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T Takagi

Publications and source records attributed to T Takagi.

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

A novel bacterial gene-finding system with improved accuracy in locating start codons.

Although a number of bacterial gene-finding programs have been developed, there is still room for improvement especially in the area of correctly detecting translation start sites. We developed a novel bacterial gene-finding program named GeneHacker Plus. Like many others, it is based on a hidden Markov model (HMM) with duration. However, it is a 'local' model in the sense that the model starts from the translation control region and ends at the stop codon of a coding region. Multiple coding regions are identified as partial paths, like local alignments in the Smith-Waterman algorithm, regardless of how they overlap. Moreover, our semiautomatic procedure for constructing the model of the translation control region allows the inclusion of an additional conserved element as well as the ribosome-binding site. We confirmed that GeneHacker Plus is one of the most accurate programs in terms of both finding potential coding regions and precisely locating translation start sites. GeneHacker Plus is also equipped with an option where the results from database homology searches are directly embedded in the HMM. Although this option does not raise the overall predictability, labeled similarity information can be of practical use. GeneHacker Plus can be accessed freely at http://elmo.ims.u-tokyo.ac.jp/GH/.

Algorithms↗
PubMed2001

Mutational analyses of cysteine residues of bovine dihydrodiol dehydrogenase 3.

The cloning, bacterial expression and purification of bovine liver cytosolic dihydrodiol dehydrogenase 3 (DD3) cDNA (1330 bp in full length) using the pKK223-3 expression vector has been reported previously. Recombinant DD3 (rDD3) was characterized in terms of its substrate specificity and inhibitor sensitivity [Terada et al., Adv. Exp. Biol. Res. 414 (1997) 543-553]. The nucleotide sequence of DD3 cDNA completely matched with that of bovine liver-type prostaglandin F synthase [Suzuki et al., J. Biol. Chem. 274 (1999) 241-248]. In the present study, we succeeded in high level expression of rDD3 in Escherichia coli BL21 (DE3) using the pET28a expression vector. rDD3 was easily and quickly purified to apparent homogeneity by one-step column chromatography using Ni(2+)-affinity resin. Furthermore, rDD3 showed essentially the same substrate specificity and inhibitor sensitivity to that of purified liver DD3. To analyze the role of cysteines (145, 154, 188, 193 and 206) in the enzymatic activity of DD3, site-directed mutagenesis of DD3 using the polymerase chain reaction method was performed. Mutants (C145S, C154S, C188S, C193S and C206S) were analyzed for substrate specificity, cofactor binding and inactivation by disulfide (dithio-bis(2-nitrobenzoic acid), alkylating reagent (N-ethylmaleimide) and oxidants (naphthoquinone and H(2)O(2)) Results indicated that these five cysteines of rDD3 may not be directly involved in substrate or cofactor binding. Mutant C193S showed strong resistance to SH-reagents unlike wild-type DD3 (WT) or other mutants. Both the WT and the other mutants showed essentially the same sensitivity to SH-reagents. Cofactor (NADP(+)) protected mutants C145S, C188S and C206S from inactivation as well as WT, while NAD(+) was not protective. Our present results indicate that Cys193, which is located close to the NADP(+)-binding site, may be involved in the alteration of enzymatic activity.

Animals↗
PubMed2001

Genomic structure of the sandworm, Perinereis vancaurica tetradentata, troponin C.

Troponin C (TnC) superfamily genes essentially possess five introns, the positions of all but the fourth being highly conserved. The fourth intron is frequently absent from protostomian invertebrate genes, such as calmodulin or TnC. We previously proposed that the common ancestor of TnC superfamily genes never possessed an intron corresponding to today's fourth introns, and that members of the superfamily independently gained a fourth intron in the evolutionary pathway of each lineage. In the present study, we isolated the TnC cDNA from the sandworm, Perinereis vancaurica tetradentata and determined its genomic structure. Sandworm TnC appears to exist as a single copy gene consisting of six exons and five introns. The positions of the first, second, third and fifth introns are identical to other TnCs, but that of the fourth intron is unique. This is in good agreement with the above-mentioned scheme, i.e. the gain of the fourth intron of sandworm TnC might have occurred within the annelid lineage after annelida/mollusca divergence.

Amino Acid Sequence↗
PubMed2001

Alterations of gene expression during colorectal carcinogenesis revealed by cDNA microarrays after laser-capture microdissection of tumor tissues and normal epithelia.

To identify a set of genes involved in the development of colorectal carcinogenesis, we compared expression profiles of colorectal cancer cells from eight tumors with corresponding noncancerous colonic epithelia using a DNA microarray consisting of 9216 human genes. These cell populations had been rendered homogeneous by laser-capture microdissection. Expression change in more than half of the tumors was observed for 235 genes, i.e., 44 up-regulated and 191 down-regulated genes. The differentially expressed genes include those associated with signal transduction, metabolizing enzymes, production of reactive oxygen species, cell cycle, transcription, mitosis, and apoptosis. Subsequent examination of 10 genes (five up-regulated and five down-regulated) by semiquantitative reverse transcription-PCR using the eight tumors together with an additional 12 samples substantiated the reliability of our analysis. The extensive list of genes identified in these experiments provides a large body of potentially valuable information of colorectal carcinogenesis and represents a source of novel targets for cancer therapy.

Colorectal Neoplasms↗
PubMed2001

In situ localization of beta-glucans in the cell wall of Schizosaccharomyces pombe.

The chemical composition of the cell wall of Sz. pombe is known as beta-1,3-glucan, beta-1,6-glucan, alpha-1,3-glucan and alpha-galactomannan; however, the three-dimensional interactions of those macromolecules have not yet been clarified. Transmission electron microscopy reveals a three-layered structure: the outer layer is electron-dense, the adjacent layer is less dense, and the third layer bordering the cell membrane is dense. In intact cells of Sz. pombe, the high-resolution scanning electron microscope reveals a surface completely filled with alpha-galactomannan particles. To better understand the organization of the cell wall and to complement our previous studies, we set out to locate the three different types of beta-glucan by immuno-electron microscopy. Our results suggest that the less dense layer of the cell wall contains mainly beta-1,6-branched beta-1,3-glucan. Occasionally a line of gold particles can be seen, labelling fine filaments radiating from the cell membrane to the alpha-galactomannan layer, suggesting that some of the radial filaments contain beta-1,6-branched beta-1,3-glucan. beta-1,6-glucan is preferentially located underneath the alpha-galactomannan layer. Linear beta-1,3-glucan is exclusively located in the primary septum of dividing cells. beta-1,6-glucan only labels the secondary septum and does not co-localize with linear beta-1,3-glucan, while beta-1,6-branched beta-1,3-glucan is present in both septa. Linear beta-1,3-glucan is present from early stages of septum formation and persists until the septum is completely formed; then just before cell division the label disappears. From these results we suggest that linear beta-1,3-glucan is involved in septum formation and perhaps the separation of the two daughter cells. In addition, we frequently found beta-1,6-glucan label on the Golgi apparatus, on small vesicles and underneath the cell membrane. These results give fresh evidence for the hypothesis that beta-1,6-glucan is synthesized in the endoplasmic reticulum-Golgi system and exported to the cell membrane.

Cell Wall↗
PubMed2001

Serum nm23-H1 protein as a prognostic factor in aggressive non-Hodgkin lymphoma.

Advances in chemotherapy have led to a favorable long-term prognosis in approximately 50% of patients with aggressive non-Hodgkin lymphoma (NHL). However, the remaining patients do not enjoy such prolonged survival after standard treatment. New prognostic factors are needed to define this poor-prognosis group and to plan an appropriate treatment strategy. It has been reported that serum nm23-H1 protein may be a new prognostic factor for aggressive NHL. In the present study involving multiple institutions and a large number of patients, the level of nm23-H1 protein was compared among different types of lymphoma; it was lowest for indolent lymphoma, followed by aggressive lymphoma and then highly aggressive lymphoma. In addition, patients with aggressive NHL and higher nm23-H1 levels had worse overall and progression-free survival rates than those with lower nm23-H1 levels. The nm23-H1 level was also compared between patients with diffuse large B-cell lymphoma and patients with peripheral T-cell lymphoma. The results suggest that the level of nm23-H1 could serve as a prognostic factor in both groups. Moreover, the prognosis of lymphoma patients could be ascertained even more precisely by combining soluble interleukin-2 receptor or soluble CD44 and nm23-H1 levels. A multivariate analysis confirmed that the nm23-H1 level is an independent and important prognostic factor in aggressive NHL. Therefore, it may provide useful information for clinicians to determine the appropriate therapy for each type of lymphoma.

Actuarial Analysis↗
PubMed2001

Site-directed mutagenesis studies of bovine liver cytosolic dihydrodiol dehydrogenase: the role of Asp-50, Tyr-55, Lys-84, His-117, Cys-145 and Cys-193 in enzymatic activity.

A previous report on the cloning, bacterial expression and purification of bovine liver cytosolic dihydrodiol dehydrogenase (DD3) cDNA (1,330 bp in full length) using pKK223-3 expression vector characterize the properties of the recombinant DD3 in the aspects of substrate specificity and inhibitor sensitivity (Terada et al., Adv. Exp. Biol. Res. 414 (1997) 543-53). The nucleotide sequence of this DD3 cDNA completely matches that of bovine liver-type prostaglandin F synthase (PGFS) (Suzuki et al., J. Biol. Chem. 274 (1999) 241-8). In the present study, a large amount of recombinant DD3 (rDD3) was expressed in Escherichia coli BL21 (DE3) with a pET28a expression vector. The recombinant DD3 (rDD3) was easily and quickly purified to an apparent homogeneity with one step column chromatography of Ni(2+)-affinity resin. The rDD3 showed essentially the same substrate specificity and inhibitor sensitivity as purified liver DD3 (DD3). To analyze the role of amino acid residues of DD3 in its enzymatic activity, site-directed mutagenesis of DD3 with PCR method was performed. The results of the analyses of these mutants in the aspects of substrate specificity and cofactor-binding suggested a variety of functions in the enzymatic activity: as an active site Tyr-55 may act as a general acid and Asp-50, Lys-84 and His-117 may play an important role in the control of protonation of Tyr-55 as a general acid in the dehydrogenase activity under higher pH conditions, though these residues may not be involved in reductase activity under lower pH conditions. Though the mutated DD3s (Cys to Ser) did not show significant differences in their substrate specificities, these mutants showed different sensitivities to SH-reagents. Present results indicate that Cys-193 may play an important role in the modulation of enzymatic activity under redox conditions generated with GSH+GSSG among five cysteines in DD3.

Alcohol Oxidoreductases↗
PubMed2001

The inducible nitric oxide synthase inhibitor ONO-1714 blunts dextran sulfate sodium colitis in mice.

In mice with acute dextran sulfate sodium colitis, we examined the effect of inducible nitric oxide synthase inhibition by (1S,5S,6R,7R)-7chloro-3-amino-5methyl-2-azabicyclo[4.1.0]heptane hydrochloride (ONO-1714) on colonic biochemistry, injury, and inflammation. Colonic luminal nitrate and nitrite were measured by the Griess reaction; inducible nitric oxide synthase messenger RNA expression by reverse transcription-polymerase chain reaction; and nitrotyrosine by immunohistochemistry. Mice with colitis showed increases in nitrate and nitrite, inducible nitric oxide synthase messenger RNA, and numbers of cells staining for nitrotyrosine. Colonic inflammation was severe. ONO-1714 inhibited increases in nitrate and nitrite and numbers of nitrotyrosine-positive cells; injury and inflammation also were reduced. Dextran sulfate sodium-induced increases in thiobarbituric acid-reactive substances, a lipid peroxidation marker, were blunted by ONO-1714, which also inhibited increases in mucosal inflammatory cytokines. Nitric oxide produced by inducible nitric oxide synthase may contribute to colonic inflammation by nitrosation, oxidative damage, and enhanced inflammatory cytokines.

Amidines↗
PubMed2001

Primary angioplasty for isolated right ventricular infarction.

We describe a case of isolated right ventricular infarction that has rarely been diagnosed antemortem. Electrocardiogram showed ST segment elevation in left precordial chest, right precordial chest, and inferior leads, which mimicked those of anterior and inferior left ventricular infarction. Coronary angiography revealed that culprit lesion was totally occluded right coronary artery. Infarcted artery was nondominant right coronary artery with branches supplying only right ventricular wall. Restoration of coronary blood flow was obtained by primary stenting and resulted in prompt ST segment normalization in all leads. Despite extensive right ventricular wall motion abnormality, subsequent right ventricular dysfunction was not observed.

Aged↗
PubMed2001

Cutting balloon angioplasty for treatment of calcified coronary lesions.

The aim of the study was to evaluate the feasibility, safety, and efficacy of cutting balloon angioplasty in treatment of angiographically moderate and severe calcified coronary lesions. Thirty-seven calcified coronary lesions (29 patients) detected by angiography were dilated with cutting balloon. Predilatation with plain balloon was performed in 27 (73.0%) lesions and stent was implanted in 23 (62.2%) lesions following cutting balloon. Acute gain following cutting balloon in predilated lesions was compared to the acute gain following plain balloon predilatation. For predilated lesions, acute gain after cutting balloon was significantly greater compared with plain balloon predilatation (1.51 +/- 0.49 vs. 0.77 +/- 0.42; P = 0.01). This result was achieved with larger size and lower pressure of cutting balloon compared with plain balloon (3.28 +/- 0.46 vs. 2.94 +/- 0.55, P = 0.01; 10.38 +/- 1.64 vs. 13.19 +/- 3.63, P = 0.001, respectively). The final gain following cutting balloon dilatation was significantly higher than the expected gain obtained by using a plain balloon of the same size (1.51 +/- 0.49 vs. 0.93 +/- 0.48; P < 0.0001), which was inflated at significantly higher pressure compared with cutting balloon. When we compared acute gain following cutting balloon in lesions with and without predilatation, we found no significant difference (P = 0.31). Angiographic success was achieved in 36 (97.3%) lesions and procedural success in 33 (89.1%) lesions. In-hospital major adverse cardiac event (MACE) occurred in three (10.3%) patients. Follow-up MACE was reported from three (10.3%) patients. In conclusion, cutting balloon angioplasty is feasible and safe in treatment of angiographically moderate and severe calcified lesions. Dilating efficiency of cutting balloon seems to be greater compared with a plain balloon of the same size, which was inflated at significantly higher pressure compared with cutting balloon. These results can be achieved with low in-hospital MACE and are associated with a good long-term outcome.

Aged↗
PubMed2001

Interferon regulatory factor 1 promoter polymorphism and response to type 1 interferon.

The clinical success of interferon-treatment has been found to vary in different individuals. To explain this, we hypothesized that responses to type 1 interferons could be partly determined by interferon regulatory factor-1 gene transcription, because the latter is an important transcription factor in the interferon system. We demonstrated that the antiproliferative effect of type 1 interferons on human liver cancer cells correlates with levels of transcription of the interferon regulatory factor-1 gene in parallel with those of p21(WAF-1) expression. Here, we investigated whether mutations in the interferon regulatory factor-1 gene cause different responses to type 1 interferons. DNA from several human liver cancer cell lines and peripheral blood mononuclear cells was investigated. Nucleotide sequences of the interferon regulatory factor-1 gene and polymerase chain reaction products of its upstream region were determined directly and after cloning. The promoter activity of the upstream region of this gene was measured by the luciferase reporter assay. We found 4 point mutations in the upstream (- 1 approximately - 495) region, and the luciferase promoter assay demonstrated that these mutations did modify promoter activity. Analysis of DNA from healthy volunteers showed that these mutations are single nucleotide polymorphisms. These results suggest that single nucleotide polymorphisms of the interferon regulatory factor-1 promoter contribute, at least in part, to determining responses to type 1 interferons. J. Cell. Biochem. Suppl. 36: 191-200, 2001.

Antineoplastic Agents↗
PubMed2001

Reduction of telomerase activity in human liver cancer cells by a histone deacetylase inhibitor.

The presence of telomerase has been demonstrated recently in many different malignancies. Several reports documented that in human hepatocellular carcinoma, the level of telomerase activity parallels its differentiation stage. In the present study, the effect of the differentiation-inducing agent sodium butyrate on telomerase activity in four human liver cancer cell lines was investigated using the telomeric repeat amplification protocol. We assayed telomerase activity before and after butyrate treatment and in cell cycle synchronized non-dividing quiescent cells. In addition, telomerase reverse transcriptase levels were measured at the mRNA level. All four cell lines possessed high but not identical levels of telomerase activity. Telomerase activity was significantly reduced by treatment with sodium butyrate as well as trichostatin A in a dose- and time-dependent fashion, paralleling the reduction of cell proliferation. Although methotrexate, hydroxyurea, and colchicine synchronized the cell cycle at G1, S, and G2/M, respectively, and thereby also caused proliferating cells to cease dividing and become quiescent, in this case telomerase activity remained essentially unaltered compared to the control cultures. Moreover, levels of mRNA encoding telomerase reverse transcriptase were not always significantly altered by either sodium butyrate treatment or cell cycle synchronization. These results suggest that sodium butyrate, as a histone deacetylase inhibitor, effectively reduces telomerase activity without affecting transcription levels of the reverse transcriptase component.

Antineoplastic Agents↗
PubMed2001

Reduction of c-myc expression by an antisense approach under Cre/loxP switching induces apoptosis in human liver cancer cells.

c-Myc has been documented to be both a positive and a negative signal for the induction of apoptosis. It is well known that overexpression of the c-myc gene induces apoptosis of normal cells, but the result of a reduction in its expression is not fully understood. We examined whether a reduction in c-myc expression would induce apoptosis in human liver cancer cells. Specifically, antisense and sense oligodeoxynucleotides (oligos) against the human c-myc mRNA were synthesized, mixed with a liposome reagent at various ratios, and were applied to the liver cancer-derived cell lines, HCC-T, HepG2, and PLC/PRF/5. To exclude effects resulting from using oligos, plasmid vectors expressing the full-length c-myc cDNA in both sense and antisense orientations under the control of the Cre/loxP system were generated. Monoclonal cell lines including these plasmid vectors were produced and Cre was supplied by adenovirus infection. Apoptosis was determined morphologically and c-Myc and Bcl-2 expression was examined by Western blotting. The antisense myc significantly inhibited the proliferation of the cells within two days, while neither the liposome reagent alone nor sense myc did so. Most of the cells were rounded up by the antisense-treatment and nuclear fragmentation and DNA ladder formation were detected after two days in antisense c-myc-treated cells. Antisense c-myc largely reduced c-Myc and partially Bcl-2 expression; overexpression of Bcl-2 partially rescued from apoptosis in HCC-T and HepG2 cells. These results suggest that the massive reduction in c-myc mRNA induces apoptosis in liver cancer cell lines and consequent decrease in Bcl-2 enhances the cell death. c-Myc reduction under the Cre/loxP switching system may be a useful tool for the clarification of c-myc-related cellular mechanisms in differentiation and proliferation.

Apoptosis↗
PubMed2001

Assessment of prediction accuracy of protein function from protein--protein interaction data.

Functional prediction of open reading frames coded in the genome is one of the most important tasks in yeast genomics. Among a number of large-scale experiments for assigning certain functional classes to proteins, experiments determining protein-protein interaction are especially important because interacting proteins usually have the same function. Thus, it seems possible to predict the function of a protein when the function of its interacting partner is known. However, in vitro experiments often suffer from artifacts and a protein can often have multiple binding partners with different functions. We developed an objective prediction method that can systematically include the information of indirect interaction. Our method can predict the subcellular localization, the cellular role and the biochemical function of yeast proteins with accuracies of 72.7%, 63.6% and 52.7%, respectively. The prediction accuracy rises for proteins with more than three binding partners and thus we present the open prediction results for 16 such proteins.

Fungal Proteins↗
PubMed2001

Systematic separation and purification of elastase, gelatinase (matrix metalloproteinase 9), and collagenase (matrix metalloproteinase 8) from polymorphonuclear leukocytes in dialyzers previously used by patients with renal failure.

We developed a simple and effective method for the systematic separation and purification of human polymorphonuclear leukocyte (PMN) proteinases, elastase, gelatinase (matrix metalloproteinase 9, type IV collagenase), and collagenase (matrix metalloproteinase 8), derived from the extracts of hollow fiber dialyzers that had been utilized in the treatment of patients with renal failure. The fraction containing elastase was grossly separated from that containing gelatinase and collagenase by heparin-Sepharose chromatography and purified in an aprotinin column. The remaining two enzymes were then separated using the gelatin-Sepharose column after gel chromatography following ammonium sulfate precipitation. Gelatinase and collagenase were further purified by gelatin-Sepharose chromatography as a latent form and by collagen-Sepharose chromatography as an activated form. This novel method offers procedural advantages over existing methods that separate PMNs from the whole blood of volunteers for experimental research purposes.

Animals↗
PubMed2001

Modified Loeffler's medial capsulotomy for osteoarthritis of the knee: 20 years' follow-up.

We reviewed 11 knees in ten patients at a mean follow-up of 23 years after a modified Loeffler's medial capsulotomy for osteoarthritis of the knee. The mean age was 59+/-8 years at surgery. The mean knee score (Hospital for Special Surgery) was 59 points before surgery and 79 points at follow-up. The long-term results of this operation were thus maintained over a prolonged period. This is a relatively simple procedure, which may be performed in the elderly, with satisfactory long-term results.

Adult↗
PubMed2001

Clinical benefits of lenograstim in patients with neutropenia due to chemotherapy for multiple myeloma (MM).

The object of this study was to determine the efficacy and safety of glycosylated recombinant human granulocyte colony-stimulating factor (rHuG-CSF; lenograstim) after combination chemotherapy consisting of ranimustine, vindesine, melphalan and prednisolone (MCNU-VMP). One hundred thirty-nine consecutive patients with newly diagnosed multiple myeloma (MM) were allocated at random to a lenograstim group (n = 70) or a placebo group (n = 69). Patients were treated with two cycles of MCNU-VMP, and either lenograstim (2 microg/kg daily, s.c.) or placebo was administered from the day neutrophils decreased to less than 1.000/microl and was discontinued when neutrophils exceeded 5,000/microl. The median duration of neutropenia (neutrophils under 1,000/microl) was significantly shorter for the lenograstim group than the placebo group (2 days vs 9 days in the first cycle; 1 day vs 13 days in the second cycle). The incidence of febrile neutropenia in the first cycle was significantly lower in the lenograstim group than in the placebo group (9.2% vs 30.4%). No life-threatening infections were observed in either group. The two cycles of MCNU-VMP therapy were completed in 90.8% of the patients, and a higher average relative dose intensity (ARDI; 0.94) was achieved in the lenograstim group. The tumor response rate of the lenograstim group (57.8%) was higher than that of the placebo group (43.1%), but the difference was not statistically significant (chi2 = 2.634, df = 1, P = 0.105). Lenograstim was well tolerated, and no unexpected adverse events occurred. Lenograstim proved effective in controlling chemotherapy-induced neutropenia in MM patients under MCNU-VMP therapy.

Adjuvants, Immunologic↗