Biomedical subjects

Koichi Ishikawa

Publications and source records attributed to Koichi Ishikawa.

At least 19 recordsLinked to original sources

PubMed2006

Statistical validation of two sample comparison methods for oligonucleotide microarray in rat ischemia model.

In gene expression analyses using a high-density oligonucleotide array in a rat ischemia model, two comparison methods, "pair-wise comparison" and "sample average comparison", were evaluated based on statistical methods. The reliability of the elements screened with a 1.2 to 10-fold threshold was also evaluated. In pair-wise comparisons, most of the elements were significantly independent of the threshold value, with the percentage of significant elements remaining above 95%, when screened at 2.5-fold or higher threshold value. Pair-wise comparison structurally provided strict screening, which resulted in genes that were not selected despite significant alterations in expression. Screening by "sample average comparison" resulted in elements with low probability of significance, which suggested the necessity for increasing the reliability by additional statistical analyses after screening. When genes with altered expression were screened using an oligonucleotide array, marked differences in the numbers and reliability were proved to exist among elements screened by each sample comparison method.

Animals↗

PubMed2006

Characteristics of hepatitis B virus in Ghana: full length genome sequences indicate the endemicity of genotype E in West Africa.

Hepatitis B virus (HBV) genotypes from A to H have distinct geographical distributions and have been shown to affect the clinical features as well as the course of the HBV infection. HBV genotype E has been found only in Africa. However, the complete genomes of this genotype, which were isolated mainly from West Africa, were available only for a few samples. In this study, five full-length genomes and seven other small S genes of HBV strains from Ghanaian blood donors were sequenced and investigated. Following phylogenetic analysis, all of the Ghanaian HBV strains were clustered closely in genotype E. All of the 12 small S genes showed the same characteristic of subtype ayw4. The complete genomes of the five Ghanaian strains showed marked similarity with each other and with the reported genotype E strains (96.7%-99.1%). Genotype E strains showed low intra-genotypic diversity (1.8%) and carried the conserved signature pattern in pre-S1 as well as in the full genome sequence. Of note, the finding of the G145R escape mutant in an unvaccinated Ghanaian blood donor might raise concern as to the ongoing nation-wide hepatitis B vaccination program in Ghana.

Amino Acid Sequence↗

PubMed2006

Long-term outcome of laparoscopic wedge resection for gastric submucosal tumor compared with open wedge resection.

Little is known about the outcomes of laparoscopic wedge resection (LWR) in comparison with conventional open wedge resection (OWR) for gastric submucosal tumor. Outcomes of 21 patients who underwent LWR (n = 14) or OWR (n = 7) for gastric submucosal tumor between 1993 and 2004 were investigated. We compared the short-term and long-term operative results between the 2 groups. LWR showed several advantages over OWR for gastric submucosal tumor: less blood loss, lower fever on day 1, lower analgesic usage rate, earlier first postoperative flatus and oral intake, lower leukocyte count on days 1 and 7, and lower C-reactive protein level on days 1 and 3. All patients, except 2 with histologically diagnosed high-risk gastrointestinal stromal tumor, survived during the mean follow-up period of 60 months. LWR is feasible for the management of patients with gastric submucosal tumor.

Aged↗

PubMed2006

Clinicopathologic features and treatment of residual early cancers after endoscopic mucosal resection of the stomach.

GOALS: We sometimes encounter residual or recurrent cancers after endoscopic mucosal resection (EMR) for early gastric cancer. The aim of the present study was to clarify the clinicopathologic characteristics of and optimal treatment for the residual cancers after EMR. STUDY: Seventy-four patients with early gastric cancer were treated with EMR between 1994 and 2004. These patients were divided into 2 groups as follows: the curative group (n=59) and the noncurative group (n=15). The clinicopathologic data were compared between the 2 groups and the outcomes of additional therapy were reviewed. RESULTS: In the noncurative group, the tumors were located significantly frequently on the upper or middle third of the stomach compared with the curative group (P<0.05). The number of fragments in EMR was significantly larger in the noncurative group than in the curative group (P<0.05). Fifteen patients required additional treatment because of the residual cancer. Nine (75%) of 12 patients requiring surgery underwent laparoscopic surgery. Three patients were treated by endoscopic therapy. CONCLUSIONS: EMR with a single fragment and with a sufficient margin is useful for the complete resection of early gastric cancer. When residual cancer occurs, laparoscopic gastrectomy may be a good alternative.

Aged↗

PubMed2006

Screening for control genes in mouse hippocampus after transient forebrain ischemia using high-density oligonucleotide array.

In conventional relative gene expression analysis (Northern blotting, RT-PCR, and in situ hybridization), housekeeping genes such as the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and beta-actin genes, whose expression levels are considered stable, have been used as control genes for normalization of RNA quantitation. However, it has been reported that the expression levels of these two control genes are affected by ischemia. Therefore, we have been searching for novel control genes whose expression levels are stable in a mouse model of transient forebrain ischemia. Using the GeneChip Mu6500 array set, we monitored the expression levels of approximately 6000 murine genes in the mouse hippocampus during 24 h of ischemia-reperfusion. To select stable genes, we applied the restricted criterion of a 1.5-fold change in expression level as the threshold. By adding statistical analysis with this criterion, we identified 10 genes as candidates for control genes from the GeneChip data. In this criterion, GAPDH and beta-actin genes were not included in the 10 genes as candidates for control genes. The present findings might be relevant to the use of control genes in quantitation of RNA, particularly in the study of mouse transient forebrain ischemia.

Animals↗

PubMed2005

Monitoring expression of cytochrome P450 genes during postischemic rat liver reperfusion using DNA microarrays.

We investigated the expression of 50 cytochrome P450 (CYP) genes in the postischemic reperfused rat liver using a DNA microarray. Thirteen CYPs showed absent expression in all experiments and 2 CYPs were induced by pentobarbital, which was used as an anesthetic. Eight of the remaining 35 CYPs showed significantly decreased expression following ischemia-reperfusion. Monitoring CYP expression may be a powerful approach for elucidation of pathways regulating drug metabolism that may be involved in postischemic reperfusion liver injury.

Animals↗

PubMed2005

Ornithine breath test as a method to evaluate functional liver volume.

BACKGROUND: The purpose of this study was to investigate whether the functional liver volume can be measured from changes in expiratory 13CO2 levels after intravenous administration of L-[1, 2-13C] ornithine, using a rat model of hepatectomy. MATERIALS AND METHODS: Under pentobarbital anesthesia, 30%, 70%, or 90% hepatectomy was performed. In the control group, simple laparotomy was performed. Then, 20 mg/kg L-[1, 2-13C] ornithine was administered to rats via the femoral vein. A breath test was conducted 20 min after laparotomy. We examined the correlation of the sum of 13CO2 output (S) or a single point of 13CO2 level (SP) with liver weight/body weight (LW/BW) (%) every 15 min. RESULTS: In all of the groups, the ornithine breath test (OBT) graph reached a plateau level at about 6 min. The correlation coefficient between S15 and LW/BW was highest 0.952 (P <0.0001). The correlation coefficient between SP14 and LW/BW was highest, 0.944 (P <0.0001). The severity of hepatic injury could be evaluated, with significant differences in S5-15 and SP5-15 in all comparisons between groups. CONCLUSION: In the breath test with intravenously administered L-[1, 2-13C] ornithine, functional liver volume could be evaluated accurately in a short period.

Animals↗

PubMed2005

The middle to 3' end of the HIV-1 vif gene sequence is important for vif biological activity and could be used for antisense oligonucleotide targets.

The human immunodeficiency virus type-1 (HIV-1)-encoded vif protein is essential for viral replication, virion production, and pathogenicity. HIV-1 Vif interacts with the endogenous human APOBEC3G protein (an mRNA editor) in target cells to prevent its encapsidation into virions. Some studies have established targets within the HIV-1 vif gene that are important for its biologic function; however, it is important to determine effective therapeutic targets in vif because of its critical role in HIV-1 infectivity and pathogenicity. The present study demonstrates that virions generated in transfected HeLa-CD4+ cells, especially from HIV-1 vif frame-shift mutant (3' delta vif; 5561-5849), were affected in splicing and had low infectivity in MT-4 cells. In addition, HIV-1 vif antisense RNA fragments constructed within the same region, notably the region spanning nucleic acid positions 5561-5705 (M-3'-AS), which corresponds to amino acid residues 96-144, significantly inhibited HIV-1 replication in MT-4 and reduced the HIV-1 vif mRNA transcripts and reporter gene (EGFP) expression. The generated virions showed low secondary infection in H9 cells. These data therefore suggest that the middle to the 3' end of vif is important for its biological activity in the target cells.

3' Flanking Region↗

PubMed2005

Lentiviral-mediated delivery of combined HIV-1 decoy TAR and Vif siRNA as a single RNA molecule that cleaves to inhibit HIV-1 in transduced cells.

RNA interference (RNAi) silences gene expression via short interfering 21-23 mer double-stranded RNA (siRNA) segments that guide cognate mRNA degradation in a sequence-specific manner. On the other hand, HIV-1 decoy TAR RNA are known to competitively interact with the HIV-1 Tat protein, to downregulate the enhanced gene expression from the long terminal repeat (LTR) promoters. Here we report that a novel expression construct, encoding both HIV-1 decoy TAR and Vif siRNA, as a single RNA substrate, was expressed under the control of the human U6 promoter, and later the TAR and siRNA were cleaved into their respective separate RNA by the endogenous RNase III-like enzyme. Each of the cleaved HIV-1 anti-genes then synergistically contributed toward enhancing the inhibition efficacy (>80%) of HIV-1 replication in transduced Jurkat cells. These results suggest that targeting HIV-1 mRNA with simultaneously expressed intracellular decoy TAR and Vif-siRNA could lead to an effective gene therapy strategy for the control and management of HIV-AIDS.

Acquired Immunodeficiency Syndrome↗

PubMed2005

A case of sporadic gastric carcinoid tumor treated successfully by laparoscopy-assisted distal gastrectomy.

A 49-year-old man was referred to us for treatment of a gastric carcinoid tumor. Gastroscopy revealed a superficial elevated lesion with a central depression covered with nonspecific gastric mucosa located in the anterior wall of the gastric body. The lesion was diagnosed on biopsy as a gastric carcinoid tumor. Preoperative ultrasound and computed tomography examinations revealed a tumor confined to the gastric submucosa and without lymph node metastasis. Therefore, laparoscopy-assisted distal gastrectomy (LADG) was performed. Macroscopically, the resected specimen contained an elevated lesion measuring 0.9 x 0.8-cm with a central depression. The postoperative course was uneventful, and the patient remains free of recurrence 10 months after surgery. There are few cases of sporadic gastric carcinoid tumor successfully treated by LADG. LADG may be useful for treatment of patients with sporadic gastric carcinoid tumor and possible lymph node metastasis.

Biopsy↗

PubMed2005

Identification of autotaxin as a neurite retraction-inducing factor of PC12 cells in cerebrospinal fluid and its possible sources.

Abstract Cerebrospinal fluid (CSF) induced neurite retraction of differentiated PC12 cells; the action was observed in 15 min (a rapid response) and the activity further increased until 6 h (a long-acting response) during exposure of CSF to the cells. The CSF action was sensitive to monoglyceride lipase and diminished by homologous desensitization with lysophosphatidic acid (LPA) and by pretreatment with an LPA receptor antagonist Ki16425. Although fresh CSF contains LPA to some extent, the LPA content in the medium was increased during culture of PC12 cells with CSF. The rapid response was mimicked by exogenous LPA, and a long-acting response was duplicated by a recombinant autotaxin, lysophospholipase D (lyso-PLD). Although the lyso-PLD substrate lysophosphatidylcholine (LPC) was not detected in CSF, lyso-PLD activity and an approximately 120-kDa autotaxin protein were detected in CSF. On the other hand, LPC but not lyso-PLD activity was detected in the conditioned medium of a PC12 cell culture without CSF. Among neural cells examined, leptomeningeal cells expressed the highest lyso-PLD activity and autotaxin protein. These results suggest that leptomeningeal cells may work as one of the sources for autotaxin, which may play a critical role in LPA production and thereby regulate axonal and neurite morphological change.

Animals↗

PubMed2004

Intracellular expression of antisense RNA transcripts complementary to the human immunodeficiency virus type-1 vif gene inhibits viral replication in infected T-lymphoblastoid cells.

The human immunodeficiency virus type-1 (HIV-1)-encoded vif protein is essential for viral replication, virion production, and pathogenicity. HIV-1 vif interacts with the endogenous human APOBEC3G protein (an mRNA editor) in target cells to prevent its virions from encapsidation. Although some studies have established targets within the HIV-1 vif gene that are important for its biologic function, it is however important to further screen for effective therapeutic targets in the vif gene that could interfere with the HIV-1 vif-dependent infectivity and pathogenicity. This report demonstrates that HIV-1 vif antisense RNA fragments constructed within mid-3' region, notably the region spanning nucleic acid positions 5561-5705 (M-3'-AS), significantly inhibited HIV-1 replication in MT-4 and H9-infected cells and reduced the HIV-1 vif mRNA transcripts. These data clearly suggest that the above vif fragment, which corresponds to amino acid residues 96-144, could be an effective novel therapeutic target site for gene therapy applications, for the control and management of HIV-1 infection, due to its strong inhibition of HIV-1 replication in cells.

Base Sequence↗

PubMed2004

Screening for control genes in rat global cerebral ischemia using high-density oligonucleotide array.

From conventional relative gene expression analyses (Northern blotting, in situ hybridization, and RT-PCR), it has been reported that the expression of control genes, such as glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and beta-actin, used as references may be affected by ischemia. Therefore, we extended searching and evaluation at the mRNA level of transcripts whose expression levels were not changed by cerebral ischemia, using a high-density oligonucleotide array and statistical analysis in a rat global cerebral ischemia and reperfusion model. We added a hyperthermic factor and localization factor to ischemia and identified transcripts with a stable expression level under conditions even more disadvantageous than ischemia only. Screening of more than 8,000 transcripts with the Rat Genome U34A array yielded 28 transcripts, which we listed and classified according to their expression level. Widely used control genes, GAPDH and beta-actin, were not included, although cyclophilin A was included. In addition, we conducted a functional classification based on gene ontology. Under the functional classification of the 28 transcripts, many genes tended to be associated with metabolism. In conclusion, use of several transcripts is recommended, such as those we identified, as references in the analysis of gene expression in pathological models of ischemia.

Animals↗

PubMed2004

Profiling of genes associated with transcriptional responses in mouse hippocampus after transient forebrain ischemia using high-density oligonucleotide DNA array.

Several cascades of changes in gene expression have been shown to be involved in the neuronal injury after transient cerebral ischemia; however, little is known about the profile of genes showing alteration of expression in a mouse model of transient forebrain ischemia. We analyzed the gene expression profile in the mouse hippocampus during 24 h of reperfusion, after 20 min of transient forebrain ischemia, using a high-density oligonucleotide DNA array. Using statistical filtration (Welch's ANOVA and Welch's t-test), we identified 25 genes with a more than 3.0-fold higher or lower level of expression on average, with statistical significance set at p<0.05, in at least one ischemia-reperfusion group than in the sham group. Using unsupervised clustering methods (hierarchical clustering and k-means clustering algorithms), we identified four types of gene expression pattern that may be associated with the response of cell populations in the hippocampus to an ischemic insult in this mouse model. Functional classification of the 25 genes demonstrated alterations of expression of several kinds of biological pathways, regulating transcription (Bhlhb2, Jun, c-fos, Egr1, Egr2, Fosb, Junb, Ifrd1, Neurod6), the cell cycle (c-fos, Fosb, Jun, Junb, Dusp1), stress response (Dusp1, Dnajb1, Dnaja4), chaperone activity (Dnajb1, Dnaja4) and cell death (Ptgs2, Gadd45g, Tdag51), in the mouse hippocampus by 24 h of reperfusion. Using hierarchical clustering analysis, we also found that the same 25 genes clearly discriminated between the sham group and the ischemia-reperfusion groups. The alteration of expression of 25 genes identified in this study suggests the involvement of these genes in the transcriptional response of cell populations in the mouse hippocampus after transient forebrain ischemia.

Analysis of Variance↗

PubMed2004

Effects of interleukin-1beta and prostaglandin E2 on prostaglandin D synthase production in cultivated rat leptomeningeal cells.

Although the interleukin (IL)-1 receptor is densely distributed in the leptomeninges constituting the blood/cerebrospinal fluid barrier, its physiologic significance has remained unclear. In the present study, we show that in cultured leptomeningeal cells, IL-1beta, tumor necrosis factors, or lipopolysaccharide causes a prominent increase in the synthesis and release of prostaglandin (PG) D synthase, which catalyzes the final step in the biosynthesis of PGD2. Although significant increases in the amount of PGD synthase were also observed with cells exposed to somatostatin, thrombin, or ciliary neurotrophic factor, these were much smaller than were those induced by the proinflammatory cytokines. Other agents tested including IGF-I had no effect upon the enzyme levels in the culture media. Furthermore, we found that the increased secretion of PGD synthase by IL-1beta was completely inhibited by 10(-7) M PGE2. The same dose of PGD2 or 15-deoxy-Delta(12-14)PGJ2 had no effect upon the IL-1beta action. In addition, PGE2 increased the level of fibronectin and eliminated the expression of zonula occludentes-1, a tight junction-associated protein from cultured cells, effects likely reflecting a loss of barrier integrity. These results demonstrate the importance of inflammatory stimuli as a physiologic regulator of the leptomeningeal cell function.

Animals↗

PubMed2004

Clinicopathologic characteristics of early-stage mucinous gastric carcinoma.

GOALS: Early mucinous gastric carcinoma (MGC) is very rare, and the clinicopathologic features are not well understood. The aim of this study is to clarify the clinicopathologic characteristics of early MGC. STUDY: A total of 806 patients with gastric cancer underwent gastrectomy between 1983 and 2002 at our department. Of these patients, 7 were found to have early MGC. MGC was defined as a tumor in which more than 50% of the tumor area contained extracellular mucin pools. Microscopic examination was performed, and particular attention was paid to the mucin component of the tumor and histologic subtype (ie, well-differentiated or poorly-differentiated). RESULTS: The incidence of early MGC among all gastric carcinomas in our series was 0.9% (7/806). Tumors ranged in size from 1.0 cm to 7.2 cm, with a mean of 3.7 cm, and 4 appeared macroscopically elevated and 3 appeared depressed. Histologically, 3 tumors were considered well-differentiated type and 4 were considered poorly differentiated type. Microscopic features were thickening of the submucosal layer due to accumulation of abundant mucin and elevation of the surrounding normal mucosa. Tumor invaded the submucosa in 6 cases, and lymph node metastasis occurred in 1 case. However, no patient died of recurrence during follow-up periods ranging from 4 to 85 months. CONCLUSIONS: Early MGC is characterized as an elevated lesion resembling submucosal tumor due to abundant mucin pools in the submucosa. Cases of early MGC have a good outcome similar to that of early non-MGC.

Adenocarcinoma, Mucinous↗

PubMed2004

Nucleotide sequence of RNA2 of Lettuce big-vein virus and evidence for a possible transcription termination/initiation strategy similar to that of rhabdoviruses.

Lettuce big-vein virus (LBVV) is the type species of the genus Varicosavirus and is a two-segmented negative-sense single-stranded RNA virus. The larger LBVV genome segment (RNA1) consists of 6797 nt and encodes an L polymerase that resembles that of rhabdoviruses. Here, the nucleotide sequence of the second LBVV genome segment (RNA2) is reported. LBVV RNA2 consisted of 6081 nt and contained antisense information for five major ORFs: ORF1 (nt 210-1403 on the viral RNA), ORF2 (nt 1493-2494), ORF3 (nt 2617-3489), ORF4 (nt 3843-4337) and ORF5 (nt 4530-5636), which had coding capacities of 44, 36, 32, 19 and 41 kDa, respectively. The gene at the 3' end of the viral RNA encoded a coat protein, while the other four genes encoded proteins of unknown functions. The 3'-terminal 11 nt of LBVV RNA2 were identical to those of LBVV RNA1, and the 5'-terminal regions of LBVV RNA1 and RNA2 contained a long common nucleotide stretch of about 100 nt. Northern blot analysis using probes specific to the individual ORFs revealed that LBVV transcribes monocistronic RNAs. Analysis of the terminal sequences, and primer extension and RNase H digestion analysis of LBVV mRNAs, suggested that LBVV utilizes a transcription termination/initiation strategy comparable with that of rhabdoviruses.

3' Flanking Region↗

PubMed2004

Gene expression analysis in the stomachs of water immersion-restraint stress rats using high-density oligonucleotide array.

BACKGROUND AND AIM: Research on gastric lesions developing in response to stress is essential to elucidating the pathogenesis of these lesions as well as the interplay with other factors, including Helicobacter pylori infection and non-steroidal anti-inflammatory drug use. Genes expressed individually or in sets, such as heat shock proteins, growth factors, proto-oncogenes and cyclooxygenases, have been investigated in the stomach. However, gene expression in the stomach after stress exposure have not yet been comprehensively examined. We investigated the gastric gene expression profile in response to stress. METHODS: A high-density oligonucleotide array, representing approximately 850 genes, was used to determine gene expression changes in the stomachs of water immersion-restraint stress (WIRS) rats. RESULTS: Fifty-eight genes including expressed sequence tag (EST) genes were upregulated more than twofold in the 30 min-WIRS rat stomach as compared with the control. Concomitantly, five genes were downregulated. Numbers of up- or downregulated genes decreased rapidly at 1 and 2 h of WIRS. Altered gene expression of heat shock proteins, cell cycle regulators, proto-oncogenes and metabolic enzymes were recognized. Several of these genes, including p38 mitogen-activated protein kinase, did not reportedly show gastric expression changes in response to stress. CONCLUSION: These results suggest that, in addition to the previously identified stress-induced genes, expression of a number of other genes in the stomach is also involved in stress response.

Animals↗