[Utility of genome databases: future perspectives].
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Animals↗
Biomedical subjects
S Tabata
Publications and source records attributed to S Tabata.
Structural analysis of Arabidopsis thaliana chromosome 5. VIII. Sequence features of the regions of 1,081,958 bp covered by seventeen physically assigned P1 and TAC clones.
A total of 17 Pl and TAC clones each representing an assigned region of chromosome 5 were isolated from P1 and TAC genomic libraries of Arabidopsis thaliana Columbia, and their nucleotide sequences were determined. The length of the clones sequenced in this study summed up to 1,081,958 bp. As we have previously reported the sequence of 9,072,622 bp by analysis of 125 P1 and TAC clones, the total length of the sequences of chromosome 5 determined so far is now 10,154,580 bp. The sequences were subjected to similarity search against protein and EST databases and analysis with computer programs for gene modeling. As a consequence, a total of 253 potential protein-coding genes with known or predicted functions were identified. The positions of exons which do not show apparent similarity to known genes were also assigned using computer programs for exon prediction. The average density of the genes identified in this study was 1 gene per 4277 bp. Introns were observed in 74% of the potential protein genes, and the average number per gene and the average length of the introns were 4.3 and 168 bp, respectively. The sequence data and gene information are available on the World Wide Web database KAOS (Kazusa Arabidopsis data Opening Site) at http://www.kazusa.or.jp/arabi/.
Arabidopsis↗
Structural analysis of Arabidopsis thaliana chromosome 5. VII. Sequence features of the regions of 1,013,767 bp covered by sixteen physically assigned P1 and TAC clones.
Sixteen P1 and TAC clones assigned to Arabidopsis thaliana chromosome 5 were sequenced, and their sequence features were analyzed using various computer programs. The total length of the sequences determined was 1,013,767 bp. Together with the nucleotide sequences of 109 clones previously reported, the regions of chromosome 5 sequenced so far now total 9,072,622 bp, which presumably covers approximately one-third of the chromosome. A similarity search against the reported gene sequences predicted the presence of a total of 225 protein-coding genes and/or gene segments in the newly sequenced regions, indicating an average gene density of one gene per 4.5 kb. Introns were identified in 72.4% of the potential protein genes for which the entire gene structure was predicted, and the average number per gene and the average length of the introns were 3.3 and 163 bp, respectively. These sequence features are essentially identical to those in the previously reported sequences. The sequence data and gene information are available on the World Wide Web database KAOS (Kazusa Arabidopsis data Opening Site) at http://www.kazusa.or.jp/arabi/.
Animals↗
Quantitative measurements for type 1 deiodinase messenger ribonucleic acid in human peripheral blood mononuclear cells: mechanism of the preferential increase of T3 in hyperthyroid Graves' disease.
To evaluate the regulatory mechanism of human Type 1 iodothyronine deiodinase (D1) gene expression, we measured the D1 mRNA levels in peripheral blood mononuclear cells (PBMC) in normal control subjects and in patients with Graves' disease. We used competitive reverse transcriptase-polymerase chain reaction with the deleted complimentary RNA of D1 as the standard for quantification. The D1 mRNA levels in PBMC were increased significantly in patients with Graves' disease compared with that in normal controls. There was a significant (p < 0.01) positive correlation (r=0.698) between D1 mRNA level and serum T3 concentration. When PBMC from the normal volunteers were cultured with various doses of T3, the quantity of D1 mRNA increased significantly in a dose-dependent manner. These findings indicate that PBMC D1 mRNA is actually up-regulated by T3 in vivo, and we postulate that a vicious spiral of increasing T3 and D1 is responsible for the exacerbation of thyrotoxicosis in hyperthyroid Graves' disease.
Gene Expression Regulation↗
A physical map of Arabidopsis thaliana chromosome 3 represented by two contigs of CIC YAC, P1, TAC and BAC clones.
We have constructed a physical map of Arabidopsis thaliana chromosome 3 by ordering the clones from CIC YAC, P1, TAC and BAC libraries using the sequences of a variety of genetic and EST markers and terminal sequences of clones. The markers used were 112 DNA markers, 145 YAC end sequences, and 156 end sequences of P1, TAC and BAC clones. The entire genome of chromosome 3, except for the centromeric and telomeric regions, was covered by two large contigs, 13.6 Mb and 9.2 Mb long. This physical map will facilitate map-based cloning experiments as well as genome sequencing of chromosome 3. The map and end sequence information are available on the KAOS (Kazusa Arabidopsis data Opening Site) web site at http://www.kazusa.or.jp/arabi/.
Arabidopsis↗
Structural analysis of Arabidopsis thaliana chromosome 5. VI. Sequence features of the regions of 1,367,185 bp covered by 19 physically assigned P1 and TAC clones.
Nineteen P1 and TAC clones, which have been mapped on the fine physical map of the Arabidopsis thaliana chromosome 5, were sequenced according to the shotgun-based strategy, and their structural features were analysed. The total length of the regions sequenced in this study was 1,367,185 bp. Combining this with the regions covered by 90 P1 and TAC clones previously reported, the total length of chromosome 5 sequenced to date becomes 8,058,855 bp. On the basis of similarity search against protein and EST databases and gene modeling with computer programs, a total of 330 potential protein-coding regions were identified, bringing an average density of the genes to approximately one gene per 4.1 kb. Introns were identified in 81.0% of the potential protein genes for which the entire gene structure was predicted, with an average number per gene of 4.2 and an average length of the introns of 180 bp. The RNA-coding genes identified were 9 tRNA genes corresponding to 8 amino acid species and 2 genes for U2 nuclear RNA. These sequence features are essentially identical to those in the previously reported sequences. The sequence data and gene information are available on the World Wide Web database KAOS (Kazusa Arabidopsis data Opening Site) at http://www.kazusa.or.jp/arabi/.
Arabidopsis↗
Structural analysis of Arabidopsis thaliana chromosome 5. V. Sequence features of the regions of 1,381,565 bp covered by twenty one physically assigned P1 and TAC clones.
The nucleotide sequences of 21 P1 and TAC clones which have been precisely localized to the fine physical map of the Arabidopsis thaliana chromosome 5, were determined, and their sequence features were analyzed. The total length of the regions sequenced in this study were 1,381,565 bp, bringing the total length of the chromosome 5 sequences determined so far to 6,691,670 bp together with the regions of the 69 clones previously reported. By computer-aided analyses including similarity search against protein and EST databases and gene modeling with computer programs, a total of 337 potential protein-coding genes and/or gene segments were identified on the basis of similarity to the reported gene sequences. An average density of the genes and/or gene segments thus assigned was 1 gene/4,100 bp. Introns were identified in 76.7% of the potential protein genes for which the entire gene structure were predicted, and the average number per gene and the average length of the introns were 3.9 and 176 bp, respectively. These sequence features are essentially identical to those in the previously reported sequences. The numbers of the Arabidopsis ESTs matched to each of the predicted genes have been counted to monitor the transcription level. The sequence data and gene information are available on the World Wide Web database KAOS (Kazusa Arabidopsis data Opening Site) at http:@www.kazusa.or.jp@arabi
Arabidopsis↗
Early development of the peripheral nervous system in a lancelet species.
The developmental pattern of the lancelet (amphioxus) peripheral nervous system from embryos to larvae has been studied by using wholemount immunostaining and transmission electron microscopy. The peripheral nerves first appeared on the anterior dorsal surface of the medulla at the middle neurula stage, when the anterior nerve cord was just closing. A single axon with a large growth cone was the progenitor of each nerve. The nerve roots adopted an asymmetric arrangement soon after. The first nerve, likely a pair of pure sensory nerves, sprouted from the anterior tip of the nerve cord. This nerve may be comparable topographically to the preoptic nerve (the posterior branch of the terminal nerve) in lungfishes. However, the neuron that first extends its axon was located in the medulla, as in the other posterior nerves. One of the extramedullary primary sensory neurons, the corpuscles of de Quatrefages, appeared in larvae with the mouth and two anterior gill pores. Their axons were seemingly fasciculated with the efferent axon of the first nerve. The second nerve, the most complex one to appear during embryonic and early larval development, innervated the preoral pit and the buccal region. The third and fourth nerves on the left side also innervated the buccal region. The larval innervation patterns in the anterior region differed from the adult organization, suggesting a segmental rearrangement of the nerve supply during development. There was no evidence to dichotomize the peripheral nerves into cranial and spinal nerves, as exist in vertebrates. These characteristics of the peripheral nervous system in the lancelet indicate that this animal has a rather derived or primitive developmental system of peripheral nerves, making the analysis of homology with vertebrates difficult.
Animals↗
Structural analysis of Arabidopsis thaliana chromosome 5. IV. Sequence features of the regions of 1,456,315 bp covered by nineteen physically assigned P1 and TAC clones.
Nineteen P1 and TAC clones, which have been precisely localized to the fine physical map of Arabidopsis thaliana chromosome 5, were newly sequenced, and their sequence features were analysed. The total length of the clones sequenced was 1,456,315 bp. Together with the previously reported sequences, the regions of chromosome 5 that have been sequenced to date is now 5,310,105 bp. When the sequences determined in this study were subjected to similarity search against protein and expressed sequence tag (EST) databases and analysis with computer programs for gene modeling, a total of 354 potential protein-coding genes and/or gene segments were identified. The average density of the assigned genes and/or gene segments was one gene per 4,114 bp. Introns were identified in 75% of the potential protein genes, and the average number per gene and the average length of the introns were 3.7 and 194 bp, respectively. These sequence features are essentially identical to those in the previously reported sequences. The numbers of the Arabidopsis ESTs matched to each of the predicted genes have been counted to monitor the transcription level. The sequence data and gene information are available on the World Wide Web database KAOS (the Kazusa Arabidopsis data Opening Site) at http://www.kazusa.or.jp/arabi/.
Arabidopsis↗
CyanoBase, a www database containing the complete nucleotide sequence of the genome of Synechocystis sp. strain PCC6803.
CyanoBase (http://www.kazusa.or.jp/cyano/) is a database containing genomic information on the cyanobacterium Synechocystis sp. strain PCC6803. It furnishes an annotation to each of the 3168 protein genes deduced from the entire nucleotide sequence of this genome. Information on the genome can be directly accessed through three different menus: a clickable physical map of the genome, a gene classification list, and a keyword search menu, all of which are accessible from the main page of the database. The entry page for a gene annotation contains the following information: the location of the gene on the genome, the nucleotide and deduced amino acid sequence of the gene, the result of a similarity search, and the classification of the deduced gene product according to its function. This page has reverse-links to the local physical map and gene classification list so that relevant genes can be searched in terms of their location on the genome and their function. In addition, the main page of CyanoBase provides engines for similarity searches between a query sequence and the entire genome sequence and for keyword searches, in addition to numerous links to pages containing related information.
Bacterial Proteins↗
Innervation of blood vessels in the rat incisor pulp: a scanning electron microscopic and immunoelectron microscopic study.
Although two types of nerve endings have been proposed to innervate blood vessels in the dental pulp, the precise innervation pattern is not well understood. This is mainly due to the lack of information regarding the positional relationships of nerve fibers with blood vessels at the electron microscopic level. The rat incisor pulp was investigated by scanning electron microscopy (SEM) after connective tissue digestion and by transmission electron microscopy after immunohistochemical localization with polyclonal anti-PGP 9.5 antibody. SEM specimens revealed that unmyelinated nerve fibers passed through the tunica adventitia of the blood vessel in the center of the pulp and that these fibers then entered the tunica media of the smaller arterioles. The nerve fibers divided into many collaterals, and these terminated on the surface of smooth muscle cells and endothelial cells. The fibers extended toward smaller vessels. The terminal fibers then reached the subodontoblastic capillary plexus and terminated on pericytes, while the odontoblastic capillary plexus had no direct innervation. In the pulpal venules, nerve fibers were located adjacent to the pericytes and endothelial cells, and they extended toward postcapillary venules. The same results were confirmed by immunoelectron microscopy. The present study demonstrated that in the rat incisor pulp the microvasculature as well as larger vessels were directly innervated by free nerve endings, suggesting that the local regulation of blood flow could take place not only at larger vessels but also at the level of the microvasculature in this tissue.
Animals↗
Maternal thyroid function in multiple pregnancy: the variable thyrotropic activity of human chorionic gonadotropin.
The present study was undertaken to evaluate thyroid function and thyrotropic action of hCG in multiple pregnancy. We examined serum samples from 9 multiple pregnant women (3 triplets and 6 twins) and 27 singleton pregnant women as control subjects. Serum hCG levels in multiple pregnancy were higher than those in singleton pregnancy in the second and third trimesters (P < 0.01). The mean free T3 and T4 concentrations in multiple pregnancy did not differ from those in singleton pregnancy in each trimester. Serum hCG levels showed a statistically significant positive correlation with free T3 and T4 levels in singleton pregnancy (P < 0.001). However, these correlations were not observed in multiple pregnancy. Thyroid stimulation activity (TSA) determined by cAMP accumulation in FRTL-5 cells in multiple pregnancy sera was significantly higher than that in singleton pregnancy in the first trimester (P < 0.05), but did not differ in the second and third trimesters. Moreover, TSA did not show any correlation with serum hCG levels in multiple pregnancy in contrast with the results in normal pregnancy. A bioactivity/immunoreactivity ratio of hCG in multiple pregnancy was lower than in singleton pregnancy in the second and third trimesters. The discrepancy between immunoreactivity and thyrotropic activity of hCG may be caused by the variable thyrotropic potency of heterogeneous hCG molecules in multiple pregnancy.
Adult↗
Induction of type 2 deiodinase activity by cyclic guanosine 3',5'-monophosphate in cultured rat glial cells.
We investigated the effects of cyclic guanosine 3',5'-monophosphate (cGMP) on type 2 iodothyronine deiodinase (D2) in cultured rat glial cells. Rat glial cells were cultured in Dulbecco's modified Eagle's medium supplemented with 15% fetal bovine serum. When cells were cultured in the presence of 8-bromo cGMP (8-Br cGMP), an analogue of cGMP, D2 activity was increased in a time- and concentration-dependent manner. Lineweaver-Burk plots revealed that the stimulation of D2 activity by 8-Br cGMP (10(-3) M) was associated with fivefold increase in maximum velocity but without a significant change in Michaelis-Menten constant, suggesting that cGMP increases D2 activity via new enzyme synthesis. Both atrial natriuretic peptide (ANP) and C-type natriuretic peptide (CNP) are well known to increase the intracellular cGMP level via their guanylate cyclase-linked receptors in rat glial cells. In the present study, ANP (10(-6) M) and CNP (10(-6) M) significantly increased the D2 activity in rat glial cells (1.9-fold [ANP] or 2.3-fold [CNP] compared with control activity, respectively). Northern blot analysis demonstrated that D2 mRNA level increased in the presence of 8-Br cGMP (10(-3) M), and reached a plateau (six-fold) after 4 hours of incubation. The increment of D2 mRNA level by 8-Br cGMP was comparable with the increase of the D2 activity by this agent. Our data suggest that cGMP induces rat D2 activity, at least in part, at the pretranslational level, and that ANP and CNP increase D2 activity most likely via their guanylate cyclase-linked receptors in rat glial cells.
8-Bromo Cyclic Adenosine Monophosphate↗
Blood vessels and nerve fibers in rat incisor pulp. Immunoelectron microscopic observation with anti-substance P antibody.
The distribution of nerve fibers with special reference to their positional relationship with blood vessels in the pulp of the rat mandibular incisor was investigated by light and electron microscopic immunohistochemistry using polyclonal anti-substance P antibody. In the center of the pulp, numerous immunoreactive nerve fibers with varicosities were found along larger blood vessels. In the periphery of the pulp, there were two layers of capillary plexus; an odontoblastic and a subodontoblastic. Many nerve fibers, showing varicosities, were located in the subodontoblastic region, and some revealed a close association with pericytes of capillaries of the subodontoblastic plexus. A few nerve fibers entered the odontoblast layer, but no nerve fibers were seen to be associated with the odontoblastic capillary plexus. The results suggest that the local regulation of blood flow takes place not only in larger blood vessels but also in the capillaries of the rat incisor pulp.
Animals↗
A novel polymorphism in the promoter region for the human osteocalcin gene: the possibility of a correlation with bone mineral density in postmenopausal Japanese women.
We present a polymorphism of the human osteocalcin gene (also known as BGP, for bone Gla protein) due to a 1 base pair (bp) substitution from cytosine to thymine at position 298 nucleotides (nt), which is at position 198 nt upstream from the BGP exon 1. This mutation was detected by single-strand conformation polymorphism analysis after polymerase chain reaction for the osteocalcin gene fragment (326 bp) and sequencing analysis. The cytosine/thymine polymorphism can be defined by restriction fragment length polymorphism analysis using a modified primer pair and the restriction endonuclease HindIII. The osteocalcin genotype was determined in 160 postmenopausal Japanese women (age 48-80 years). Osteocalcin alleles were designated according to the absence (H) or presence (h) of the HindIII restriction site. There were 12 HH, 49 Hh, and 99 hh individuals, and the allele frequencies were 22.8% for H and 77.2% for h. To determine if genetic variation influences bone mineral density (BMD) and thus can be a determinant of susceptibility to osteoporosis in older women, we examined the association of BMD with the osteocalcin genotypes found in the present study. The subjects with genotype HH had the smallest BMD and those with hh had the greatest BMD among subjects, but these differences did not reach statistical significance. The HindIII genotype showed a significant effect on the prevalence of osteopenia in the subjects, that is, women with genotype HH had a 5.74 times greater risk for osteopenia (p < 0.05) and those with genotype Hh had a 1.59 times greater risk than women with genotype hh. We identified the osteocalcin gene polymorphism, detected with the HindIII genotype, which was suggested to influence bone density and is a possible genetic marker for bone metabolism.
Aged↗
Occult papillary thyroid carcinoma in Hashimoto's thyroiditis presenting as a metastatic bone tumor.
Some occult thyroid carcinomas are hypothesized to regress and be eventually obliterated. We report here a patient whose condition supports this hypothesis. A 51-year-old male with primary hypothyroidism due to Hashimoto's thyroiditis suffered from a rib bone tumor. He had a diffuse goiter with no nodular lesion. Serum FT4 and TSH concentrations were 0.8 ng/dl and 36.4 microU/ml on taking 100 microg/day of T4. Anti-Tg- and -TPO-Ab were strongly positive (99 and 1380 U/ml). The iodine 123 scintigraphy demonstrated clear accumulation in the rib tumor, whereas the thyroid was scarcely visible. Biopsy of the rib tumor showed papillary proliferation of large atypical cells, which were immunohistochemically positive for thyroglobulin. Metastatic bone tumor of papillary thyroid carcinoma was therefore strongly suspected. He underwent a total thyroidectomy and the thyroid was stepwise sectioned completely at 3 mm intervals. The thyroid condition was diagnosed as Hashimoto's thyroiditis demonstrating diffuse and dense fibrosis, lymphocyte infiltration with lymphoid follicles and flattened atrophied follicles, but no carcinomatous foci were found. He was treated with I-131 and scintigraphy after the ingestion showed distinct accumulation in the rib tumors similar to that before thyroidectomy. No other abnormal uptake was observed. It is suggested that the primary occult thyroid papillary carcinoma regressed and was obliterated possibly by some immunologic or other host-resistance factors after it metastasized to the distant bone.
Bone Neoplasms↗
Cellular size of bone marrow cells from rats and beagle dogs.
The usefulness of cellular size measurement for differentiating erythroid and myeloid cells was investigated using rat and canine bone marrow film prepared by the Cytospin method and Wright-Giemsa staining. 1. In the erythroid series, basophilic and polychromatic erythroblasts were distinguishable in terms of cellular diameter; i.e., 99% of rat and 95% of canine polychromatic erythroblasts were distributed in a range < or = 9.5 microns, at which basophilic erythroblasts did not exist. 2. In the myeloid series, myelocytes and metamyelocytes were to some extent distinguishable by their diameters; in rats, myelocytes (75% of the population) were > or = 13.5 microns, and metamyelocytes (61%) < or = 11 microns; and in dogs, myelocytes (45%) were > or = 16 microns, and metamyelocytes (66%) < or = 12 microns. 3. With regard to the metamyelocytes and myelocytes existing in the same range, their nuclear sizes (width) allowed further differentiation; in rats, the nuclear width of myelocytes (87%) was > or = 5 microns, and that of metamyelocytes (84%) < 5 microns; and in dogs, myelocytes (96%) > or = 7 microns, and metamyelocytes (88%) < 7 microns. The present results indicate that cellular size, together with nuclear size, contribute to distinguish the active mitotic group from less- or non-mitotic group in erythroids and myeloids, thus being helpful for toxicological evaluation on chemicals.
Animals↗
A fine physical map of Arabidopsis thaliana chromosome 5: construction of a sequence-ready contig map.
A fine physical map of Arabidopsis thaliana chromosome 5 was constructed by ordering the clones from YAC, P1, TAC and BAC libraries of the genome using the sequences of a variety of genetic and EST markers and terminal sequences of clones. The markers used were 88 genetic markers, 13 EST markers, 87 YAC end probes, 100 YAC subclone end probes, and 390 end probes of P1, TAC and BAC clones. The entire genome of chromosome 5, except for the centromeric and telomeric regions, was covered by two large contigs 11.6 Mb and 14.2 Mb long separated by the centromeric region. The minimum tiling path of the chromosome was constituted by a total of 430 P1, TAC and BAC clones. The map information is available at the Web site http://www.kazusa.or.jp/arabi/.
Arabidopsis↗