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K Nakai

Publications and source records attributed to K Nakai.

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

DBTBS: a database of Bacillus subtilis promoters and transcription factors.

With the completion of the determination of its entire genome sequence, one of the next major targets of Bacillus subtilis genomics is to clarify the whole gene regulatory network. To this end, the results of systematic experiments should be compared with the rich source of individual experimental results accumulated so far. Thus, we constructed a database of the upstream regulatory information of B.subtilis (DBTBS). The current version was constructed by surveying 291 references and contains information on 90 binding factors and 403 promoters. For each promoter, all of its known cis-elements are listed according to their positions, while these cis-elements are aligned to illustrate their consensus sequence for each transcription factor. All probable transcription factors coded in the genome were classified with the Pfam motifs. Using this database, we compared the character of B.subtilis promoters with that of Escherichia coli promoters. Our database is accessible at http://elmo.ims.u-tokyo.ac.jp/dbtbs/.

Bacillus subtilis↗
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

Billroth I gastrectomy using a circular stapler to treat gastric cancer.

We describe herein our technique of performing gastrectomy followed by side-to-end gastroduodenostomy. Because the clamp is removed at the resection line of the greater curvature, there is no need to perform an additional gastrotomy for insertion of the instrument. This feature differentiates our technique from previous methods of anastomosis using the circular stapler. We believe that our technique is superior in simplicity and security to the traditional hand-sewn anastomosis. Moreover, it allows for a shorter operative time. This technique is recommended for practical surgery over conventional techniques.

Anastomosis, Surgical↗
PubMed2001

Combined surgery and endovascular stenting for basilar artery stenosis refractory to balloon angioplasty: technical case report.

The authors report a case of symptomatic basilar artery stenosis treated by stenting via the surgically exposed C1 vertebral artery. This case was initially treated by percutaneous transluminal angioplasty via a transfemoral route but resulted in unsatisfactory dilatation. Stenting via a transfemoral route also resulted in failure because of the coiling of the proximal vertebral artery. Direct puncture of the vertebral artery beyond the coiling portion was tried but a stent could not be delivered beyond the C2 vertebrae. Finally, the vertebral artery was surgically exposed between C1 and the occipital bone and a stent was introduced into the lesion from this portion under fluoroscopic control. The basilar artery was fully opened by stenting without new neurological deficits. Stenting of the basilar artery via a transfemoral route is not always possible even with newer generation stents if the vertebral artery has elongated tortuous curves. Combined surgery and endovascular stenting is one of the alternatives in such cases including our case.

Aged↗
PubMed2001

Successful application of nonmyeloablative transplantation for paroxysmal nocturnal hemoglobinuria.

OBJECTIVE: Paroxysmal nocturnal hemoglobinuria (PNH) is an acquired clonal hematopoietic stem cell disorder that manifests as hemolytic anemia, venous thrombosis, and deficient hematopoiesis. Although allogeneic hematopoietic stem cell transplantation is considered the only curative therapeutic measure, transplant-related mortality is not negligible. Several studies supported the use of nonmyeloablative stem cell transplantation (NST) for patients of advanced age or with organ dysfunction. Hence, we used NST in a PNH patient who suffered from acute renal failure due to repeated episodes of hemolysis. MATERIALS AND METHODS: We performed NST using a conditioning regimen consisting of cladribine 0.11 mg/kg x 6, busulfan 4 mg/kg x 2, and rabbit anti-thymocyte globulin 2.5 mg/kg x 2. He received peripheral blood stem cells from his human leukocyte antigen-matched brother. Prophylaxis against graft-vs-host disease was performed with cyclosporine A alone. Chimerism of peripheral blood mononuclear cells was evaluated serially using short tandem repeat analysis and flow cytometry. RESULTS: No meaningful regimen-related toxicities were documented. Donor chimerism of 90 to 100% was achieved on day 14 and thereafter. The patient is doing well, without any recurrence of hemolysis 6 months after transplant. Follow-up chimerism studies confirmed stable and functioning donor-type hematopoiesis. CONCLUSIONS: NST may become a safe and curative approach in patients with PNH. Further studies are needed to establish the role of NST for treatment of PNH.

Antilymphocyte Serum↗
PubMed2001

Diffusion-weighted echo-planar MR imaging of CNS involvement in systemic lupus erythematosus.

RATIONALE AND OBJECTIVES: The purpose of this study was to determine the range of findings at diffusion-weighted magnetic resonance (MR) imaging in patients with systemic lupus erythematosus (SLE) and central nervous system involvement. MATERIALS AND METHODS: Diffusion-weighted MR images were reviewed in 20 patients with SLE and correlated with clinical symptoms and findings at computed tomography, conventional MR imaging, MR angiography, or conventional angiography. RESULTS: Diffusion-weighted MR imaging showed acute or subacute lesions in nine of 20 patients (45%). In the other 11, it showed no abnormal findings or chronic lesions. In four of the nine patients with lesions, diffusion-weighted imaging primarily showed hyperintense lesions with decreased apparent diffusion coefficient (ADC), which indicates acute or subacute infarcts. In four other patients, it primarily showed iso- or slightly hyperintense lesions with increased ADC, suggesting vasogenic edema. In two of these four patients, the findings were consistent with hypertensive encephalopathy. In the other two, small hyperintense foci on diffusion-weighted images with decreased ADC were seen within the vasogenic edema. These foci presumably represent microinfarcts associated with SLE vasculopathy. In the ninth patient, diffusion-weighted imaging showed a small linear hyperintense lesion with normal ADC in the left parietooccipital region. CONCLUSION: Diffusion-weighted imaging shows primarily two patterns of acute or subacute parenchymal lesions in patients with SLE: acute or subacute infarction and vasogenic edema with or without microinfarcts.

Adult↗
PubMed2001

Dose-dependent conjugation of sulfobromophthalein and hepatic transit time in bile fistula rats: role of the microtubule-dependent vesicle pathway.

Sulfobromophthalein (BSP) is selectively taken up by the liver and secreted into the bile as unconjugated and conjugated forms. Our previous study demonstrated that unconjugated BSP, but not conjugated BSP, caused the dissociation of biliary lipid secretion from that of bile acids, suggesting that the hepatic BSP conjugation rate partly regulated biliary lipid secretion. To evaluate the mechanisms through which biliary lipid secretion is regulated by exogenous organic anions, we intravenously administered BSP to male Sprague-Dawley rats at various doses either continuously or as a bolus. Then the relationship of the dose of BSP to its conjugation rate, hepatic transit time, and biliary lipid secretion was determined. BSP decreased biliary secretion of cholesterol and phospholipids in a dose-dependent manner without affecting bile acid secretion. In contrast, the proportion of conjugated BSP in bile was associated with the dose. Although the serum clearance of BSP after bolus infusion was constant regardless of the dose administered (50 or 200 nmol/100 g), BSP secretion was delayed with increasing doses: unconjugated BSP was secreted predominantly in the early phase (0-15 min after bolus injection), and conjugated BSP was the predominant form in the late phase (15-30 min). Pretreatment with colchicine reduced the conjugation rate and hepatic transit time of BSP, suggesting that the microtubule-dependent vesicle pathway plays a role in biliary excretion and conjugation of BSP. We conclude that biliary lipid secretion is influenced by organic anions with an affinity for bile acids such as BSP and that this effect is dependent upon the hepatic metabolic rate, i.e., conjugation rate. The hepatic transit time also plays a key role in this process by influencing metabolism.

Animals↗
PubMed2001

Phospholipid alterations in hepatocyte membranes and transporter protein changes in cholestatic rat model.

Biliary components are transported by hepatic adenosine triphosphate-binding cassette (ABC) transporters that are located in canalicular membranes. Physiological transporter function is related to membrane fluidity, which is modulated by the phospholipid composition of the lipid bilayer. We hypothesized that cholestasis may alter transporter function by modifying phospholipid species to protect the cell from cholestatic damage. Therefore, we examined the expression of ABC transport proteins and their mRNA levels in canalicular membrane vesicles isolated from rat liver 6 hr or three days after bile duct ligation. Membrane lipid composition and membrane fluidity of both sinusoidal and canalicular membrane vesicles were also examined. By 6 hr after bile duct ligation, we found a clear increase of mdr2 and bsep mRNA. These changes were associated with an increase of mdr-Pgp and with a clear decrease of mrp2 protein, and small decrease of bsep protein. In addition, mdrlb mRNA showed a strong increase by three days after bile duct ligation. Canalicular membrane fluidity decreased in a marked time-dependent manner, whereas sinusoidal membranes showed biphasic changes: increased fluidity at 6 hr and a decrease at three days. These changes were closely related to the changes of membrane lipid constitution; the saturated/unsaturated fatty acid ratio increased for phosphatidylcholine in canalicular membrane and the reverse occurred in sinusoidal membrane, and those for sphingomyelin showed the opposite pattern. We conclude that cholestasis causes modulation of ABC transporters as well as that of the lipid constitution in lipid bilayer. These may confer cytoprotective resistance to hepatocytes against cholestatic stress.

ATP-Binding Cassette Transporters↗
PubMed2001

Association of BMI with the beta3-adrenergic receptor gene polymorphism in Japanese: meta-analysis.

OBJECTIVE: To assess the effect of the Trp64Arg polymorphism in the beta3-adrenergic receptor gene (ADRB3) on body mass index (BMI) in the Japanese population. RESEARCH METHODS AND PROCEDURES: We selected studies that evaluated the association between BMI and ADRB3 polymorphism among Japanese, using MEDLINE and PubMed. After data collection, an extension of ANOVA was performed to assess the differences according to the genotype. RESULTS: In a total of 35 subgroups including 2316 subjects with the Trp64Arg variant and 4266 subjects without this variant, the weighted mean difference in BMI was 0.26 kg/m(2) (95% confidence interval: 0.18 to 0.42; p < 0.01), indicating that variant carriers exhibited higher BMI than did normal homozygous subjects. DISCUSSION: Although it is known that the allele frequency of the ADRB3 polymorphism differs among races, this study focuses on the Japanese population, which has a high allele frequency of ADRB3 polymorphism. We assumed that statistical errors would be prevented due to the sufficient number of subjects. In conclusion, the results support the hypothesis that ADRB3 gene polymorphism is associated with BMI.

Alleles↗
PubMed2001

Pre-emptive therapy against cytomegalovirus (CMV) disease guided by CMV antigenemia assay after allogeneic hematopoietic stem cell transplantation: a single-center experience in Japan.

From April 1998 to March 2000, a cytomegalovirus (CMV) antigenemia-guided pre-emptive approach for CMV disease was evaluated in 77 adult patients who received allogeneic hematopoietic stem cell transplantation at the National Cancer Center Hospital. A CMV antigenemia assay was performed at least once a week after engraftment. High-level antigenemia was defined as a positive result with 10 or more positive cells per 50 000 cells and low-level antigenemia was defined as less than 10 positive cells. Among the 74 patients with initial engraftment, 51 developed positive antigenemia. Transplantation from alternative donors and the development of grade II-IV GVHD were independent risk factors for positive antigenemia. Ganciclovir was administered as pre-emptive therapy in 39 patients in a risk-adapted manner. None of the nine low-risk patients with low-level antigenemia as their initial positive result developed high-level antigenemia even though ganciclovir was withheld. Only one patient developed early CMV disease (hepatitis) during the study period. CMV antigenemia resolved in all but two cases, in whom ganciclovir was replaced with foscarnet. In eight patients, however, the neutrophil count decreased to 0.5 x 10(9)/l or less after starting ganciclovir, including three with documented infections and two with subsequent secondary graft failure. The total amount of ganciclovir and possibly the duration of high-dose ganciclovir might affect the incidence of neutropenia. We concluded that antigenemia-guided pre-emptive therapy with a decreased dose of ganciclovir and response-oriented dose adjustment might be appropriate to decrease the toxicity of ganciclovir without increasing the risk of CMV disease.

Adolescent↗
PubMed2001

Long-term low-dose acyclovir against varicella-zoster virus reactivation after allogeneic hematopoietic stem cell transplantation.

To evaluate the efficacy of long-term administration of acyclovir as prophylaxis against varicella-zoster virus (VZV) reactivation, we analyzed the medical records of 86 consecutive adult patients who obtained engraftment after allogeneic hematopoietic stem cell transplantation from January 1996 to March 2000. We started long-term low-dose (400 mg/day) oral administration of acyclovir in June 1999, and this was continued until the end of immunosuppressive therapy after transplantation. There was no breakthrough reactivation of VZV in patients receiving acyclovir. Five patients who were receiving cyclosporine or prednisolone developed VZV reactivation after discontinuing acyclovir. With this prophylaxis, the cumulative incidence of VZV reactivation at 1 year after transplantation decreased from 33% to 10% (P = 0.025). On multivariate analysis, the use of long-term acyclovir was identified as a significant independent parameter for the development of VZV reactivation. These findings suggest the efficacy of long-term prophylaxis with low-dose acyclovir. Resumption of acyclovir upon restarting immunosuppressive therapy might be important for the further prevention of VZV reactivation. The benefit of long-term low-dose acyclovir should be confirmed prospectively.

Acyclovir↗
PubMed2001

Gangliosides GD1b, GT1b, and GQ1b suppress the growth of human melanoma by inhibiting interleukin-8 production: the inhibition of adenylate cyclase.

We studied the effects of various gangliosides on in vitro growth of human metastatic melanoma WM266-4. GD1b, GT1b, and GQ1b inhibited 3H-thymidine uptake and growth rate of WM266-4 whereas the other gangliosides were ineffective. The growth inhibition by GD1b, GT1b, and GQ1b was counteracted by interleukin-8 but not by the other growth factors. The growth inhibition by gangliosides was not detected in the presence of anti-interleukin-8 antibody. GD1b, GT1b, and GQ1b reduced the constitutive interleukin-8 secretion and mRNA levels in WM266-4. Transient transfection showed that GD1b, GT1b, and GQ1b inhibited the constitutive chloramphenicol acetyltransferase expression driven by interleukin-8 promoter in WM266-4. Transfection with a series of 5'-deleted mutants demonstrated that the sequences between -98 and -62 bp on interleukin-8 promoter may be involved in the transcriptional repression by these gangliosides. Cyclic AMP analog dibutyryl cAMP counteracted GD1b, GT1b, and GQ1b-induced inhibition of interleukin-8 production at the levels of protein secretion, mRNA expression, and promoter activity. GD1b, GT1b, and GQ1b reduced cAMP level and protein kinase A activity in WM266-4. These gangliosides suppressed adenylate cyclase activity without altering that of cyclic nucleotide phosphodiesterase in WM266-4. The data indicate that GD1b, GT1b, and GQ1b may suppress the growth of melanoma by inhibiting interleukin-8 production via the inhibition of adenylate cyclase.

3',5'-Cyclic-AMP Phosphodiesterases↗
PubMed2001

Jargonagraphia with severe aphasia due to a right hemisphere lesion: case report.

The authors report a case of a patient who developed jargonagraphia, severe aphasia, unilateral spatial neglect and apraxia due to a right hemisphere lesion. Jargonagraphia with severe aphasia, unilateral spatial neglect and apraxia is quite rare. The mechanisms of jargonagraphia remain unknown. A possible mechanism underlying this case of jargonagraphia is discussed.

Agraphia↗