A and GABP, found in the promoters of some other r-protein genes were also conserved in both genes. These structural features were included in the typical CpG island identified in the 5'-end sequences, suggesting that RPL27A/Rpl27a cloned here are authentic and transcriptionally active. Fluorescence in situ hybridization (FISH) analysis localized the mouse intron-containing Rpl27a to chromosome 7E2-F1 syntenic to human chromosome 11p15, where human RPL27A was located. [ABSTRACT FROM AUTHOR]
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- 1999
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17. Primary culture of chicken hepatocytes in serum-free medium (pH 7.8) secreted albumin and transferrin for a long period in free gas exchange with the atmosphere
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Fujii, M., Yoshino, I., Suzuki, M., Higuchi, T., Mukai, S., Aoki, T., Fukunaga, T., Sugimoto, Y., Inoue, Y., and Kusuda, J.
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- 1996
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18. Molecular cloning of a novel human CC chemokine secondary lymphoid-tissue chemokine that is a potent chemoattractant for lymphocytes and mapped to chromosome 9p13.
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Nagira, M, Imai, T, Hieshima, K, Kusuda, J, Ridanpää, M, Takagi, S, Nishimura, M, Kakizaki, M, Nomiyama, H, and Yoshie, O
- Abstract
By searching the Expressed Sequence Tag (EST) data base, we identified partial cDNA sequences potentially encoding a novel human CC chemokine. We determined the entire cDNA sequence which encodes a highly basic polypeptide of 134 amino acids total with a putative signal peptide of 23 amino acids. The predicted mature protein of 111 amino acids has the four canonical cysteine residues and shows 21-33% identity to other human CC chemokines, but has a unique carboxyl-terminal extension of about 30 amino acids which contains two extra cysteine residues. The mRNA was expressed strongly in tissues such as the lymph nodes, Appendix, and spleen. The recombinant protein, which was produced by the baculovirus system and purified to homogeneity, was a highly efficient chemoattractant for certain human T cell lines and a highly potent one for freshly isolated peripheral blood lymphocytes and cultured normal T cells expanded by phytohemagglutinin and interleukin 2. Unlike most other CC chemokines, however, this novel chemokine was not chemotactic for monocytes or neutrophils, suggesting that it is specific for lymphocytes. From these results, we designated this novel CC chemokine as SLC from secondary lymphoid-tissue chemokine. SLC fused with the secreted form of alkaline phosphatase (SLC-SEAP) was used to characterize the SLC receptor. Binding of SLC-SEAP to freshly isolated lymphocytes was blocked by SLC (IC50, 0.12 nM) but not by any other CC chemokine so far tested, suggesting that resting lymphocytes express a class of receptors highly specific for SLC. By using somatic cell hybrids, radiation hybrids, and selected yeast and bacterial artificial chromosome clones, we mapped the SLC gene (SCYA21) at chromosome 9p13 and between chromosomal markers, D9S1978(WI-8765) and AFM326vd1, where the gene for another novel CC chemokine termed ELC from EBI1-ligand chemokine (SCYA19) also exists. Collectively, SLC is a novel CC chemokine specific for lymphocytes and, together with ELC, constitutes a new group of chemokines localized at chromosome 9p13.
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- 1997
19. The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression
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Shinozaki, K., Ohme, M., Tanaka, M., Wakasugi, T., Hayashida, N., Matsubayashi, T., Zaita, N., Chunwongse, J., Obokata, J., Yamaguchi‐Shinozaki, K., Ohto, C., Torazawa, K., Meng, B.Y., Sugita, M., Deno, H., Kamogashira, T., Yamada, K., Kusuda, J., Takaiwa, F., Kato, A., Tohdoh, N., Shimada, H., and Sugiura, M.
- Abstract
The complete nucleotide sequence (155 844 bp) of tobacco (Nicotiana tabacumvar. Bright Yellow 4) chloroplast DNA has been determined. It contains two copies of an identical 25 339 bp inverted repeat, which are separated by a 86 684 bp and a 18 482 bp single‐copy region. The genes for 4 different rRNAs, 30 different tRNAs, 39 different proteins and 11 other predicted protein coding genes have been located. Among them, 15 genes contain introns. Blot hybridization revealed that all rRNA and tRNA genes and 27 protein genes so far analysed are transcribed in the chloroplast and that primary transcripts of the split genes hitherto examined are spliced. Five sequences coding for proteins homologous to components of the respiratory‐chain NADH dehydrogenase from human mitochondria have been found. The 30 tRNAs predicted from their genes are sufficient to read all codons if the ‘two out of three’ and ‘U:N wobble’ mechanisms operate in the chloroplast. Two sequences which autonomously replicate in yeast have also been mapped. The sequence and expression analyses indicate both prokaryotic and eukaryotic features of the chloroplast genes.
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- 1986
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20. Molecular cloning of a novel human CC chemokine EBI1-ligand chemokine that is a specific functional ligand for EBI1, CCR7.
- Author
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Yoshida, R, Imai, T, Hieshima, K, Kusuda, J, Baba, M, Kitaura, M, Nishimura, M, Kakizaki, M, Nomiyama, H, and Yoshie, O
- Abstract
By searching the expressed sequence tag (EST) data base, we identified partial cDNA sequences encoding a novel human CC chemokine. We determined the complete cDNA sequence that encodes a highly basic polypeptide of a total 98 amino acids with 20 to 30% identity to other human CC chemokines. We termed this novel chemokine from EBI1-Ligand Chemokine as ELC (see below). The ELC mRNA was most strongly expressed in the thymus and lymph nodes. Recombinant ELC protein was expressed as a fusion protein with the Flag tag (ELC-Flag). For receptor-binding assays, recombinant ELC protein fused with the secreted form of alkaline phosphatase (SEAP) was used. By stably expressing five CC chemokine receptors (CCR1 to 5) and five orphan receptors, ELC-SEAP was found to bind specifically to an orphan receptor EBI1. Only ELC-Flag, but not MCP-1, MCP-2, MCP-3, eotaxin, MIP-1alpha, MIP-1beta, RANTES (regulated on activation normal T cell expressed and secreted), thymus and activation-regulated chemokine (TARC), or liver and activation-regulated chemokine (LARC), competed with ELC-SEAP for EBI1. ELC-Flag-induced transient calcium mobilization and chemotactic responses in EBI1-transfected cells. ELC-Flag also induced chemotaxis in HUT78 cells expressing endogenous EBI1 at high levels. By somatic hybrid and radiation hybrid analyses, the gene for ELC (SCYA19) was mapped to chromosome 9p13 instead of chromosome 17q11.2 where the genes for CC chemokines are clustered. Taken together, ELC is a highly specific ligand for EBI1, which is known to be expressed in activated B and T lymphocytes and strongly up-regulated in B cells infected with Epstein-Barr virus and T cells infected with herpesvirus 6 or 7. ELC and EBI1 may thus play roles in migration and homing of normal lymphocytes, as well as in pathophysiology of lymphocytes infected with these herpesviruses. We propose EBI1 to be designated as CCR7.
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- 1997
21. Cloning and chromosomal localization of a paralog and a mouse homolog of the human transaldolase gene
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Kusuda, J., Hirai, M., Toyoda, A., Tanuma, R., Nomura-Kitabayashi, A., and Hashimoto, K.
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- 1998
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22. Human rasGTPase-activating protein (human counterpart of GAP1^m): sequence of the cDNA, primary structure of the protein, production and chromosomal localization
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Kobayashi, M., Masui, T., Kusuda, J., Kameoka, Y., Hashimoto, K., and Iwashita, S.
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- 1996
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23. Identification of the gene-richest bands in human chromosomes
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Saccone, S., Caccio, S., Kusuda, J., Andreozzi, L., and Bernardi, G.
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- 1996
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24. Molecular cloning of a novel human CC chemokine liver and activation-regulated chemokine (LARC) expressed in liver. Chemotactic activity for lymphocytes and gene localization on chromosome 2.
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Hieshima, K, Imai, T, Opdenakker, G, Van Damme, J, Kusuda, J, Tei, H, Sakaki, Y, Takatsuki, K, Miura, R, Yoshie, O, and Nomiyama, H
- Abstract
Partial overlapping cDNA sequences likely to encode a novel human CC chemokine were identified from the GenBank Expressed Sequence Tag data base. Using these sequences, we isolated full-length cDNA encoding a protein of 96 amino acid residues with 20-28% identity to other CC chemokines. By Northern blot, this chemokine was mainly expressed in liver among various tissues and strongly induced in several human cell lines by phorbol myristate acetate. We thus designated this chemokine as LARC from Liver and Activation-Regulated Chemokine. We mapped the LARC gene close to the chromosomal marker D2S159 at chromosome 2q33-q37 by somatic cell and radiation hybrid mappings and isolated two yeast artificial chromosome clones containing the LARC gene from this region. To prepare LARC, we subcloned the cDNA into a baculovirus vector and expressed it in insect cells. The secreted protein started at Ala-27 and was significantly chemotactic for lymphocytes. At a concentration of 1 microg/ml, it also showed a weak chemotactic activity for granulocytes. Unlike other CC chemokines, however, LARC was not chemotactic for monocytic THP-1 cells or blood monocytes. LARC tagged with secreted alkaline phosphatase-(His)6 bound specifically to lymphocytes, the binding being competed only by LARC and not by other CC or CXC chemokines. Scatchard analysis revealed a single class of receptors for LARC on lymphocytes with a Kd of 0.4 nM and 2100 sites/cell. Collectively, LARC is a novel CC chemokine, which may represent a new group of CC chemokines localized on chromosome 2.
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- 1997
25. Organization and nucleotide sequence of a densovirus genome imply a host-dependent evolution of the parvoviruses
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Bando, H, Kusuda, J, Gojobori, T, Maruyama, T, and Kawase, S
- Abstract
The genome structure of a densovirus from a silkworm was determined by sequencing more than 85% of the complete genome DNA. This is the first report of the genome organization of an insect parvovirus deduced from the DNA sequence. In the viral genome, two large open reading frames designated 1 and 2 and one smaller open reading frame designated 3 were identified. The first two open reading frames shared the same strand, while the third was found in the complementary sequence. Computer analysis suggested that open reading frame 2 may encode all four structural proteins. The genome organization and a part of the nucleotide sequence were conserved among the insect densovirus, rodent parvoviruses, and a human dependovirus. These viruses may have diverged from a common ancestor.
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- 1987
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26. cDNA cloning and chromosome mapping of the mouse casein kinase I epsilon gene (Csnk1e).
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Kusuda, J., Hirai, M., Tanuma, R., and Hashimoto, K.
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PROTEIN kinases , *MOLECULAR cloning , *GENE mapping , *SERINE , *CASEINS , *LABORATORY mice - Abstract
Casein kinase I (CKI) is a family of serine/threonine protein kinases found in all eukaryotes, first described over 20 years ago as having the ability to phosphorylate preferentially acidic proteins like casein and phosvitin using ATP, but not GTP. To date, seven isoforms of CKI, termed α, β, γl, γ2, γ3, &b.delta; and &b.epsi;, have been identified in higher eukaryotes. CKI has been implicated in a number of unrelated important biological functions in mouse.
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- 1999
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27. Cloning and chromosome mapping of the human casein kinase I γ3 gene (CSNK1G3).
- Author
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Kusuda, J., Hirai, M., Toyoda, A., Tanuma, R., and Hashimoto, K.
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CASEINS , *MOLECULAR cloning , *GENE mapping , *YEAST genetic engineering , *TESTIS , *HUMAN chromosomes - Abstract
The article presents information on cloning and chromosome mapping of the human casein kinase I &ggr;3 gene. Casein kinase I (CKI) is a ubiquitious Ser/Thr protein kinase found in the nuclei, cytoplasm and membrane fractions of eukaryotic cells. The yeast CKI gene, HRR25 is essential for growth and viability and is known to be involved in the regulation of DNA repair. cDNA for the CKI &ggr;3gene from a human testis cDNA library was isolated to establish the chromosomal locations of human CKI isoform genes.
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- 1998
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28. Collection of Macaca fascicularis cDNAs derived from bone marrow, kidney, liver, pancreas, spleen, and thymus
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Kameoka Yosuke, Kusuda Jun, Terao Keiji, Sugano Sumio, Suzuki Yutaka, Tanuma Reiko, Hirata Makoto, Osada Naoki, Hashimoto Katsuyuki, and Takahashi Ichiro
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Medicine ,Biology (General) ,QH301-705.5 ,Science (General) ,Q1-390 - Abstract
Abstract Background Consolidating transcriptome data of non-human primates is essential to annotate primate genome sequences, and will facilitate research using non-human primates in the genomic era. Macaca fascicularis is a macaque monkey that is commonly used for biomedical and ecological research. Findings We constructed cDNA libraries of Macaca fascicularis, derived from tissues obtained from bone marrow, liver, pancreas, spleen, and thymus of a young male, and kidney of a young female. In total, 5'-end sequences of 56,856 clones were determined. Including the previously established cDNA libraries from brain and testis, we have isolated 112,587 cDNAs of Macaca fascicularis, which correspond to 56% of the curated human reference genes. Conclusion These sequences were deposited in the public sequence database as well as in-house macaque genome database http://genebank.nibio.go.jp/qfbase/. These data will become valuable resources for identifying functional parts of the genome of macaque monkeys in future studies.
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- 2009
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29. Extensive expansion and diversification of the chemokine gene family in zebrafish: Identification of a novel chemokine subfamily CX
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Tanase Sumio, Kikuchi Yutaka, Yoshizawa Akio, Takegawa Sumio, Izawa Toshiaki, Otsuka-Ono Kaori, Kato-Unoki Yoko, Osada Naoki, Hieshima Kunio, Nomiyama Hisayuki, Miura Retsu, Kusuda Jun, Nakao Miki, and Yoshie Osamu
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Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background The chemokine family plays important roles in cell migration and activation. In humans, at least 44 members are known. Based on the arrangement of the four conserved cysteine residues, chemokines are now classified into four subfamilies, CXC, CC, XC and CX3C. Given that zebrafish is an important experimental model and teleost fishes constitute an evolutionarily diverse group that forms half the vertebrate species, it would be useful to compare the zebrafish chemokine system with those of mammals. Prior to this study, however, only incomplete lists of the zebrafish chemokine genes were reported. Results We systematically searched chemokine genes in the zebrafish genome and EST databases, and identified more than 100 chemokine genes. These genes were CXC, CC and XC subfamily members, while no CX3C gene was identified. We also searched chemokine genes in pufferfish fugu and Tetraodon, and found only 18 chemokine genes in each species. The majority of the identified chemokine genes are unique to zebrafish or teleost fishes. However, several groups of chemokines are moderately similar to human chemokines, and some chemokines are orthologous to human homeostatic chemokines CXCL12 and CXCL14. Zebrafish also possesses a novel species-specific subfamily consisting of five members, which we term the CX subfamily. The CX chemokines lack one of the two N-terminus conserved cysteine residues but retain the third and the fourth ones. (Note that the XC subfamily only retains the second and fourth of the signature cysteines residues.) Phylogenetic analysis and genome organization of the chemokine genes showed that successive tandem duplication events generated the CX genes from the CC subfamily. Recombinant CXL-chr24a, one of the CX subfamily members on chromosome 24, showed marked chemotactic activity for carp leukocytes. The mRNA was expressed mainly during a certain period of the embryogenesis, suggesting its role in the zebrafish development. Conclusion The phylogenic and genomic organization analyses suggest that a substantial number of chemokine genes in zebrafish were generated by zebrafish-specific tandem duplication events. During such duplications, a novel chemokine subfamily termed CX was generated in zebrafish. Only two human chemokines CXCL12 and CXCL14 have the orthologous chemokines in zebrafish. The diversification observed in the numbers and sequences of chemokines in the fish may reflect the adaptation of the individual species to their respective biological environment.
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- 2008
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30. Large-scale analysis of Macaca fascicularis transcripts and inference of genetic divergence between M. fascicularis and M. mulatta
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Sugano Sumio, Suzuki Yutaka, Hida Munetomo, Inoue Itsuro, Uno Yasuhiro, Tanuma Reiko, Hirata Makoto, Kameoka Yosuke, Hashimoto Katsuyuki, Osada Naoki, Terao Keiji, Kusuda Jun, and Takahashi Ichiro
- Subjects
Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Cynomolgus macaques (Macaca fascicularis) are widely used as experimental animals in biomedical research and are closely related to other laboratory macaques, such as rhesus macaques (M. mulatta). We isolated 85,721 clones and determined 9407 full-insert sequences from cynomolgus monkey brain, testis, and liver. These sequences were annotated based on homology to human genes and stored in a database, QFbase http://genebank.nibio.go.jp/qfbase/. Results We found that 1024 transcripts did not represent any public human cDNA sequence and examined their expression using M. fascicularis oligonucleotide microarrays. Significant expression was detected for 544 (51%) of the unidentified transcripts. Moreover, we identified 226 genes containing exon alterations in the untranslated regions of the macaque transcripts, despite the highly conserved structure of the coding regions. Considering the polymorphism in the common ancestor of cynomolgus and rhesus macaques and the rate of PCR errors, the divergence time between the two species was estimated to be around 0.9 million years ago. Conclusion Transcript data from Old World monkeys provide a means not only to determine the evolutionary difference between human and non-human primates but also to unveil hidden transcripts in the human genome. Increasing the genomic resources and information of macaque monkeys will greatly contribute to the development of evolutionary biology and biomedical sciences.
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- 2008
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31. Human chemokines fractalkine (SCYD1), MDC (SCYA22) and TARC (SCYA17) are clustered on chromosome 16q13<FOOTREF>[sup 1] </FOOTREF>.
- Author
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Nomiyama, H., Imai, T., Kusuda, J., Miura, R., Callen, D.F., and Yoshie, O.
- Subjects
GENE mapping ,CHEMOKINES ,HUMAN chromosomes ,POLYMERASE chain reaction ,SOMATIC hybrids ,GENES - Abstract
Abstract. Chemokines are a large family of small secreted proteins that regulate migration of white blood cells. Based on the arrangement of the first two of the four conserved cysteine residues, chemokines are classified into four subfamilies, CXC, CC, C and recently identified CX[sub 3] C. Most of the human genes for the CC chemokines are clustered at chromosome 17q11.2 (Naruse et al., 1996). Previously we identified a novel CC chemokine TARC (thymus and activation-regulated chemokine) (Imai et al., 1996) and localized its gene (SCYA17) at chromosome 16q13 (Nomiyama et al., 1996). Recently, Bazan et al. (1997) and Pan et al. (1997) mapped the CX[sub 3] C chemokine fractalkine/neurotactin gene (SCYD1) to chromosome 16. [ABSTRACT FROM AUTHOR]
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- 1998
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32. Cynomolgus monkey testicular cDNAs for discovery of novel human genes in the human genome sequence
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Terao Keiji, Hirai Momoki, Suto Yumiko, Hirata Makoto, Tanuma Reiko, Kusuda Jun, Hida Munetomo, Osada Naoki, Sugano Sumio, and Hashimoto Katsuyuki
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Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background In order to contribute to the establishment of a complete map of transcribed regions of the human genome, we constructed a testicular cDNA library for the cynomolgus monkey, and attempted to find novel transcripts for identification of their human homologues. Result The full-insert sequences of 512 cDNA clones were determined. Ultimately we found 302 non-redundant cDNAs carrying open reading frames of 300 bp-length or longer. Among them, 89 cDNAs were found not to be annotated previously in the Ensembl human database. After searching against the Ensembl mouse database, we also found 69 putative coding sequences have no homologous cDNAs in the annotated human and mouse genome sequences in Ensembl. We subsequently designed a DNA microarray including 396 non-redundant cDNAs (with and without open reading frames) to examine the expression of the full-sequenced genes. With the testicular probe and a mixture of probes of 10 other tissues, 316 of 332 effective spots showed intense hybridized signals and 75 cDNAs were shown to be expressed very highly in the cynomolgus monkey testis, but not ubiquitously. Conclusions In this report, we determined 302 full-insert sequences of cynomolgus monkey cDNAs with enough length of open reading frames to discover novel transcripts as human homologues. Among 302 cDNA sequences, human homologues of 89 cDNAs have not been predicted in the annotated human genome sequence in the Ensembl. Additionally, we identified 75 dominantly expressed genes in testis among the full-sequenced clones by using a DNA microarray. Our cDNA clones and analytical results will be valuable resources for future functional genomic studies.
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- 2002
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33. Identification of the gene-richest bands in human chromosomes [Gene 174 (1996) 85-94]
- Author
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Saccone, S., Caccio, S., Kusuda, J., Andreozzi, L., and Bernardi, G.
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- 1997
- Full Text
- View/download PDF
34. Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators.
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Fujimoto A, Totoki Y, Abe T, Boroevich KA, Hosoda F, Nguyen HH, Aoki M, Hosono N, Kubo M, Miya F, Arai Y, Takahashi H, Shirakihara T, Nagasaki M, Shibuya T, Nakano K, Watanabe-Makino K, Tanaka H, Nakamura H, Kusuda J, Ojima H, Shimada K, Okusaka T, Ueno M, Shigekawa Y, Kawakami Y, Arihiro K, Ohdan H, Gotoh K, Ishikawa O, Ariizumi S, Yamamoto M, Yamada T, Chayama K, Kosuge T, Yamaue H, Kamatani N, Miyano S, Nakagama H, Nakamura Y, Tsunoda T, Shibata T, and Nakagawa H
- Subjects
- Adult, Aged, Aged, 80 and over, Carcinoma, Hepatocellular pathology, Carcinoma, Hepatocellular virology, Female, Genome, Viral genetics, Hepatitis B genetics, Hepatitis B virus genetics, Hepatitis C genetics, Humans, Liver Neoplasms pathology, Liver Neoplasms virology, Male, Middle Aged, Telomerase genetics, Virus Integration genetics, Carcinoma, Hepatocellular genetics, Chromatin genetics, Liver Neoplasms genetics, Mutation
- Abstract
Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related death worldwide. We sequenced and analyzed the whole genomes of 27 HCCs, 25 of which were associated with hepatitis B or C virus infections, including two sets of multicentric tumors. Although no common somatic mutations were identified in the multicentric tumor pairs, their whole-genome substitution patterns were similar, suggesting that these tumors developed from independent mutations, although their shared etiological backgrounds may have strongly influenced their somatic mutation patterns. Statistical and functional analyses yielded a list of recurrently mutated genes. Multiple chromatin regulators, including ARID1A, ARID1B, ARID2, MLL and MLL3, were mutated in ∼50% of the tumors. Hepatitis B virus genome integration in the TERT locus was frequently observed in a high clonal proportion. Our whole-genome sequencing analysis of HCCs identified the influence of etiological background on somatic mutation patterns and subsequent carcinogenesis, as well as recurrent mutations in chromatin regulators in HCCs.
- Published
- 2012
- Full Text
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35. High-resolution characterization of a hepatocellular carcinoma genome.
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Totoki Y, Tatsuno K, Yamamoto S, Arai Y, Hosoda F, Ishikawa S, Tsutsumi S, Sonoda K, Totsuka H, Shirakihara T, Sakamoto H, Wang L, Ojima H, Shimada K, Kosuge T, Okusaka T, Kato K, Kusuda J, Yoshida T, Aburatani H, and Shibata T
- Subjects
- Carcinoma, Hepatocellular virology, Exons, Gene Rearrangement, Genes, Tumor Suppressor, Genetic Variation, Genomic Library, Genomics, Hepacivirus pathogenicity, Humans, INDEL Mutation, Liver Neoplasms virology, Mutation, Oncogenes, Polymorphism, Single Nucleotide, Selection, Genetic, Carcinoma, Hepatocellular genetics, Liver Neoplasms genetics
- Abstract
Hepatocellular carcinoma, one of the most common virus-associated cancers, is the third most frequent cause of cancer-related death worldwide. By massively parallel sequencing of a primary hepatitis C virus-positive hepatocellular carcinoma (36× coverage) and matched lymphocytes (>28× coverage) from the same individual, we identified more than 11,000 somatic substitutions of the tumor genome that showed predominance of T>C/A>G transition and a decrease of the T>C substitution on the transcribed strand, suggesting preferential DNA repair. Gene annotation enrichment analysis of 63 validated non-synonymous substitutions revealed enrichment of phosphoproteins. We further validated 22 chromosomal rearrangements, generating four fusion transcripts that had altered transcriptional regulation (BCORL1-ELF4) or promoter activity. Whole-exome sequencing at a higher sequence depth (>76× coverage) revealed a TSC1 nonsense substitution in a subpopulation of the tumor cells. This first high-resolution characterization of a virus-associated cancer genome identified previously uncharacterized mutation patterns, intra-chromosomal rearrangements and fusion genes, as well as genetic heterogeneity within the tumor.
- Published
- 2011
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36. Collection of Macaca fascicularis cDNAs derived from bone marrow, kidney, liver, pancreas, spleen, and thymus.
- Author
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Osada N, Hirata M, Tanuma R, Suzuki Y, Sugano S, Terao K, Kusuda J, Kameoka Y, Hashimoto K, and Takahashi I
- Abstract
Background: Consolidating transcriptome data of non-human primates is essential to annotate primate genome sequences, and will facilitate research using non-human primates in the genomic era. Macaca fascicularis is a macaque monkey that is commonly used for biomedical and ecological research., Findings: We constructed cDNA libraries of Macaca fascicularis, derived from tissues obtained from bone marrow, liver, pancreas, spleen, and thymus of a young male, and kidney of a young female. In total, 5'-end sequences of 56,856 clones were determined. Including the previously established cDNA libraries from brain and testis, we have isolated 112,587 cDNAs of Macaca fascicularis, which correspond to 56% of the curated human reference genes., Conclusion: These sequences were deposited in the public sequence database as well as in-house macaque genome database http://genebank.nibio.go.jp/qfbase/. These data will become valuable resources for identifying functional parts of the genome of macaque monkeys in future studies.
- Published
- 2009
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37. Casein kinase I{gamma}2 down-regulates trafficking of ceramide in the synthesis of sphingomyelin.
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Tomishige N, Kumagai K, Kusuda J, Nishijima M, and Hanada K
- Subjects
- Amino Acid Sequence, Animals, CHO Cells, Casein Kinase I genetics, Cricetinae, Cricetulus, Endoplasmic Reticulum metabolism, Gene Knockdown Techniques, Golgi Apparatus metabolism, Humans, Isoenzymes genetics, Isoenzymes metabolism, Molecular Sequence Data, Protein Serine-Threonine Kinases genetics, Protein Serine-Threonine Kinases metabolism, Recombinant Fusion Proteins genetics, Recombinant Fusion Proteins metabolism, Sequence Alignment, Toxins, Biological metabolism, Casein Kinase I metabolism, Ceramides metabolism, Sphingomyelins biosynthesis
- Abstract
Intracellullar trafficking of lipids is fundamental to membrane biogenesis. For the synthesis of sphingomyelin, ceramide is transported from the endoplasmic reticulum to the Golgi apparatus by the ceramide transfer protein CERT. CERT is phosphorylated by protein kinase D at S132 and subsequently multiple times in a serine-repeat motif, resulting in its inactivation. However, the kinase involved in the multiple phosphorylation remains unclear. Here, we identify the gamma2 isoform of casein kinase I (CKIgamma2) as a kinase whose overexpression confers sphingomyelin-directed toxin-resistance to Chinese hamster ovary cells. In a transformant stably expressing CKIgamma2, CERT was hyperphosphorylated, and the intracellular trafficking of ceramide was retarded, thereby reducing de novo sphingomyelin synthesis. The reduction in the synthesis of sphingomyelin caused by CKIgamma2 was reversed by the expression of CERT mutants that are not hyperphosphorylated. Furthermore, CKIgamma2 directly phosphorylated CERT in vitro. Among three gamma isoforms, only knockdown of gamma2 isoform caused drastic changes in the ratio of hypo- to hyperphosphorylated form of CERT in HeLa cells. These results indicate that CKIgamma2 hyperphosphorylates the serine-repeat motif of CERT, thereby inactivating CERT and down-regulating the synthesis of sphingomyelin.
- Published
- 2009
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38. Extensive expansion and diversification of the chemokine gene family in zebrafish: identification of a novel chemokine subfamily CX.
- Author
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Nomiyama H, Hieshima K, Osada N, Kato-Unoki Y, Otsuka-Ono K, Takegawa S, Izawa T, Yoshizawa A, Kikuchi Y, Tanase S, Miura R, Kusuda J, Nakao M, and Yoshie O
- Subjects
- Animals, Base Sequence, Chemokines chemistry, Chemokines classification, Chemotaxis, Leukocyte drug effects, DNA Primers genetics, DNA, Complementary genetics, Gene Expression Regulation, Developmental, Humans, Phylogeny, Recombinant Proteins genetics, Recombinant Proteins pharmacology, Species Specificity, Terminology as Topic, Zebrafish growth & development, Zebrafish Proteins chemistry, Zebrafish Proteins classification, Chemokines genetics, Multigene Family, Zebrafish genetics, Zebrafish immunology, Zebrafish Proteins genetics
- Abstract
Background: The chemokine family plays important roles in cell migration and activation. In humans, at least 44 members are known. Based on the arrangement of the four conserved cysteine residues, chemokines are now classified into four subfamilies, CXC, CC, XC and CX3C. Given that zebrafish is an important experimental model and teleost fishes constitute an evolutionarily diverse group that forms half the vertebrate species, it would be useful to compare the zebrafish chemokine system with those of mammals. Prior to this study, however, only incomplete lists of the zebrafish chemokine genes were reported., Results: We systematically searched chemokine genes in the zebrafish genome and EST databases, and identified more than 100 chemokine genes. These genes were CXC, CC and XC subfamily members, while no CX3C gene was identified. We also searched chemokine genes in pufferfish fugu and Tetraodon, and found only 18 chemokine genes in each species. The majority of the identified chemokine genes are unique to zebrafish or teleost fishes. However, several groups of chemokines are moderately similar to human chemokines, and some chemokines are orthologous to human homeostatic chemokines CXCL12 and CXCL14. Zebrafish also possesses a novel species-specific subfamily consisting of five members, which we term the CX subfamily. The CX chemokines lack one of the two N-terminus conserved cysteine residues but retain the third and the fourth ones. (Note that the XC subfamily only retains the second and fourth of the signature cysteines residues.) Phylogenetic analysis and genome organization of the chemokine genes showed that successive tandem duplication events generated the CX genes from the CC subfamily. Recombinant CXL-chr24a, one of the CX subfamily members on chromosome 24, showed marked chemotactic activity for carp leukocytes. The mRNA was expressed mainly during a certain period of the embryogenesis, suggesting its role in the zebrafish development., Conclusion: The phylogenic and genomic organization analyses suggest that a substantial number of chemokine genes in zebrafish were generated by zebrafish-specific tandem duplication events. During such duplications, a novel chemokine subfamily termed CX was generated in zebrafish. Only two human chemokines CXCL12 and CXCL14 have the orthologous chemokines in zebrafish. The diversification observed in the numbers and sequences of chemokines in the fish may reflect the adaptation of the individual species to their respective biological environment.
- Published
- 2008
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39. Intraoperative radiotherapy for oncological and function-preserving surgery in patients with advanced lower rectal cancer.
- Author
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Masaki T, Takayama M, Matsuoka H, Abe N, Ueki H, Sugiyama M, Tonari A, Kusuda J, Mizumoto S, and Atomi Y
- Subjects
- Aged, Autonomic Nervous System radiation effects, Combined Modality Therapy, Disease-Free Survival, Female, Humans, Japan, Kaplan-Meier Estimate, Lymphatic Metastasis pathology, Male, Middle Aged, Neoplasm Recurrence, Local etiology, Neoplasm Recurrence, Local mortality, Neoplasm Staging, Postoperative Complications etiology, Postoperative Complications mortality, Prognosis, Radiotherapy, Adjuvant, Rectal Neoplasms mortality, Rectal Neoplasms pathology, Risk Factors, Urinary Catheterization, Urination Disorders etiology, Autonomic Nervous System surgery, Intraoperative Care, Lymph Node Excision, Microsurgery, Pelvis innervation, Rectal Neoplasms radiotherapy, Rectal Neoplasms surgery, Rectum innervation
- Abstract
Background: Pelvic autonomic nerve preservation (PANP) with lateral lymph node dissection (LLND) has been introduced in rectal cancer surgery in Japan; however, its indication has not been standardized yet., Materials and Methods: Forty-four patients with advanced lower rectal cancer were randomized to either the standard treatment group (control group) or the intraoperative radiotherapy (IORT) group. All patients underwent potentially curative resection of the rectum with total mesorectal excision. The control group underwent bilateral LLND and limited PANP. The IORT group underwent bilateral LLND, complete PANP, and IORT. Patients allocated to the IORT group received IORT to the bilateral preserved pelvic nerve plexuses. Patients' clinicopathologic parameters, postoperative complications, voiding function, and prognosis were compared between the two groups., Results: Among 44 patients enrolled, three patients were excluded from the analysis, resulting in 19 patients in the IORT group and 22 patients in the control group. Patients' demographic and pathological parameters and postoperative complications were well balanced between the two groups. Oncological outcomes including overall and disease-free survival were also similar. Local recurrence was observed in one patient in each group. Among the 34 patients not complicated with intrapelvic abscess, the mean duration of urinary catheter indwelling was 8 days in the IORT group and 13 days in the control group (p = 0.055). In the long term, medication for urination was necessitated in four patients in the control group, whereas in none in the IORT group (p = 0.059)., Discussions: Oncological outcomes in the IORT group are equal to those in the control group, and voiding functions in the IORT group are superior to those in the control group. These results suggest that IORT may be useful to expand the indication of complete PANP with LLND for advanced lower rectal cancer.
- Published
- 2008
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40. Large-scale analysis of Macaca fascicularis transcripts and inference of genetic divergence between M. fascicularis and M. mulatta.
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Osada N, Hashimoto K, Kameoka Y, Hirata M, Tanuma R, Uno Y, Inoue I, Hida M, Suzuki Y, Sugano S, Terao K, Kusuda J, and Takahashi I
- Subjects
- Animals, DNA, Complementary chemistry, DNA, Complementary genetics, Databases, Genetic, Female, Gene Expression Profiling, Gene Library, Genetic Variation, Genome, Human genetics, Humans, Male, Models, Biological, Molecular Sequence Data, Oligonucleotide Array Sequence Analysis, Polymorphism, Genetic, Sequence Analysis, DNA, Transcription, Genetic, Evolution, Molecular, Genomics methods, Macaca fascicularis genetics, Macaca mulatta genetics
- Abstract
Background: Cynomolgus macaques (Macaca fascicularis) are widely used as experimental animals in biomedical research and are closely related to other laboratory macaques, such as rhesus macaques (M. mulatta). We isolated 85,721 clones and determined 9407 full-insert sequences from cynomolgus monkey brain, testis, and liver. These sequences were annotated based on homology to human genes and stored in a database, QFbase http://genebank.nibio.go.jp/qfbase/., Results: We found that 1024 transcripts did not represent any public human cDNA sequence and examined their expression using M. fascicularis oligonucleotide microarrays. Significant expression was detected for 544 (51%) of the unidentified transcripts. Moreover, we identified 226 genes containing exon alterations in the untranslated regions of the macaque transcripts, despite the highly conserved structure of the coding regions. Considering the polymorphism in the common ancestor of cynomolgus and rhesus macaques and the rate of PCR errors, the divergence time between the two species was estimated to be around 0.9 million years ago., Conclusion: Transcript data from Old World monkeys provide a means not only to determine the evolutionary difference between human and non-human primates but also to unveil hidden transcripts in the human genome. Increasing the genomic resources and information of macaque monkeys will greatly contribute to the development of evolutionary biology and biomedical sciences.
- Published
- 2008
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41. Mapping of chimpanzee full-length cDNAs onto the human genome unveils large potential divergence of the transcriptome.
- Author
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Sakate R, Suto Y, Imanishi T, Tanoue T, Hida M, Hayasaka I, Kusuda J, Gojobori T, Hashimoto K, and Hirai M
- Subjects
- 3' Untranslated Regions genetics, 5' Untranslated Regions genetics, Alu Elements, Animals, Chromosome Mapping, DNA Transposable Elements genetics, DNA, Complementary genetics, Humans, Genetic Variation, Genome, Human genetics, Pan troglodytes genetics, Transcription, Genetic
- Abstract
The genetic basis of the phenotypic difference between human and chimpanzee is one of the most actively pursued issues in current genomics. Although the genomic divergence between the two species has been described, the transcriptomic divergence has not been well documented. Thus, we newly sequenced and analyzed chimpanzee full-length cDNAs (FLcDNAs) representing 87 protein-coding genes. The number of nucleotide substitutions and sites of insertions/deletions (indels) was counted as a measure of sequence divergence between the chimpanzee FLcDNAs and the human genome onto which the FLcDNAs were mapped. Difference in transcription start/termination sites (TSSs/TTSs) and alternative splicing (AS) exons was also counted as a measure of structural divergence between the chimpanzee FLcDNAs and their orthologous human transcripts (NCBI RefSeq). As a result, we found that transposons (Alu) and repetitive segments caused large indels, which strikingly increased the average amount of sequence divergence up to more than 2% in the 3'-UTRs. Moreover, 20 out of the 87 transcripts contained more than 10% structural divergence in length. In particular, two-thirds of the structural divergence was found in the 3'-UTRs, and variable transcription start sites were conspicuous in the 5'-UTRs. As both transcriptional and translational efficiency were supposed to be related to 5'- and 3'-UTR sequences, these results lead to the idea that the difference in gene regulation can be a major cause of the difference in phenotype between human and chimpanzee.
- Published
- 2007
- Full Text
- View/download PDF
42. [Exposure dose, complication of radiation therapy for breast cancer].
- Author
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Tonari A, Takayama M, and Kusuda J
- Subjects
- Esophageal Neoplasms etiology, Esophagitis etiology, Female, Humans, Lung Neoplasms etiology, Radiation Dosage, Radiodermatitis etiology, Skin Neoplasms etiology, Breast Neoplasms radiotherapy, Radiotherapy adverse effects
- Published
- 2007
43. Aberrant termination of reproduction-related TMEM30C transcripts in the hominoids.
- Author
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Osada N, Hashimoto K, Hirai M, and Kusuda J
- Subjects
- Animals, Base Sequence, Evolution, Molecular, Gene Expression Profiling, Genetic Linkage, Humans, Male, Mice, Pan troglodytes genetics, Phylogeny, RNA, Messenger analysis, Hominidae genetics, Hominidae physiology, Infertility genetics, Membrane Glycoproteins genetics, Membrane Proteins genetics, Reproduction genetics
- Abstract
Finding genetic novelties that may contribute to human-specific physiology and diseases is a key issue of current biomedical studies. TMEM30C is a gene containing two transmembrane (TM) domains and homologous to the yeast CDC50 family, which is related to polarized cell division. It is conserved among mammals along with two other paralogs, TMEM30A and TMEM30B. We found that TMEM30C is expressed specifically in the testis of mammals, in contrast to the relatively wide expression distributions of the other paralogs. While macaques expressed two alternative splicing isoforms which include one or two TM domains, humans and chimpanzees predominantly expressed truncated transcripts because of the mutations in the splicing and/or poly(A) signal sites. The major transcript in humans harbored non-stop ORF (open reading frame) while the chimpanzee counterpart encoded a protein with one TM domain. The difference was due to the 1-bp indel upstream of the poly(A) signal site. In addition, both the hominoids expressed minor transcripts encoding short proteins with one TM domain. Phylogenetic analysis has showed the acceleration of amino acid substitution after the human and chimpanzee divergence, which may have been caused by a recent relaxation in functional constraints or positive selection on TMEM30C. Elucidating the precise reproductive function of TMEM30C in mammals will be important to the foundation of divergence in higher primates at a molecular level.
- Published
- 2007
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44. Identification of a novel CXCL1-like chemokine gene in macaques and its inactivation in hominids.
- Author
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Nomiyama H, Otsuka-Ono K, Miura R, Osada N, Terao K, Yoshie O, and Kusuda J
- Subjects
- Amino Acid Sequence, Animals, Chemokine CXCL1, Chemokines, CXC metabolism, Humans, Macaca fascicularis, Macaca mulatta, Molecular Sequence Data, Pan troglodytes, Chemokines, CXC antagonists & inhibitors, Chemokines, CXC genetics, Gene Silencing, Hominidae genetics, Macaca genetics
- Abstract
Chemokines are a rapidly evolving cytokine gene family. Because of various genome rearrangements after divergence of primates and rodents, humans and mice have different sets of chemokine genes, with humans having members outnumbering those of mice. Here, we report the occurrence of lineage-specific chemokine gene generation or inactivation events within primates. By using human chemokine sequences as queries, we isolated a novel cynomolgus macaque CXC chemokine cDNA. The encoded chemokine, termed CXCL1L (from CXCL1-like) showed the highest similarity to human CXCL1. A highly homologous gene was also found in the rhesus macaque genome. By comparing the genome organization of the major CXC chemokine clusters among the primates, we found that one copy of the duplicated CXCL1 genes turned into a pseudogene in the hominids, whereas the gene in macaques has been maintained as a functionally active CXCL1L. In addition, cynomolgus macaque was found to contain an additional CXC chemokine highly homologous to CXCL3, termed CXCL3L (from CXCL3-like). These results demonstrate the birth-and-death process of a new gene in association with gene duplication within the primates.
- Published
- 2007
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- View/download PDF
45. Substitution rate and structural divergence of 5'UTR evolution: comparative analysis between human and cynomolgus monkey cDNAs.
- Author
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Osada N, Hirata M, Tanuma R, Kusuda J, Hida M, Suzuki Y, Sugano S, Gojobori T, Shen CK, Wu CI, and Hashimoto K
- Subjects
- Animals, Amino Acid Substitution, Evolution, Molecular, Humans, 5' Untranslated Regions genetics, DNA, Complementary genetics, Genetic Variation, Macaca fascicularis genetics
- Abstract
The substitution rate and structural divergence in the 5'-untranslated region (UTR) were investigated by using human and cynomolgus monkey cDNA sequences. Due to the weaker functional constraint in the UTR than in the coding sequence, the divergence between humans and macaques would provide a good estimate of the nucleotide substitution rate and structural divergence in the 5'UTR. We found that the substitution rate in the 5'UTR (K5UTR) averaged approximately 10%-20% lower than the synonymous substitution rate (Ks). However, both the K5UTR and nonsynonymous substitution rate (Ka) were significantly higher in the testicular cDNAs than in the brain cDNAs, whereas the Ks did not differ. Further, an in silico analysis revealed that 27% (169/622) of macaque testicular cDNAs had an altered exon-intron structure in the 5'UTR compared with the human cDNAs. The fraction of cDNAs with an exon alteration was significantly higher in the testicular cDNAs than in the brain cDNAs. We confirmed by using reverse transcriptase-polymerase chain reaction that about one-third (6/16) of in silico "macaque-specific" exons in the 5'UTR were actually macaque specific in the testis. The results imply that positive selection increased K5UTR and structural alteration rate of a certain fraction of genes as well as Ka. We found that both positive and negative selection can act on the 5'UTR sequences.
- Published
- 2005
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46. Radiation-induced apoptosis of oligodendrocytes in the adult rat optic chiasm.
- Author
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Nagayama K, Kurita H, Nakamura M, Kusuda J, Tonari A, Takayama M, Fujioka Y, and Shiokawa Y
- Subjects
- Analysis of Variance, Animals, Cell Count, Corpus Callosum radiation effects, Dose-Response Relationship, Radiation, Immunohistochemistry methods, In Situ Nick-End Labeling, Male, Nucleoside-Triphosphatase metabolism, Oligodendroglia cytology, Optic Chiasm radiation effects, Radiation Injuries, Experimental metabolism, Rats, Rats, Wistar, Time Factors, Apoptosis radiation effects, Oligodendroglia radiation effects, Optic Chiasm cytology, Radiation, Radiation Injuries, Experimental pathology
- Abstract
Objectives: The present study characterized glial cell injury provoked in adult rat chiasm within 24 hours after a single, high-dose irradiation of 20 Gy., Methods: All chiasmal glial cells in a section were counted, and the percentage of TUNEL-positive glial cells exhibiting apoptotic morphology was defined as the apoptotic rate., Results: Numbers of apoptotic cells increased significantly (p<0.0001) from 3 to 8 hours after exposure, but returned to baseline levels by 24 hours. Little evidence of apoptosis was observed in non-irradiated chiasms. Similar patterns of increase in apoptotic rate were observed in the genu of the corpus callosum, but the extent was significantly lower (p=0.047) in the optic chiasm, with a maximal rate of 1.9%. Immunohistochemically, apoptotic cells were positive for CNP, a marker for oligodendrocytes., Discussion: These data indicate that chiasmal irradiation induces limited, but significant apoptotic depletion of the oligodendroglial population, and may participate in the development of radiation-induced optic neuropathy.
- Published
- 2005
- Full Text
- View/download PDF
47. Comparative DNA sequence analysis of mouse and human CC chemokine gene clusters.
- Author
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Nomiyama H, Egami K, Tanase S, Miura R, Hirakawa H, Kuhara S, Ogasawara J, Morishita S, Yoshie O, Kusuda J, and Hashimoto K
- Subjects
- Animals, Chromosome Mapping, Chromosomes, Artificial, Bacterial genetics, Chromosomes, Human, Pair 17 genetics, Evolution, Molecular, Humans, Mice, Molecular Sequence Data, Phylogeny, Sequence Analysis, DNA, Species Specificity, Chemokines, CC genetics, DNA genetics, Multigene Family
- Abstract
The CC chemokines are a closely related subfamily of the chemokine superfamily. Most of the CC chemokine genes form a cluster on chromosome 11 in mice and chromosome 17 in humans. To date, 11 and 16 functional genes have been localized within the mouse and human clusters, respectively. Notably, some of the genes within these clusters appear to have no counterparts between the two species, and the orthologous relationships of some of the genes are difficult to establish solely on the basis of amino acid similarity. In this study, we have taken a comparative genomic approach to reveal some of the features that may be involved in the dynamic evolution of these gene clusters. We sequenced a 122-kb region containing five chemokine genes of the mouse CC cluster. This mouse sequence was combined with those determined by the Mouse Genome Sequencing Project, and the entire sequence of the mouse CC cluster was compared with that of the corresponding cluster in the human genome by percent identity plot and dot-plot analyses. Although no additional chemokine genes have been found in these clusters, our analysis has revealed that numerous gene rearrangements have occurred even after the diversification of rodents and primates, resulting in several species-specific chemokine genes and pseudogenes. In addition, phylogenetic analysis and comparison of the genomic sequences unambiguously identified the orthologous relationships of some of the chemokine genes in the mouse and human CC gene clusters.
- Published
- 2003
- Full Text
- View/download PDF
48. Cynomolgus monkey testicular cDNAs for discovery of novel human genes in the human genome sequence.
- Author
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Osada N, Hida M, Kusuda J, Tanuma R, Hirata M, Suto Y, Hirai M, Terao K, Sugano S, and Hashimoto K
- Abstract
Background: In order to contribute to the establishment of a complete map of transcribed regions of the human genome, we constructed a testicular cDNA library for the cynomolgus monkey, and attempted to find novel transcripts for identification of their human homologues., Result: The full-insert sequences of 512 cDNA clones were determined. Ultimately we found 302 non-redundant cDNAs carrying open reading frames of 300 bp-length or longer. Among them, 89 cDNAs were found not to be annotated previously in the Ensembl human database. After searching against the Ensembl mouse database, we also found 69 putative coding sequences have no homologous cDNAs in the annotated human and mouse genome sequences in Ensembl. We subsequently designed a DNA microarray including 396 non-redundant cDNAs (with and without open reading frames) to examine the expression of the full-sequenced genes. With the testicular probe and a mixture of probes of 10 other tissues, 316 of 332 effective spots showed intense hybridized signals and 75 cDNAs were shown to be expressed very highly in the cynomolgus monkey testis, but not ubiquitously., Conclusions: In this report, we determined 302 full-insert sequences of cynomolgus monkey cDNAs with enough length of open reading frames to discover novel transcripts as human homologues. Among 302 cDNA sequences, human homologues of 89 cDNAs have not been predicted in the annotated human genome sequence in the Ensembl. Additionally, we identified 75 dominantly expressed genes in testis among the full-sequenced clones by using a DNA microarray. Our cDNA clones and analytical results will be valuable resources for future functional genomic studies.
- Published
- 2002
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- View/download PDF
49. Search for genes positively selected during primate evolution by 5'-end-sequence screening of cynomolgus monkey cDNAs.
- Author
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Osada N, Kusuda J, Hirata M, Tanuma R, Hida M, Sugano S, Hirai M, and Hashimoto K
- Subjects
- Animals, Cytochrome c Group genetics, DNA, Complementary chemistry, DNA, Complementary genetics, Databases, Nucleic Acid, Electron Transport Complex IV genetics, Genes genetics, Molecular Sequence Data, Phylogeny, Sequence Analysis, DNA, Evolution, Molecular, Macaca fascicularis genetics, Primates genetics, Selection, Genetic
- Abstract
It is possible to assess positive selection by using the ratio of K(a) (nonsynonymous substitutions per plausible nonsynonymous sites) to K(s) (synonymous substitutions per plausible synonymous sites). We have searched candidate genes positively selected during primate evolution by using 5'-end sequences of 21,302 clones derived from cynomolgus monkey (Macaca fascicularis) brain cDNA libraries. Among these candidates, 10 genes that had not been shown by previous studies to undergo positive selection exhibited a K(a)/K(s) ratio > 1. Of the 10 candidate genes we found, 5 were included in the mitochondrial respiratory enzyme complexes, suggesting that these nuclear-encoded genes coevolved with mitochondrial-encoded genes, which have high mutation rates. The products of other candidate genes consisted of a cell-surface protein, a member of the lipocalin family, a nuclear transcription factor, and hypothetical proteins.
- Published
- 2002
- Full Text
- View/download PDF
50. Prediction of unidentified human genes on the basis of sequence similarity to novel cDNAs from cynomolgus monkey brain.
- Author
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Osada N, Hida M, Kusuda J, Tanuma R, Hirata M, Hirai M, Terao K, Suzuki Y, Sugano S, and Hashimoto K
- Subjects
- Animals, DNA, Complementary chemistry, DNA, Complementary genetics, Gene Expression Regulation, Genes genetics, Genome, Human, Humans, Reverse Transcriptase Polymerase Chain Reaction, Sequence Alignment methods, Sequence Analysis, DNA, Software, Brain metabolism, Macaca fascicularis genetics, RNA genetics
- Abstract
Background: The complete assignment of the protein-coding regions of the human genome is a major challenge for genome biology today. We have already isolated many hitherto unknown full-length cDNAs as orthologs of unidentified human genes from cDNA libraries of the cynomolgus monkey (Macaca fascicularis) brain (parietal lobe and cerebellum). In this study, we used cDNA libraries of three other parts of the brain (frontal lobe, temporal lobe and medulla oblongata) to isolate novel full-length cDNAs., Results: The entire sequences of novel cDNAs of the cynomolgus monkey were determined, and the orthologous human cDNA sequences were predicted from the human genome sequence. We predicted 29 novel human genes with putative coding regions sharing an open reading frame with the cynomolgus monkey, and we confirmed the expression of 21 pairs of genes by the reverse transcription-coupled polymerase chain reaction method. The hypothetical proteins were also functionally annotated by computer analysis., Conclusions: The 29 new genes had not been discovered in recent explorations for novel genes in humans, and the ab initio method failed to predict all exons. Thus, monkey cDNA is a valuable resource for the preparation of a complete human gene catalog, which will facilitate post-genomic studies.
- Published
- 2002
- Full Text
- View/download PDF
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