PubMed Health⌕ Search

Biomedical subjects

Ikuo Nakamura

Publications and source records attributed to Ikuo Nakamura.

At least 19 recordsLinked to original sources
PubMed2006

Immune responses of liver-infiltrating lymphocytes and peripheral blood mononuclear cells to hepatitis C virus core and NS3 antigens.

BACKGROUND AND AIM: Th1/Th2 cytokine balance is thought to play an important role in antiviral immunity and pathogenesis in viral infection. Ex vivo hepatitis C virus (HCV) antigen-specific T-cell responses were investigated. METHODS: Using enzyme-linked immunospot assay, HCV core and NS3 antigen-specific interferon-gamma-, interleukin-4- and interleukin-10-secreting cells were enumerated in peripheral blood mononuclear cells (PBMCs) from 30 chronic hepatitis C patients and 16 healthy controls, and in liver-infiltrating lymphocytes (LILs) from 17 of the 30 patients. RESULTS: IFN-gamma- and IL-10-secreting cells in response to stimulation with HCV core and NS3 antigen were detectable in both PBMCs and LILs from patients with chronic hepatitis C, although frequencies of the cytokine-secreting cells were much higher in LILs than PBMCs. They were not detectable in PBMCs of healthy controls except for IL-10-secreting cells in response to HCV NS3 antigen stimulation. IL-4-secreting cells were hardly detectable in both PBMC and LIL in both the patients and the healthy controls. Frequencies of HCV NS3 antigen-specific IFN-gamma- and IL-10-secreting cells in PBMCs correlated with those in LILs (rho=0.599, p=0.044 and rho=0.716, p=0.004, respectively). CONCLUSIONS: These data provide further evidence of the immunomodulatory role of the CD4(+)CD25(+) regulatory T lymphocytes in chronic HCV infection.

Journal Article↗
PubMed2006

Production of marker-free transgenic Nierembergia caerulea using MAT vector system.

Agrobacterium tumefaciens strain EHA105 harboring an ipt-type MAT vector, pNPI132, was used to produce morphologically normal transgenic Nierembergia caerulea cv. Mont Blanc employing ipt gene as the selectable marker gene. beta-glucuronidase (GUS) gene was used as model gene of interest. The MAT vector system is a positive selection system that gives the advantage of regeneration to the transgenic cells without killing the non-transgenic cells. Infected explants were cultured on hormone- and antibiotic-free MS medium, and 65% of the regenerated shoots developed ipt shooty phenotype-morphologically abnormal shoots, within approximately 3 months after co-cultivation. Twenty morphologically normal shoots were produced from 12 transgenic ipt shoots 7 months after co-cultivation. The normal shoots rooted well on hormone-free MS medium. Ninety percent of the normal shoots were ipt (-), GUS(+) and excision(+) as determined by PCR and Southern blot analyses. These results indicate that ipt-type MAT vector system can be used successfully in Nierembergia to produce marker-free transgenic plants without using phytohormones and selective chemical agents.

Agrobacterium tumefaciens↗
PubMed2006

Primary liposarcoma of gallbladder diagnosed by preoperative imagings: a case report and review of literature.

A 49-year-old Japanese woman was referred to our department because of high fever and a huge abdominal mass. Computed tomography (CT) and magnetic resonance (MR) imagings revealed a tumor, about 30 cm in diameter,occupied the right hepatic lobe and the peritoneal cavity. Abdominal angiography showed that the tumor was fed mainly by the cystic artery. We preoperatively diagnosed angiosarcoma of the gallbladder and performed tumor resection with cholecystectomy because the tumor was almost capsulated,however the posterior wall of the gallbladder attached to the tumor firmly. Histologically,the tumor was composed of spindle cells including lipoblasts with cellular pleomorphism, which were also detected in the muscular layer of the gallbladder. We finally diagnosed pleomorphic liposarcoma of the gallbladder. At 10 mo and 29 mo after the first operation, she underwent two more operations because of recurrence. Now she has a good quality of life 3 yr and 6 mo after the first operation.

Angiography↗
PubMed2006

The sequences of the spacer region between the atpF and atpA genes in the plastid genome allows discrimination among three varieties of medicinal Angelica.

The dried roots of Angelica acutiloba Kitagawa var. acutiloba Kitagawa, A. acutiloba Kitagawa var. iwatensis Hikino and A. acutiloba Kitagawa var. sugiyamae Hikino have been used as the herbal medicine known in Japan as Japanese Angelica Root. The respective morphological features of, in particular, A. acutiloba var. sugiyamae and A. acutiloba var. iwatensis are similar, and they are not easy to distinguish morphologically from each other. In an attempt to find a method for discriminating among these three varieties, we compared the nucleotide sequence of the spacer region between the atpF and atpA genes among the respective plastid genomes. Comparison of these sequences allowed us to identify each of the three varieties unequivocally.

Angelica↗
PubMed2005

Activation tagging approach in a model legume, Lotus japonicus.

We constructed T-DNA insertional lines of a model legume, Lotus japonicus, using a multifunctional vector for gene and exon activation tagging. The vector had the CaMV 35S promoter together with two additional enhancer elements, the start codon, and splice donor and acceptor sites facing the left border, in anticipation of the activation of T-DNA flanking genes and forced expression of flanking exons. The improved transformation technique yielded more than 3,500 lines, including 45 dominant mutant candidates with abnormal phenotypes with respect to aerial parts, nodules, and roots. Among the 44 selected lines, one copy of T-DNA was inserted into the genome of 37 lines (84%). The T-DNA flanking regions of seven lines were isolated by thermal asymmetric interlaced (TAIL)-PCR or reverse transcription (RT)-PCR, and the corresponding genomic clones were analyzed. The transcripts of four genes adjacent to T-DNA out of 11 genes tested were increased in the T(1) generation, demonstrating that gene and exon activation effects by the newly developed tagging vector are heritable. The T-DNA insertional population of L. japonicus will provide legume-specific dominant mutants.

Base Sequence↗
PubMed2005

The sequences of the plastid gene rpl16 and the rpl16-rpl14 spacer region allow discrimination among six species of Scutellaria.

Dried aerial parts of Scutellaria galericulata L. (Labiatae; marsh skullcap) and Scutellaria lateriflora L. (Labiatae; mad dog skullcap) are mainly used as skullcap, a medicinal herb, in Europe and the United States. The respective dried aerial parts of the two species are difficult to distinguish morphologically from each other. We attempted to discriminate among six species (Scutellaria altissima L. (Labiatae), Scutellaria baicalensis Georgi (Labiatae), Scutellaria galericulata, Scutellaria incana Spreng. (Labiatae), Scutellaria indica L. (Labiatae) and Scutellaria lateriflora) of Scutellaria, which include three medicinal species (Scutellaria galericulata, Scutellaria lateriflora and Scutellaria baicalensis), by comparing the respective nucleotide sequences of the plastid rpl16 gene and the rpl16-rpl14 spacer region. Comparisons of these sequences allowed us to identify each of the six species unequivocally.

Amino Acid Sequence↗
PubMed2004

Identification and characterization of a QTL on chromosome 2 for cytosolic glutamine synthetase content and panicle number in rice.

A quantitative trait locus (QTL) associated with the protein content of cytosolic glutamine synthetase (GS1; EC 6.3.1.2) in senescing leaves, panicle number, and panicle weight was characterized in rice (Oryza sativa L.). A near-isogenic line (NIL), C-22, developed by marker-assisted selection was grown under different nitrogen levels in the greenhouse and in a paddy field. Chromosome 2 of C-22 had an approximately 50-cM segment substituted from the Kasalath (indica) chromosome in a Koshihikari (japonica) genetic background. C-22 showed a 12-37% lower content of GS1 protein in leaf blades than Koshihikari, which was in good agreement with a QTL region positively affected by the japonica chromosome. At an early vegetative stage, C-22 had more active tillers than Koshihikari in the greenhouse. At the reproductive stage, both panicle number and total panicle weight of C-22 were significantly higher than those of Koshihikari, particularly when the plants were grown under a low-nitrogen condition. These traits of C-22 were further confirmed in a paddy field. Thus, tiller development was positively affected by the Kasalath chromosome at an early vegetative stage, which resulted in an increased panicle number and panicle weight at the mature stage in C-22. These data indicate that the target QTL (Pnn1; panicle number 1) is important in the development of tillers and panicles in rice. Linkage analyses for panicle number and ratio of developing tiller formation in the second axil (RDT) revealed that Pnn1 was delimited at the 6.7-cM region.

Alleles↗
PubMed2004

Genomic structure and differential expression of two tandem-arranged GSTZ genes in rice.

Glutathione S-transferases (GSTs) are scavenging enzymes that detoxify cellular xenobiotics and toxins by catalyzing the conjugation of these substrates with a tripeptide glutathione. GSTs are classified depending on gene organization and sequence similarity. The sequence analysis of genomic DNA for zeta class GST (GSTZ) locus in rice indicated that two homologous GSTZ genes lay in a tandem orientation with a short (0.4 kb) intergenic spacer. The upstream OsGSTZ1 and downstream OsGSTZ2 spanned 3.5 and 3.2 kb with nine coding exons, respectively. The transcript of OsGSTZ1 had a long 3' untranslated region (3' UTR) that was mostly encoded by a 10th noncoding exon, whereas OsGSTZ2 mRNA contained a long 5' UTR. Northern blot analysis showed that OsGSTZ1/2 messages were strongly expressed in leaf blades, while transcripts from roots were low level. Because OsGSTZ1/2 messages in leaf tissues were strongly induced only by water treatment, it was difficult to assay for the induction of OsGSTZ1/2 transcripts by various stress treatments. Thus, using rice culture cells, we analyzed the respective responses of OsGSTZ1 and OsGSTZ2 genes against various treatments by real-time reverse transcriptase-polymerase chain reaction (RT-PCR). The results showed that OsGSTZ1 was expressed at a level ca. 1000-fold higher than OsGSTZ2 in suspension cells without stress treatment. OsGSTZ1 was expressed constitutively under various stress conditions. In contrast, the expression of OsGSTZ2 gene was strongly enhanced to 30-fold by treatment with jasmonic acid. These observations suggested that the expression of OsGSTZ1 and OsGSTZ2 genes are differentially regulated in the culture cell of rice.

Amino Acid Sequence↗
PubMed2004

Discrimination among species of Papaver based on the plastid rpl16 gene and the rpl16-rpl14 spacer sequence.

An attempt was made to discriminate among six species of Papaver (P. bracteatum, P. orientale, P. pseudo-orientale, P. rhoeas, P. setigerum and P. somniferum) by comparing the nucleotide sequences of the plastid rpl16 gene and the rpl16-rpl14 spacer region. Comparison of sequences allowed us to distinguish five species, namely P. bracteatum, P. orientale, P. pseudo-orientale, P. rhoeas and P. setigerum plus P. somniferum from one another, but sequences from P. setigerum and P. somniferum were identical. It is difficult to distinguish between P. bracteatum, P. orientale and P. pseudo-orientale at the vegetative stage of growth. However, our method allowed us to distinguish between these three species and the others using nucleotide sequences and should allow identification of P. bracteatum that has been cultivated illegally in the garden in Japan. Furthermore, P. rhoeas was clearly discriminated from P. setigerum and P. somniferum by reference to the sequence of the rpl16 exon using young seedlings.

Base Sequence↗
PubMed2004

Identification of SNPs in the waxy gene among glutinous rice cultivars and their evolutionary significance during the domestication process of rice.

Common non-waxy ( Wx) rice cultivars contain two different alleles at the waxy locus, designated Wx(a) and Wx(b), which encode different levels of granule-bound starch synthases and are hence involved in the control of endosperm amylose content. The Wx(a) allele was predominant in non-waxy indica cultivars, whereas the Wx(b) allele was common to the non-waxy japonica variety. Recently, some of the molecular mechanisms underlying the differentiation of Wx(a) from Wx(b) have been characterized. One structural difference between these two alleles was shown to be due to alternative splicing caused by a single-base substitution (AG GT to AG TT) at a donor site of the first intron within the Wx gene. In the case of waxy ( wx) rice, it was not possible to distinguish whether the each wx allele was derived from Wx(a) or Wx(b) alleles by phenotypic analysis. However, we succeeded in developing a derived cleaved amplified polymorphic sequence (dCAPS) marker for the detection of the one-base splicing mutation without the need for sequencing. A mismatch primer was used to generate a restriction site in the Wx(a) allele (AGGT) but not in the Wx(b) allele (AGTT). Three hundred fifty-three waxy rice strains that are widely found in Asia were then employed for analysis using this dCAPS marker. Our findings suggested that waxy rice strains have both Wx(a)- and Wx(b)-derived alleles, but that the Wx(b)-derived allele was predominant, and its distribution was independent of indica- japonica differentiation. The wild relatives of cultivated rice all possessed the AGGT allele. It was concluded that the waxy mutations, and the corresponding rice cultivation, originated from japonica during the evolution and domestication process of rice and was preferentially selected by most Asian peoples.

Alleles↗
PubMed2004

Phagocytic function of neutrophils of patients with decompensated liver cirrhosis is restored by oral supplementation of branched-chain amino acids.

It has been reported that phagocytic function of neutrophils is impaired in cirrhotic patients. We examined the effects of oral supplementation of branched-chain amino acids (BCAA) on phagocytic function of neutrophils in peripheral blood of patients with decompensated cirrhosis. Five patients with decompensated cirrhosis received 12g of BCAA daily for 3 months. Phagocytic function of neutrophils and NK activities of lymphocytes in peripheral blood as well as serum albumin levels and Fisher's ratios were determined before and at 1 and 3 months of BCAA supplementation. Phagocytic function of neutrophils was significantly improved by 3-month BCAA oral supplementation. NK activity of lymphocytes was improved in four of five patients at 3 months of BCAA supplementation, although the changes were not statistically different. In conclusion, BCAA supplementation improved phagocytic function of neutrophils in cirrhotic patients. BCAA supplementation may reduce the risk of bacterial infection in patients with decompensated liver cirrhosis.

Journal Article↗
PubMed2004

Identification of novel hepatitis C virus-specific cytotoxic T lymphocyte epitopes by ELISpot assay using peptides with human leukocyte antigen-A*2402-binding motifs.

The human leukocyte antigen (HLA)-A*2402 is common in Asians. The authors attempted to identify epitopes for HLA-A*2402-restricted, hepatitis C virus (HCV)-specific CD8(+) T cells by an enzyme-linked immunospot (ELISpot) assay using peripheral blood CD8(+) T cells from HLA-A*2402-positive hepatitis C patients and synthetic HCV peptides based on HLA-A*2402-binding motifs and the amino acid sequence of type 1b HCV. Ten novel epitopes were identified in five of seven HLA-A*2402-positive patients with acute or short-term chronic HCV infection (<3 years), but in none of four with longer-term chronic infection (>10 years). Only one of the ten epitopes proved to be definitely HLA-A*2402-restricted. Another epitope was identified in one of two HLA-A*2402-negative acute hepatitis C patients. In two of the six patients with positive CD8(+) T cell responses, the targeted epitopes were multiple. The same epitope was targeted in two patients. When patients with unresolved acute HCV infection were treated with alpha interferon, peripheral blood HCV-specific CD8(+) T cells decreased with resolution of the hepatitis. In conclusion, CD8(+) T cell responses to HCV infection are heterogeneous. One definite HLA-A*2402-restricted and ten probably non-HLA-A*2402-restricted epitopes were identified. Patients with short-term HCV infection are suitable for searching for novel HCV epitopes, but peripheral blood HCV-specific CD8(+) T cells decrease markedly after loss of antigenic stimulation.

Binding Sites↗
PubMed2003

Characterization of topological structure on complex networks.

Characterizing the topological structure of complex networks is a significant problem especially from the viewpoint of data mining on the World Wide Web. "Page rank" used in the commercial search engine Google is such a measure of authority to rank all the nodes matching a given query. We have investigated the page-rank distribution of the real Web and a growing network model, both of which have directed links and exhibit a power law distributions of in-degree (the number of incoming links to the node) and out-degree (the number of outgoing links from the node), respectively. We find a concentration of page rank on a small number of nodes and low page rank on high degree regimes in the real Web, which can be explained by topological properties of the network, e.g., network motifs, and connectivities of nearest neighbors.

Journal Article↗
PubMed2003

Frequencies of interferon-gamma and interleukin-10 secreting cells in peripheral blood mononuclear cells and liver infiltrating lymphocytes in chronic hepatitis B virus infection.

Cytokine balance may play an important role in effective antiviral immunity. We determined the frequencies of interferon-gamma (IFN-gamma)-, interleukin-4 (IL-4)-, and interleukin-10 (IL-10)-secreting cells in response to HBV antigens in peripheral blood mononuclear cells (PBMCs) and liver-infiltrating lymphocytes (LILs) using an enzyme-linked immuno spot (ELISpot) assay and related them to serum ALT and HBV DNA levels, and hepatic histological findings. PBMCs were obtained from 25 patients with chronic hepatitis B, from eight of whom LILs were also obtained, and 12 healthy controls. On stimulation with hepatitis B core antigen (HBcAg), the median (range) frequencies of IFN-gamma- and IL-10-secreting cells were 25 (7-71) and 54 (26-101) cells/10(4) PBMCs, respectively, in patients with chronic hepatitis B, and 4 (0-12) and 36 (7-63) cells/10(4) PBMCs, respectively, in healthy controls. The frequencies of HBcAg-specific IFN-gamma-secreting cells in PBMCs and LILs of chronic hepatitis B patients correlated with serum ALT levels. Those of LILs correlated with serum ALT levels and HAI scores. In conclusion, HBcAg-specific IFN-gamma-secreting cells may play a role in liver damage in chronic HBV infection. Excessive IL-10 production by PBMCs and LILs in response to HBcAg may suppress antiviral immune responses and contribute to persistent infection.

Journal Article↗