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Biomedical subjects

K Shibata

Publications and source records attributed to K Shibata.

At least 55 records · Page 3Linked to original sources
PubMed2001

Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays.

We have systematically characterized gene expression patterns in 49 adult and embryonic mouse tissues by using cDNA microarrays with 18,816 mouse cDNAs. Cluster analysis defined sets of genes that were expressed ubiquitously or in similar groups of tissues such as digestive organs and muscle. Clustering of expression profiles was observed in embryonic brain, postnatal cerebellum, and adult olfactory bulb, reflecting similarities in neurogenesis and remodeling. Finally, clustering genes coding for known enzymes into 78 metabolic pathways revealed a surprising coordination of expression within each pathway among different tissues. On the other hand, a more detailed examination of glycolysis revealed tissue-specific differences in profiles of key regulatory enzymes. Thus, by surveying global gene expression by using microarrays with a large number of elements, we provide insights into the commonality and diversity of pathways responsible for the development and maintenance of the mammalian body plan.

Animals↗
PubMed2001

Functional annotation of a full-length mouse cDNA collection.

The RIKEN Mouse Gene Encyclopaedia Project, a systematic approach to determining the full coding potential of the mouse genome, involves collection and sequencing of full-length complementary DNAs and physical mapping of the corresponding genes to the mouse genome. We organized an international functional annotation meeting (FANTOM) to annotate the first 21,076 cDNAs to be analysed in this project. Here we describe the first RIKEN clone collection, which is one of the largest described for any organism. Analysis of these cDNAs extends known gene families and identifies new ones.

Animals↗
PubMed2001

Identification of a novel member of the snail/Gfi-1 repressor family, mlt 1, which is methylated and silenced in liver tumors of SV40 T antigen transgenic mice.

DNA methylation is the only known mechanism for an epigenetic genomic DNA modification that is capable of altering gene expression. A recent study reveals that the pattern of CpG island methylation is largely characteristic of tumor type, suggesting that distinct sets of genes are inactivated by methylation during development of each tumor type. We compared previously the methylation status between normal liver and liver tumors in SV40 T/t antigen transgenic mice (MT-D2 mice) using Restriction Landmark Genomic Scanning for Methylation (RLGS-M) and identified several loci/spots that appeared to be methylated frequently in liver tumors. One of these spots, B236, identified a locus on chromosome 12 (D12Ncvs7) syntenic with human 14q12-q21 that is frequently lost in certain human cancers. Shotgun sequencing of a bacterial artificial chro mosome clone containing this spot/locus was performed to identify genes within this region. The Genescan program predicted an open reading frame of a novel, intron-less gene adjacent to the B236 spot that encodes a putative 493-amino acid protein containing the SNAG repressor motif in the NH2-terminal region and five C2H2-type zinc finger motifs in the COOH-terminal half. This putative gene, methylated in liver tumor (mlt 1), is a novel member of the SNAG transcriptional repressor family with 43% amino acid identity to insulinoma-associated protein 1. An open reading frame encoding a protein quite similar to mouse mlt 1 (56% amino acid identity) was located in the syntenic region of the human genome, indi cating that mlt 1 is evolutionarily conserved in human. Northern blot analysis revealed that mlt 1 is normally expressed in brain, spleen, stom ach, and liver. However, mlt 1 expression was silenced in the liver tumors of MT-D2 mice. The putative promoter region of mlt 1 is unmethylated in normal tissues but methylated in all liver tumors from 11 MT-D2 mice We also found that mlt 1 was methylated and not expressed in N18TG-22 cells, a mouse neuroblastoma cell line. Treatment of N18TG-2 cells with a demethylating agent, 5-aza-deoxycytidine, resulted in an expression of mlt 1, indicating that the repression of mlt 1 is attributable to methylation Thus, mlt 1 is a novel target gene that is silenced by methylation during liver tumorigenesis initiated by SV40 T antigen.

Amino Acid Sequence↗
PubMed2001

Comparative evaluation of 5'-end-sequence quality of clones in CAP trapper and other full-length-cDNA libraries.

To enhance the usefulness of the laboratory mouse and to facilitate the rapid assay of gene functions we have been collecting the entire set of mouse full-length cDNA by one-pass sequencing. To collect full-length cDNA clones efficiently, it is critical to construct high-quality cDNA libraries. In recent years, we have been developing a way to construct full-length cDNA libraries by using biotinylation of the cap structure (the 'CAP-trapper' method) coupled with treatment to increase reverse transcriptase efficiency at high temperature by the addition of trehalose. In this paper we report our evaluation of the quality of CAP trapper and a number of other full-length cDNA libraries, including the results of 5' end analysis of clones in CAP trapper and the other libraries. We used a procedure that compared the 5'-ends of cDNA clones with those of genes in the public databases. Our analysis showed that 63% of cDNA clones in CAP trapper libraries had sequences that were either the same length as those of equivalent genes in the public database or 5'-extended, and that 90% of these clones maintained their coding sequences. These results indicate that the CAP trapper library is a promising tool for collecting full-length cDNA in large-scale projects. Comparison of the quality of CAP trapper with that of other full-length-cDNA libraries confirmed the value of these libraries.

Algorithms↗
PubMed2001

Upregulation of immunoreactive angiotensin II release and angiotensinogen mRNA expression by high-frequency preganglionic stimulation at the canine cardiac sympathetic ganglia.

The possible involvement of the local angiotensin system in ganglionic functions was investigated in the canine cardiac sympathetic ganglia. Positive chronotropic responses to preganglionic stellate stimulation at high frequencies, after intravenous administration of pentolinium plus atropine, were inhibited by the nonpeptide angiotensin AT(1) receptor antagonist forasartan or the angiotensin I-converting enzyme inhibitor captopril, whereas the rate increases elicited by the postganglionic stellate stimulation and norepinephrine given intravenously failed to be inhibited by these antagonists. The levels of endogenous immunoreactive angiotensin II, as determined by radioimmunoassay in the incubation medium of the stellate and inferior cervical ganglia, were increased after the high-frequency preganglionic stimulation of the isolated ganglia. The increment of the peptide was also antagonized by the pretreatment with captopril but not by a chymase inhibitor, chymostatin. The expression of angiotensinogen mRNA was observed in the stellate ganglion, adrenal, liver, and lung but not in the ovary and spleen. The expression of the mRNA in the stellate and inferior cervical ganglia increased after high-frequency preganglionic stimulation of the in vivo dogs for a period of 1 hour. These results indicate that an intrinsic angiotensin I-converting enzyme-dependent angiotensin system exists in the cardiac sympathetic ganglia, which is activated by high-frequency preganglionic stimulation.

Angiotensin II↗
PubMed2001

Novel components of the plant cytoskeleton: a beginning to plant 'cytomics'

The bulk of our knowledge concerning the plant cytoskeleton has come primarily from the use of techniques and probes derived from animal research. However, in comparison with animal tissues, relatively few plant cytoskeleton proteins have been identified. We presume this is not because the plant cytoskeleton is really made up of such few proteins, but rather that only rarely have attempts been made to identify plant-specific cytoskeleton proteins, using plant-specific methods. Here we outline methods that we have developed both for the isolation and identification of novel cytoskeleton proteins as well as for the visualization of novel filamentous structures in plant cells, and we describe several novel cytoskeleton proteins and two novel cytoskeleton structures, 'nanofilaments' and 'nanotubules'. We postulate that use of such approaches will lead to a rapid expansion of our knowledge of the plant cytoskeleton.

Journal Article↗
PubMed2001

Balanced-size and long-size cloning of full-length, cap-trapped cDNAs into vectors of the novel lambda-FLC family allows enhanced gene discovery rate and functional analysis.

We have developed a new class of cloning vectors: lambda-full-length cDNA (lambda-FLC) cloning vectors. These vectors can be bulk-excised for preparing full-length cDNA libraries in which a high proportion of the plasmids carry large inserts that can be transferred into other (for example, functional) vectors. Unlike other cloning vectors, lambda-FLC vectors accommodate a broad range of sizes of eukaryotic cDNA inserts because they contain "size balancers." Further, the main protocol we use for direct bulk excision of plasmids is mediated by a Cre-lox system and is apparently free of size bias. The average size of the inserts from excised plasmid cDNA libraries was 2.9 kb for standard and 6.9 kb for size-selected cDNA. The average insert size of the full-length cDNA libraries was correlated to the rate of new gene discovery, suggesting that effectively cloning rarely expressed mRNAs requires vectors that can accommodate large inserts from a variety of sources. Part of the vectors are also suitable for bulk transfer of inserts into various functional vectors.

Animals↗
PubMed2001

Left ventricular contractility is reduced by hypercapnic acidosis and thoracolumbar epidural anesthesia in rabbits.

PURPOSE: We have previously observed that sympathetic blockade by epidural anesthesia (EA) modifies the cardiovascular response to marked hypercapnic acidosis in dogs. Our objective was to determine whether the combination of marked hypercapnic acidosis and EA reduce left ventricular contractility. METHODS: We randomly assigned 22 Japanese white rabbits anesthetized with isoflurane (1.0%) to two groups according to the absence (control group, n= 11) or presence (EA group, n= 11) of thoracolumbar EA. After epidural injection (0.5 mL.kg(-1) of 0.9% saline in the control group or 1% mepivacaine in the EA group) and during subsequent hypercapnia (mean arterial CO2 tension 85 mmHg), we measured left ventricular pressure, left ventricular volume by using conductance catheter and plasma catecholamine concentrations. Left ventricular contractility was assessed by the slope of the linear approximation of the left ventricular end-systolic pressure-volume relationship, [i.e., end-systolic elastance (Ees)]. RESULTS: The combination of hypercapnic acidosis and thoracolumbar EA caused a 65% decrease in Ees (P <0.05). Hypercapnic acidosis alone caused a 16% decrease (P <0.05) and thoracolumbar EA alone caused a 49% decrease in Ees (P <0.05). In the EA group, epidural injection caused an 85% decrease in the epinephrine concentration (P <0.05) and a 39% decrease in the norepinephrine concentration (P <0.05), even during hypercapnic acidosis. However, in the control group, hypercapnic acidosis caused no change in the circulating epinephrine concentration but a 74% increase in the circulating norepinephrine concentration (P <0.05). CONCLUSION: Combined hypercapnic acidosis and EA markedly reduce left ventricular contractility in an additive fashion in rabbits receiving general anesthesia.

Acidosis↗
PubMed2001

Computational analysis of full-length mouse cDNAs compared with human genome sequences.

Although the sequencing of the human genome is complete, identification of encoded genes and determination of their structures remain a major challenge. In this report, we introduce a method that effectively uses full-length mouse cDNAs to complement efforts in carrying out these difficult tasks. A total of 61,227 RIKEN mouse cDNAs (21,076 full-length and 40,151 EST sequences containing certain redundancies) were aligned with the draft human sequences. We found 35,141 non-redundant genomic regions that showed a significant alignment with the mouse cDNAs. We analyzed the structures and compositional properties of the regions detected by the full-length cDNAs, including cross-species comparisons, and noted a systematic bias of GENSCAN against exons of small size and/or low GC-content. Of the cDNAs locating the 35,141 genomic regions, 3,217 did not match any sequences of the known human genes or ESTs. Among those 3,217 cDNAs, 1,141 did not show any significant similarity to any protein sequence in the GenBank non-redundant protein database and thus are candidates for novel genes.

Algorithms↗
PubMed2001

Synthesis and biological activity of 26-norbrassinolide, 26-norcastasterone and 26-nor-6-deoxocastasterone.

26-Norbrassinolide, identified as a metabolite of brassinolide in cultured cells of the liverwort, Marchantia polymorpha, as well as 26-norcastasterone and 26-nor-6-deoxocastasterone were synthesized. Synthesis of these new brassinosteroids was conducted by employing the orthoester Claisen rearrangement and asymmetric dihydroxylation as key reactions. The modified rice lamina inclination test indicated that these three 26-norbrassinosteroids were less active than their corresponding C28 brassinosteroids. Growth-promoting activities were also examined by using the brassinosteroid-deficient, dwarf mutant lkb of garden pea (Pisum sativum L.). In this assay, 26-norbrassinolide was as effective as brassinolide and 26-norcastasterone was more effective than castasterone although 26-nor-6-deoxocastasterone was much less effective than 6-deoxocastasterone. Therefore, removal of C-26 of brassinosteroids does not necessarily reduce the biological activity. The role of C-26 removal in Marchantia cells remains unclear.

Plants↗
PubMed2001

E1 mice epilepsy shows genetic polymorphism for S-Adenosyl-L-homocysteine hydrolase.

E1 mice are an animal model of human epilepsy (idiopathic complex partial seizures). We have previously demonstrated abrupt poly(A)(+) RNA expression in liver from 1-day-old E1 mouse [Mita et al., 1991. Devl. Brain Res. 64, 27-35]. In the present study, we constructed a cDNA library of the poly(A)(+) RNA. By analyzing cDNA clones and nucleotide sequences, we found a clone that was homologous to a rat gene of S-adenosyl-L-homocysteine hydrolase (EC 3.3.1.1.) (SAHH) (a key enzyme in the active methyl transfer pathway) and showed the gene polymorphism/RFLP(PstI) between the epileptic strain, E1, and the non-epileptic mother strain, ddY, as indicated in a gel electrophoresis by cleaving 2.6 kb with PstI into 1.9 kb and 0.7 kb fragment bands. F1(E1xddY) showed the heterozygosity. An attempt to determine the mutation on the genomic SAHH gene in the E1 disclosed a single nucleotide polymorphism indicated by a C-->T transition in the 8th intron, by which the PstI site was created. SAHH enzymatic activity in the liver in 1-day-old E1 mice was slight (approximately 10%), and in fact was significantly lower than that of the control ddY. Results suggested that the abrupt primary mRNA transcribed on the SAHH gene in the liver of 1-day-old E1 mice was processed partially or incompletely because of the presence of the point mutation in the intron. Accordingly, poor energy supply by the insufficient SAHH enzymatic activity in the brain postnatally may be responsible for epileptogenesis in this animal model. It is concluded that a single nucleotide SAHH gene polymorphism may be associated with epilepsy in E1 mice.

Adenosylhomocysteinase↗
PubMed2001

Doppler ultrasonographic identification of the critical segmental artery for spinal cord protection.

OBJECTIVE: The purpose of this study is to evaluate the possibility of identifying critical segmental arteries (CSAs) based on Doppler ultrasonographic hemodynamics. METHODS: In 18 mongrel dogs, the descending aorta was scanned directly with a 5-MHz linear probe through left thoracotomies and the flow velocities in segmental arteries were measured by pulsed Doppler. The aorta was cross-clamped between Th13 and L1, and flow velocity changes were recorded. According to flow increases, segmental arteries were divided into three groups: arteries with the largest flow increase (L-arteries), arteries with the smallest increase (S-arteries) and other arteries (O-arteries). Animals were divided into three groups. One aortic segment including an L-artery or an S-artery was perfused via a temporary shunt during 30-min aortic cross-clamping distal to the left subclavian artery (Group L or Group S) and neurological outcomes were compared with those of animals without shunting (Group N) after 24 and 48 h. RESULTS: L-arteries had significantly larger flow increases than S- and O-arteries (74.3+/-33.8, 20.4+/-9.8 and 33.3+/-17.8 cm/s, P<0.01). In Group N, five of the six animals were completely paraplegic (Tarlov Grade 0) and the other was Grade 1. In Group S, four animals were Grade 4 and two were Grade 0 after 24h. However, two animals showed delayed paraplegia. Therefore, four animals were Grade 0 and two were Grade 4 after 48 h. All animals in Group L were neurologically normal (Grade 4) at both after 24h (vs. Group N, P=0.0013) and 48 h (vs. Group N, P=0.0013; vs. Group S, P=0.019). CONCLUSIONS: Flow responses to aortic cross-clamping differed among segmental arteries and selective perfusion of L-arteries completely prevented paraplegia. Therefore, L-arteries were considered to be CSAs. Hemodynamic measurement of segmental arterial flow using Doppler ultrasonography could be clinically useful for spinal cord protection during thoracoabdominal aortic surgery.

Animals↗
PubMed2001

Arterial blood gas management in retrograde cerebral perfusion: the importance of carbon dioxide.

OBJECTIVES: Many interventional physiological assessments for retrograde cerebral perfusion (RCP) have been explored. However, the appropriate arterial gas management of carbon dioxide (CO2) remains controversial. The aim of this study is to determine whether alpha-stat or pH-stat could be used for effective brain protection under RCP in terms of cortical cerebral blood flow (CBF), cerebral metabolic rate for oxygen (CMRO2), and distribution of regional cerebral blood flow. METHODS: Fifteen anesthetized dogs (25.1+/-1.1 kg) on cardiopulmonary bypass (CPB) were cooled to 18 degrees C under alpha-stat management and had RCP for 90 min under: (1), alpha-stat; (2), pH-stat; or (3), deep hypothermic (18 degrees C) antegrade CPB (antegrade). RCP flow was regulated for a sagittal sinus pressure of around 25 mmHg. CBF was monitored by a laser tissue flowmeter. Serial analyses of blood gas were made. The regional cerebral blood flow was measured with colored microspheres before discontinuation of RCP. CBF and CMRO2 were evaluated as the percentage of the baseline level (%CBF, %CMRO2). RESULTS: The oxygen content of arterial inflow and oxygen extraction was not significantly different between the RCP groups. The %CBF and %CMRO2 were significantly higher for pH-stat RCP than for alpha-stat RCP. The regional cerebral blood flow, measured with colored microspheres, tended to be higher for pH-stat RCP than for alpha-stat RCP, at every site in the brain. Irrespective of CO2 management, regional differences were not significant among any site in the brain. CONCLUSIONS: CO2 management is crucial for brain protection under deep hypothermic RCP. This study revealed that pH-stat was considered to be better than alpha-stat in terms of CBF and oxygen metabolism in the brain. The regional blood flow distribution was considered to be unchanged irrespective of CO2 management.

Animals↗
PubMed2001

Occurrence of N-methyl-L-aspartate in bivalves and its distribution compared with that of N-methyl-D-aspartate and D,L-aspartate.

The presence of N-methyl-L-aspartate (NMLA) was demonstrated in bivalves, Corbicula sandai and Tapes japonica. To our knowledge, this is the first report on the occurrence of NMLA in animal tissues. NMLA in bivalve tissues was identified according to the following findings; (a) its derivatives with (+)- and (-)- 1-(9-fluorenyl)ethyl chloroformate (FLEC) behaved identically with those of authentic NMLA, respectively, on high-performance liquid chromatography (HPLC), (b) its derivatives with (+)- and (-)- FLEC behaved identically with (-)- and (+)-FLEC derivatives of authentic N-methyl-D-aspartate (NMDA), respectively, on HPLC and (c) its behavior on thin-layer chromatography was the same as those of authentic NMLA. We also describe the distribution of NMDA, and D- and L-aspartate, to which N-methylaspartate enantiomers are structurally related. NMDA was more widely dirtributed than NMLA in bivalves. These bivalves containing NMLA showed lower D-aspartate contents and D/(D+L) ratios of aspartate, than the bivalves containing NMDA.

Animals↗
PubMed2001

Accumulation of beta-catenin in the cytoplasm and the nuclei during the early hepatic tumorigenesis.

Hepatocellular carcinomas (HCCs) are thought to develop as well-differentiated tumors and progress to less-differentiated tumors. However, the genetic changes underlying the development and progression of HCCs are not well understood. Recent studies have shown frequent beta-catenin gene activation in HCCs by somatic alterations involving exon 3, resulting in the activation of the Wnt/Wingless signal transduction pathway. However, the exact process in which activation of Wnt/Wingless signal transduction pathway occurs during hepatic tumorigenesis remains to be elucidated. The aim of the present study was to investigate at what stage of hepatocellular tumorigenesis this pathway was activated. Altered expression of beta-catenin was investigated immunohistochemically with special reference to the grade of histological differentiation in 41 HCCs and eight dysplastic nodules. Mutational analysis of the beta-catenin gene with single-strand conformation polymorphism method and polymerase chain reaction amplification was related with the expression of this protein. beta-Catenin was expressed in the cytoplasm and the nuclei in three cases among eight dysplastic nodules, in four cases among 20 well differentiated HCCs, in five cases among 15 moderately differentiated HCCs, and one case among six poorly differentiated HCCs, respectively. Expression of beta-catenin in the cytoplasm and the nuclei was associated in one case with mutation and two cases without mutation for beta-catenin gene among 11 screened HCCs. It was concluded that beta-catenin was accumulated in the cytoplasm and the nuclei in pre-cancerous lesions of the liver and might contribute, at least in part, to hepatic tumorigenesis.

Journal Article↗
PubMed2001

Decreased amount of mpl and reduced expression of glycoprotein IIb/IIIa and glycoprotein Ib on platelets from patients with refractory anemia: analysis by a non-isotopic quantitative ligand binding assay and immunofluorescence.

Using a non-isotopic ligand binding assay and immunofluorescence, we examined the amount of mpl, glycoprotein IIb/IIIa (gpIIb/IIIa) and glycoprotein Ib (gpIb) on platelets from healthy volunteers and patients with refractory anemia (RA). For the analysis of mpl expression, we applied both a non-isotopic ligand binding assay and immunofluorescence using anti-mpl monoclonal antibody, and compared the results from both methods. The non-isotopic ligand binding assay has been developed in our laboratory and is suitable for the quantitative analysis of a small amount of cytokine receptors such as mpl on platelets. In platelets from patients with RA, the amount of mpl expressed by the D value was 0.05+/-0.03 (mean+/-standard deviation), and was significantly lower than that in healthy volunteers (0.15+/-0.05, p<0.0001). The mean fluorescence intensities (MFI) of gpIIb/IIIa and gpIb on platelets from RA patients were 28.8+/-8.8 and 20.8+/-7.7, respectively, and were significantly lower than those on normal subjects (93.2+/-22.6 and 67.4+/-9.1, p<0.0001 and p<0.0001, respectively). There was a good correlation between the amount of mpl and the MFI of gpIIb/IIIa (p=0.794, p<0.0001) or gpIb (p=0.774, p<0.0001), and between those of gpIIb/IIIa and gpIb (p=0.728, p<0.0001). We demonstrated a decreased amount of mpl as well as a reduced expression of gpIIb/IIIa and gpIb on platelets from RA patients.

Adult↗