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Biomedical subjects

N Shimizu

Publications and source records attributed to N Shimizu.

At least 163 records · Page 9Linked to original sources
PubMed2000

The DNA sequence of human chromosome 21.

Chromosome 21 is the smallest human autosome. An extra copy of chromosome 21 causes Down syndrome, the most frequent genetic cause of significant mental retardation, which affects up to 1 in 700 live births. Several anonymous loci for monogenic disorders and predispositions for common complex disorders have also been mapped to this chromosome, and loss of heterozygosity has been observed in regions associated with solid tumours. Here we report the sequence and gene catalogue of the long arm of chromosome 21. We have sequenced 33,546,361 base pairs (bp) of DNA with very high accuracy, the largest contig being 25,491,867 bp. Only three small clone gaps and seven sequencing gaps remain, comprising about 100 kilobases. Thus, we achieved 99.7% coverage of 21q. We also sequenced 281,116 bp from the short arm. The structural features identified include duplications that are probably involved in chromosomal abnormalities and repeat structures in the telomeric and pericentromeric regions. Analysis of the chromosome revealed 127 known genes, 98 predicted genes and 59 pseudogenes.

Base Sequence↗
PubMed2000

Isolation and initial characterization of a novel zinc finger gene, DNMT3L, on 21q22.3, related to the cytosine-5-methyltransferase 3 gene family.

We have isolated the DNMT3L gene that is related to the cytosine-5-methyltransferase 3 (DNMT3) family. The gene is located on chromosome 21q22.3 between the AIRE and the KIAA0653 genes and spans approximately 16 kb of genomic sequence. The encoded protein of 387 amino acids has a cysteine-rich region containing a novel-type zinc finger domain that is conserved in DNMT3A and DNMT3B but also in ATRX, a member of the SNF2 protein family. The novel domain, called an ADD (ATRX, DNMT3, DNMT3L)-type zinc finger, contains two subparts: a C2C2 and an imperfect PHD zinc finger. Expression of the DNMT3L mRNA was not detectable by Northern blotting; however, RT-PCR amplification revealed that it is expressed at low levels in several tissues including testis, ovary, and thymus.

Amino Acid Sequence↗
PubMed2000

Criteria for gene identification and features of genome organization: analysis of 6.5 Mb of DNA sequence from human chromosome 21.

To establish criteria for and the limitations of novel gene identification, to identify novel genes of potential relevance to Down Syndrome and to investigate features of genome organization, 6. 550kb. In total, 41 novel gene models were predicted, and for a subset of these, RT-PCR experiments helped to verify and refine the models, and were used to assess expression in early development and in adult brain regions of potential relevance to Down syndrome. Results suggest generally low and/or restricted patterns of expression, and also reveal examples of complex alternative processing, especially in brain, that may have important implications for regulation of protein function. Analysis of complete gene structures of the known genes identified a number of very large introns, a number of very short intergenic distances, and at least one potentially bi-directional promoter. At least 3/4 of known genes and 1/2 of predicted genes are associated with CpG islands. For novel genes, three cases of overlapping genes are predicted. Results of these analyses illustrate some of the complexities inherent in mammalian genome organization and some of the limitations of current sequence analysis technologies. They also doubled the number of potential genes within the region.

Adult↗
PubMed2000

Synthesis of a model compound related to an anti-ulcer pectic polysaccharide.

A stereocontrolled synthesis of the model compound for an anti-ulcer active polysaccharide (Bupleuran 2IIc) is described. Glycosidation of the disaccharide acceptor, 2-O-acetyl-3-O-benzyl-4-O-(p-methoxybenzyl)-alpha-L-rhamnopyranosyl-(1-- >4)-2,3,6-tri-O-benzyl-alpha-D-galactopyranosyl trichloroacetimidate, with the disaccharide receptor, allyl 3,4-di-O-benzyl-alpha-L-rhamnopyranosyl-(1-->4)-2,3,6-tri-O-benzyl-beta- D-galactopyranoside, using silver triflate (AgOTf) as a promoter gave the desired tetrasaccharide derivative, which was transformed into the acidic tetrasaccharide, corresponding to a segment of the rhamnogalacturonan (Bupleuran 2IIc) polysaccharide, propyl alpha-L-Rha-(1-->4)-alpha-D-GalA-(1-->2)-alpha-L-Rha-(1-->4)-beta-D-GalA , via removal of the corresponding ether and ester protecting groups, followed by oxidation.

Anti-Ulcer Agents↗
PubMed2000

The human homolog of insect-derived growth factor, CECR1, is a candidate gene for features of cat eye syndrome.

Cat eye syndrome (CES) is a developmental disorder with multiple organ involvement, associated with the duplication of a 2-Mb region of 22q11.2. Using exon trapping and genomic sequence analysis, we have isolated and characterized a gene, CECR1, that maps to this critical region. The protein encoded by CECR1 is similar to previously identified novel growth factors: IDGF from Sarcophaga peregrina (flesh fly) and MDGF from Aplysia californica (sea hare). The CECR1 gene is alternatively spliced and expressed in numerous tissues, with most abundant expression in human adult heart, lung, lymphoblasts, and placenta as well as fetal lung, liver, and kidney. In situ hybridization of a human embryo shows specific expression in the outflow tract and atrium of the developing heart, the VII/VIII cranial nerve ganglion, and the notochord. The location of this gene in the CES critical region and its embryonic expression suggest that the overexpression of CECR1 may be responsible for at least some features of CES, particularly the heart defects.

Abnormalities, Multiple↗
PubMed2000

Eradication diminishes enhancing effects of Helicobacter pylori infection on glandular stomach carcinogenesis in Mongolian gerbils.

To investigate the nature of the link between Helicobacter pylori (Hp) infection and stomach carcinogenesis, a study of the glandular stomach of Mongolian gerbils (MGs) was performed. MGs were treated with N-methyl-N-nitrosourea (MNU), followed by inoculation with Hp (groups 1 and 2) or without Hp (group 3), or infected with Hp (groups 4 and 5) or inoculation without Hp (group 6) followed by MNU administration. At week 21, the animals in groups 2 and 5 underwent an eradication procedure. At week 50, the incidences of adenocarcinomas in group 1 (15 of 23) and group 4 (9 of 26) were significantly higher than in group 3 (1 of 15) and group 6 (1 of 18), respectively. Moreover, those in group 2 (5 of 24) and group 5 (2 of 22) were lower than in groups 1 and 4, respectively. This study shows that Hp eradication may be useful as a prevention approach against stomach cancer.

Adenocarcinoma↗
PubMed2000

Selective elimination of acentric double minutes from cancer cells through the extrusion of micronuclei.

Several lines of evidences from us or other authors had shown that tumor cells revert their phenotypes and differentiate by the elimination of oncogenes amplified on the acentric double minutes (DMs). The selective incorporation of DMs into the cytoplasmic micronuclei was thought to be involved in this elimination, however, the mechanism by which the content of micronuclei was eliminated from the cells remains to be discovered. In this report, we show the finding and the characterization of the extruded micronuclei in the culture fluid of human COLO 320DM tumor line, and suggest that the extrusion of micronuclei mediates the selective elimination of DMs. The extracellular micronuclei enriched with DMs had an apparently normal cytoplasmic membrane, decondensed chromatin and nuclear lamin protein, and their DNA did not suffer any extensive degradation. These characteristics were closely related to their cytoplasmic counterpart and clearly differentiated from the apoptotic bodies. We also developed a method for purifying the extracellular micronuclei. In this paper, the implications of the micronuclear extrusion are discussed.

Cell Nucleus↗
PubMed2000

Hox cluster genomics in the horn shark, Heterodontus francisci.

Reconstructing the evolutionary history of Hox cluster origins will lead to insights into the developmental and evolutionary significance of Hox gene clusters in vertebrate phylogeny and to their role in the origins of various vertebrate body plans. We have isolated two Hox clusters from the horn shark, Heterodontus francisci. These have been sequenced and compared with one another and with other chordate Hox clusters. The results show that one of the horn shark clusters (HoxM) is orthologous to the mammalian HoxA cluster and shows a structural similarity to the amphioxus cluster, whereas the other shark cluster (HoxN) is orthologous to the mammalian HoxD cluster based on cluster organization and a comparison with noncoding and Hox gene-coding sequences. The persistence of an identifiable HoxA cluster over an 800-million-year divergence time demonstrates that the Hox gene clusters are highly integrated and structured genetic entities. The data presented herein identify many noncoding sequence motifs conserved over 800 million years that may function as genetic control motifs essential to the developmental process.

Animals↗
PubMed2000

Mechanical stress enhances expression and production of plasminogen activator in aging human periodontal ligament cells.

Plasminogen activator (PA) converts plasminogen to plasmin, and plasmin activates the kinin cascade and latent extracellular matrix metalloproteases. The periodontal ligament serves to anchor the tooth to the alveolus and functions as a cushion between these hard tissues to migrate occlusal force during mastication. We reported previously that repeated mechanical tension force (MTF) as an experimental model of a traumatic occlusion, increased PA activity in human periodontal ligament derived fibroblast (hPLF) cells. In this study, the influence of in vitro cellular aging on MTF-stimulated PA activity in hPLF cells was studied. Aged hPLF cells produced a significantly higher PA activity when compared with those of young hPLF cells in response to MTF in a time- and magnitude-dependent manner. tPA mRNA levels in aged cells were higher than those in young cells, whereas PAI-1 mRNA remained unchanged and uPA mRNA was not detected. Because MTF-stimulated PA activity from hPLF cells was increased by in vitro cellular aging, aging of the periodontal ligament may affect the severity of the inflammation and the degradation of the extracellular matrix of periodontal ligament tissue by producing a large amount of PA in response to excessive force such as a traumatic occlusion.

Bite Force↗
PubMed2000

Keio Mutation Database (KMDB) for human disease gene mutations.

A database of mutations in human disease-causing genes has been constructed and named as Keio Mutation Database (KMDB). This KMDB utilizes a database software called MutationView which was designed to compile various mutation data and to provide graphical presentation of data analysis. Currently, the KMDB accommodates mutation data of 38 different genes for 35 different diseases which are involved in eye, heart, ear and brain. These KMDBs are accessible through http://mutview.dmb.med.keio.ac.jp with advanced internet browsers.

Computer Graphics↗
PubMed2000

Effects of low-energy laser irradiation on bone remodeling during experimental tooth movement in rats.

BACKGROUND AND OBJECTIVE: Low-energy laser irradiation has many anabolic effects such as the acceleration of bone formation. However, its effects on tooth movement, performed by bone resorption and formation, have not been well characterized. STUDY DESIGN/MATERIALS AND METHODS: A total of 10 g of orthodontic force was applied to rat molars to cause experimental tooth movement. A Ga-Al-As diode laser was used to irradiate the area around the moved tooth, and after 12 days, the amount of tooth movement was measured. Calcein was injected subcutaneously to label the newly formed alveolar bone for quantitative analysis. Immunohistochemical staining of proliferating cell nuclear antigen was performed to evaluate cellular proliferation. TRAPase staining was also performed to facilitate the identification of osteoclasts. RESULTS: In the laser irradiation group, the amount of tooth movement was significantly greater (1. 3-fold) than that of the nonirradiation group in the end of the experiment. The amount of bone formation and rate of cellular proliferation in the tension side and the number of osteoclasts in the pressure side were all significantly increased in the irradiation group when compared with the nonirradiation group (P < 0. 01). CONCLUSION: These findings suggest that low-energy laser irradiation can accelerate tooth movement accompanied with alveolar bone remodeling.

Alveolar Process↗
PubMed2000

Interruption of NFkappaB-STAT1 signaling mediates EGF-induced cell-cycle arrest.

It is known that EGF induces the cell-cycle arrest in A431 cells that possess high numbers of EGF receptors and it was previously suggested that p21/WAF1 protein was a major effector molecule of the EGF-mediated cell-cycle arrest of A431 cells. Here, we further investigate this phenomenon using the decoy double-strand oligonucleotides for STAT-binding sequence (STAT decoy) and IkappaB, an inhibitor of the nuclear factor kappa B (NFkappaB). Addition of STAT decoy restored EGF-induced A431 cell-growth arrest. Interestingly, infection of adenovirus vectors to express IkappaB (AxIkappaBalphaDeltaN) as the inhibitor of NFkappaB also reversed the A431 cell-growth inhibition. The individual treatment of two inhibitors partially inhibited the WAF1 gene expression, whereas simultaneous treatment of two inhibitors exhibited more efficient inhibition. These observations suggest the activation of NFkappaB via IkappaB degradation and STAT1 via specific receptor kinase activity synergistically induce WAF1 gene expression in A431 cells. Thus, NFkappaB and STAT1 pathways mutually interact to play an important role in the EGF-induced intracellular reaction.

Carcinoma, Squamous Cell↗
PubMed2000

Eye disorder database "KMeyeDB".

The KMeyeDB (http://mutview.dmb.med.keio.ac.jp) has been developed as a database of mutations in human eye disorder genes using software called MutationView which provides graphical presentation of various data analysis. Here, we present several display windows from the KMeyeDB for data analysis of mutations in the RB-1 gene, which is responsible for the pathogenesis of retinoblastoma, a malignant tumor in the retina.

Amino Acid Sequence↗
PubMed2000

Novel mutations in the myocilin gene in Japanese glaucoma patients.

Myocilin is a gene responsible for juvenile onset primary open angle glaucoma (POAG) mapped as the GLC1A locus and, many mutations have been reported worldwide. Some mutations were found not only in patients with juvenile onset POAG, but also in patients with late onset POAG and in patients with normal tension glaucoma. To investigate the mutation prevalence in Japan, we performed a mutation analysis in 140 unrelated Japanese patients. We have identified the 10 sequence variants, of which four were highly probable for disease-causing mutations (Arg46ter, Arg158Gln, Ile360Asn, and Ala363Thr), and six polymorphisms (Gln19His, Arg76Lys, Asp208Glu, Val439Val, Arg470His, and Ala488Ala). Thus, myocilin mutations were found at the rate of 4/140 (2.9%) probands, similar to previous reports with other ethnic populations.

Adult↗
PubMed2000

Effects of cyclic polylactate (CPL) on the growth of cloned leukemic cells in vitro.

A novel supramolecular oligomer, cyclic polylactate (CPL), was first discovered in the culture medium of HeLa-S tumour cells, and was reported to inhibit the growth of FM3A ascites tumour cells by inhibiting the activities of pyruvate kinase (PK) and lactic dehydrogenase (LDH). We have now synthesized CPL-containing oligomers with polymerization numbers ranging from 9 to 19, by prolonged heating and rapid mixing of a carbohydrate compound of the L-lactic acid monomer (C(3)H(6)O(3)) under decreased pressure and have studied its effects on the growth of leukemic cells. Treatment with 0.02 mg/ml CPL inhibited the growth of HL60 and TF-1 cells, while the growth of K562 cells was inhibited by 0.2 mg/ml CPL. A concentration of 2 mg/ml CPL was required to inhibit granulocyte-macrophage progenitor cell (CFU-GM) and burst-forming unit erythroid (BFU-E) precursor colony formation among normal bone marrow cells. Furthermore, 7A6 antigen expression and DNA ladder formation were observed in leukemic cells cultured with CPL, indicating that CPL induces apoptotic changes in these cells. These findings suggest that CPL might be a useful chemotherapeutic agent for leukemia.

Antineoplastic Agents↗
PubMed2000

RNA and protein expression of the murine autoimmune regulator gene (Aire) in normal, RelB-deficient and in NOD mouse.

Mutations in the putative transcription factor autoimmune regulator (AIRE) gene are responsible for autoimmune polyendocrinopathy-candidiosis-ectodermal dystrophy (APECED; OMIM#240300), a monogenic recessively inherited disease characterized by destructive autoimmune diseases of the endocrine organs, chronic candidiosis of mucous membranes and ectodermal dystrophies. In this study the expression of murine homolog for AIRE protein, Aire, was detected in a fraction of thymic medullary epithelial cells. Subcellularly, in thymus the protein appears as concentrated into nuclear dot-like structures, whereas in transfected cells the protein is also bound along a cytosolic fibrillar network. By RT-PCR Aire mRNA was detected in thymus, lymph node, spleen and testis although the second round PCR amplified Aire specific band from most mouse tissues analyzed. Furthermore, the Aire mRNA was detected in dendritic cell (DC) populations isolated from thymus and spleen, representing both myeloid- and lymphoid-related lineages of DC. We also demonstrate that the Aire protein is absent in the thymus of RelB-deficient mouse and in NOD thymus most of the Aire positive cells showed an abnormal morphology. These results suggest that the Aire protein is associated with the normal development and/or action of a subset of thymic medullary stromal cells involved in tolerance induction.

Alternative Splicing↗
PubMed2000

PARKIN as a pathogenic gene for autosomal recessive juvenile parkinsonism.

Parkinson's disease is a common neurodegenerative disease with complex clinical features. Recently, we idenfied a novel gene named Parkin to be responsible for the pathogenesis of autosomal recessive juvenile parkinsonism (AR-JP). Various mutations were found in AR-JP patients of Japanese and other ethnic origins, providing a definitive evidence for the Parkin to be a causative gene for AR-JP. The predicted structure of Parkin protein and its mutation provide important clues for studying the functional role of the Parkin protein in leading to selective degeneration of nigral neurons in the brains of AR-JP patients.

Amino Acid Motifs↗