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Search Results: 1 - 10 of 2803 matches for " Satoshi Nishikawa "
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Calcified Nodule Formation in Vitro Using Rat Mandibular Incisor Pulp Cells  [PDF]
Hideaki Ikenaga, Masataka Yoshikawa, Ayano Miyamoto, Hitomi Nakama, Ikuo Nishikawa, Satoshi Teramoto, Hiroaki Aso, Nozomi Matsuo, Hiroshi Maeda
Journal of Biomedical Science and Engineering (JBiSE) , 2018, DOI: 10.4236/jbise.2018.1112027
Abstract: One great advantage of bone marrow is that a large number of stem cells can be obtained. However, stem cells cannot be taken from the bone marrow of a patient for the purpose of regenerating teeth. In dental practice, it may not be practical to obtain mesenchymal stem cells for the regeneration of the tooth from iliac bone marrow, as in orthopedics. Therefore, establishment of a cell source for tooth regeneration is one of the important problems in the field of regenerative medicine. Although the isolation of undifferentiated mesenchymal stem cells or odontoblasts from dental pulp may be difficult, dental pulp may be a favorable source for stem cells to regenerate a tooth via tissue engineering. As a fundamental study for tooth regeneration, this study was performed in order to clarify the culture periods for proliferation and differentiation using rat dental pulp-derived cells. The results of this study were as follows: Primary culture of the dental pulp cells does not require a long period of time. However, for sufficient proliferation of dental pulp cells to form a calcified nodule in the secondary culture, a long culture period is required. Dexamethasone was essential for the formation of calcified nodules by dental pulp-derived cells. Calcified nodule formation by dental pulp-derived cells in vitro required more than one month. The duration of the secondary culture for the dental pulp-derived cells will be much longer.
Computational Prediction of O-linked Glycosylation Sites that Preferentially Map on Intrinsically Disordered Regions of Extracellular Proteins
Ikuko Nishikawa,Yukiko Nakajima,Masahiro Ito,Satoshi Fukuchi,Keiichi Homma,Ken Nishikawa
International Journal of Molecular Sciences , 2010, DOI: 10.3390/ijms11124991
Abstract: O-glycosylation of mammalian proteins is one of the important posttranslational modifications. We applied a support vector machine (SVM) to predict whether Ser or Thr is glycosylated, in order to elucidate the O-glycosylation mechanism. O-glycosylated sites were often found clustered along the sequence, whereas other sites were located sporadically. Therefore, we developed two types of SVMs for predicting clustered and isolated sites separately. We found that the amino acid composition was effective for predicting the clustered type, whereas the site-specific algorithm was effective for the isolated type. The highest prediction accuracy for the clustered type was 74%, while that for the isolated type was 79%. The existence frequency of amino acids around the O-glycosylation sites was different in the two types: namely, Pro, Val and Ala had high existence probabilities at each specific position relative to a glycosylation site, especially for the isolated type. Independent component analyses for the amino acid sequences around O-glycosylation sites showed the position-specific existences of the identified amino acids as independent components. The O-glycosylation sites were preferentially located within intrinsically disordered regions of extracellular proteins: particularly, more than 90% of the clustered O-GalNAc glycosylation sites were observed in intrinsically disordered regions. This feature could be the key for understanding the non-conservation property of O-glycosylation, and its role in functional diversity and structural stability.
E-Cadherin Promotes Incorporation of Mouse Epiblast Stem Cells into Normal Development
Satoshi Ohtsuka, Satomi Nishikawa-Torikai, Hitoshi Niwa
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0045220
Abstract: Mouse epiblast stem cells (mEpiSCs) are pluripotent stem cells derived from epiblasts of postimplantation mouse embryos. Their pluripotency is distinct from that of mouse embryonic stem cells (mESCs) in several cell biological criteria. One of the distinctions is that mEpiSCs contribute either not at all or at much lower efficiency to chimeric embryos after blastocyst injection compared to mESCs. However, here we showed that mEpiSCs can be incorporated into normal development after blastocyst injection by forced expression of the E-cadherin transgene for 2 days in culture. Using this strategy, mEpiSCs gave rise to live-born chimeras from 5% of the manipulated blastocysts. There were no obvious signs of reprogramming of mEpiSCs toward the mESC-like state during the 2 days after induction of the E-cadherin transgene, suggesting that mEpiSCs possess latent ability to integrate into the normal developmental process as its origin, epiblasts.
Binary classification of protein molecules into intrinsically disordered and ordered segments
Satoshi Fukuchi, Kazuo Hosoda, Keiichi Homma, Takashi Gojobori, Ken Nishikawa
BMC Structural Biology , 2011, DOI: 10.1186/1472-6807-11-29
Abstract: In contrast to other available ID prediction programs that merely identify likely ID regions, the DICHOT system we previously developed classifies the entire protein sequence into SDs and ID regions. Application of DICHOT to the human proteome revealed that residue-wise ID regions constitute 35%, SDs with similarity to PDB structures comprise 52%, while SDs with no similarity to PDB structures account for the remaining 13%. The last group consists of novel structural domains, termed cryptic domains, which serve as good targets of structural genomics. The DICHOT method applied to the proteomes of other model organisms indicated that eukaryotes generally have high ID contents, while prokaryotes do not. In human proteins, ID contents differ among subcellular localizations: nuclear proteins had the highest residue-wise ID fraction (47%), while mitochondrial proteins exhibited the lowest (13%). Phosphorylation and O-linked glycosylation sites were found to be located preferentially in ID regions. As O-linked glycans are attached to residues in the extracellular regions of proteins, the modification is likely to protect the ID regions from proteolytic cleavage in the extracellular environment. Alternative splicing events tend to occur more frequently in ID regions. We interpret this as evidence that natural selection is operating at the protein level in alternative splicing.We classified entire regions of proteins into the two categories, SDs and ID regions and thereby obtained various kinds of complete genome-wide statistics. The results of the present study are important basic information for understanding protein structural architectures and have been made publicly available at http://spock.genes.nig.ac.jp/~genome/DICHOT webcite.Understanding of human proteins is doubtlessly essential for both basic and applied sciences. With protein structures accumulating and protein structure prediction improving, it is becoming increasingly accurate to assign structural domains (SD
Development of an accurate classification system of proteins into structured and unstructured regions that uncovers novel structural domains: its application to human transcription factors
Satoshi Fukuchi, Keiichi Homma, Yoshiaki Minezaki, Takashi Gojobori, Ken Nishikawa
BMC Structural Biology , 2009, DOI: 10.1186/1472-6807-9-26
Abstract: The new dichotomic system first identifies domains of known structures, followed by assignment of structural domains and ID regions with a combination of pre-existing tools and a newly developed program based on sequence divergence, taking un-aligned regions into consideration. The system was found to be highly accurate: its application to a set of proteins with experimentally verified ID regions had an error rate as low as 2%. Application of this system to human TFs (401 proteins) showed that 38% of the residues were in structural domains, while 62% were in ID regions. The preponderance of ID regions makes a sharp contrast to TFs of Escherichia coli (229 proteins), in which only 5% fell in ID regions. The method also revealed that 4.0% and 11.8% of the total length in human and E. coli TFs, respectively, are comprised of structural domains whose structures have not been determined.The present system verifies that sequence divergence including information of unaligned regions is a good indicator of ID regions. The system for the first time estimates the complete fractioning of structured/un-structured regions in human TFs, also revealing structural domains without homology to known structures. These predicted novel structural domains are good targets of structural genomics. When applied to other proteins, the system is expected to uncover more novel structural domains.Recent studies revealed that a high fraction of proteins in eukaryotes have long stretches of intrinsically disordered (ID) regions [1,2]. Proteins with ID regions, abundant in the cytosol and nucleus but scarce in mitochondria [3], are frequently involved in cellular regulatory processes such as transcription, translation, and cellular signaling transduction [4-7]. The abundance of proteins with ID regions in the cells can be tightly controlled by regulation of transcript clearance, proteolytic degradation, and translational rate[8]. Transcription factors (TFs) such as activators, repressors, or enhan
Gene cluster analysis method reliably identifies horizontally transferred genes and reveals their involvement in operon formation
Keiichi Homma,Satoshi Fukuchi,Yoji Nakamura,Takashi Gojobori,Ken Nishikawa
Quantitative Biology , 2006,
Abstract: The formation mechanism of operons remains controversial despite the proposal of many models. Although acquisition of genes from other species, horizontal gene transfer, is considered to occur, definitive concrete cases have been unavailable. It is desirable to select horizontally transferred genes reliably and examine their relationship to operons. We here developed a method to identify candidates of horizontally transferred genes based on minimization of gene cluster insertions/deletions. To select a benchmark set of positively horizontally transferred genes against which the candidate set can be appraised, we devised another procedure using intergenetic alignments. Comparison with the benchmark set of horizontally transferred genes demonstrated the absence of a significant number of false positives in the candidates, showing that the method identifies horizontally transferred genes with a high degree of confidence. Horizontally transferred genes constitute at least 5.5% of the genes in Escherichia, Shigella, and Salmonella and ~46% of which originate from other gamma-proteobacteria. Not only informational genes, but also operational genes (those involved in housekeeping) are horizontally transferred less frequently than expected. A gene-cluster analysis of Escherichia coli K-12 operons revealed that horizontal transfer produced four entire operons and expanded two operons, but deletion of intervening genes accounts for the formation of no operons. We propose that operons generally form by horizontal gene transfer. We further suggest that genes with related essential functions tend to reside in conserved operons, while genes in nonconserved operons generally confer slight advantage to the organisms and frequently undergo horizontal transfer and decay.
Novel gene cluster analysis method identifies horizontally transferred genes with high reliability and reveals their involvement in operon formation
Keiichi Homma,Satoshi Fukuchi,Yoji Nakamura,Takashi Gojobori,Ken Nishikawa
Quantitative Biology , 2005,
Abstract: This paper was withdrawn by the authors.
Hyperbaric oxygen therapy for painful bladder syndrome/interstitial cystitis resistant to conventional treatments: long-term results of a case series in Japan
Tomoaki Tanaka, Yujiro Nitta, Kazuya Morimoto, Noriaki Nishikawa, Chikako Nishihara, Satoshi Tamada, Hidenori Kawashima, Tatsuya Nakatani
BMC Urology , 2011, DOI: 10.1186/1471-2490-11-11
Abstract: HBO treatment (2.0 ATA for 60 minutes/day × 5 days/week for 2 or 4 weeks) was performed on 11 patients with severe symptoms that had not been improved by previous therapy regimens between December 2004 and July 2009.Seven of the 11 patients demonstrated persistent improvement in symptoms during the 12 months after HBO treatment. These responders demonstrated a decrease in the pelvic pain scale and urgency scale from 7.7 ± 1.0 and, 6.6 ± 0.9 to 3.4 ± 2.5 and 4.3 ± 2.4 after 12 months, respectively (p < 0.05). The total score of the interstitial cystitis symptom index and 24-hour urinary frequency demonstrated a significant sustained decrease from the baseline. Two responders, who received an additional course of HBO 12 and 13 months after initial treatment, respectively, did not suffer impairment for more than two years. There was one case of transient eustachian tube dysfunction and three cases of reversible exudative otitis media as a consequence of HBO treatment.HBO is a potent treatment for PBS/IC patients resistant to conventional therapy. It was well tolerated and provided maintained amelioration of pain, urgency and urinary frequency for at least 12 months.Painful bladder syndrome/interstitial cystitis (PBS/IC) is a collective term covering a range of clinical complaints and pathological findings. Approximately 10-50% of PBS/IC patients demonstrate a classical mucosal ulcer (Hunner's ulcer), and the majority are diagnosed on the basis of positive factors and exclusions derived from the diagnostic criteria of the National Institute of Diabetes and Digestive and Kidney Diseases for IC [1,2]. The etiology of PBS/IC includes a diversity of factors and remains poorly understood. Therefore, appropriate therapy has not been established from clinical evidence [3-5]. Hyperbaric oxygen (HBO) therapy has been reported to be effective in patients with cyclophosphamide-induced hemorrhagic cystitis and chronic radiation cystitis for approximately 20 years [6-9]. The patholo
Reconsideration of Augmentation Strategies in Electroconvulsive Therapy: Effects of the Concurrent Use of a Reduced Dose of Propofol with Divided Supplemental Remifentanil and Moderate Hyperventilation on Electroconvulsive Therapy-Induced Seizure Production and Adverse Events  [PDF]
Kohki Nishikawa, Michiaki Yamakage
Open Journal of Anesthesiology (OJAnes) , 2015, DOI: 10.4236/ojanes.2015.510040
Abstract: Background: Although several treatment strategies to enhance the efficacy of electroconvulsive therapy (ECT) have been discussed, there have been no reports on the combined use of these treatments. The purpose of this study was to evaluate the efficacy and safety of concurrent use of moderate hyperventilation and a reduced dose of propofol combined with divided remifentanil in ECT practice. Methods: Sixty patients scheduled to receive a total of 300 ECT treatments were randomly assigned to have the three interventions: a standard dose (1 mg/kg) of propofol (group P/N); a standard dose of propofol and moderate hyperventilation with end-tidal pressure of carbon dioxide (ETCO2) of 30 - 35 mmHg (group P/H); and a reduced dose (0.5 mg/kg) of propofol with divided supplemental remifentanil and moderate hyperventilation (group RP/H). Patients in group RP/H received remifentanil 1 μg/kg followed by propofol 0.5 mg/kg for unconsciousness and thereafter remifentanil 1 μg/kg immediately before the ECT stimulus. Results: Patients in group RP/H showed significantly longer durations of electroencephalographic (EEG) seizures in the early phase of ECT course (P < 0.01 and 0.05) and lower electrical stimulus in the late phase of ECT course (P < 0.05 in each) than those in groups P/N and P/H, respectively. Conclusions: The use of a reduced dose of propofol combined with divided supplemental remifentanil under moderate hyperventilation during ECT can offer advantages over the use of a standard dose of propofol with or without moderate hyperventilation in terms of more seizure augmentation and/or lower electrical stimulus.
Direct Process to Prepare Crystallized Freestanding Membranes of Hydroxyapatite Using Sacrificial Layer of Barium-Compounds  [PDF]
Hiroaki Nishikawa, Takafumi Nishii
Journal of Crystallization Process and Technology (JCPT) , 2017, DOI: 10.4236/jcpt.2017.72003
Abstract: Freestanding membrane (FSM) of hydroxyapatite (HA) is a thin sheet of pure HA without any supporting substrates. Our original preparation process of FSM of HA had three steps: The first was the deposition of HA layer on sacrificial layer of solvent-soluble materials, the second was separation of FSM of HA by means of dissolution of sacrificial layer, and the third was post-annealing to crystallize FSM of HA. To date, the post-annealing process was a serious bottleneck of productivity owing to its too long time. In this short report, we proposed a novel sacrificial layer, heatproof and water-soluble Ba-compound, which makes the direct deposition of crystallized HA possible due to its heatproof property because the problem on the original process was that the previous sacrificial layers have no heatproof property and HA layer should be deposited as amorphous. We can deposit the Ba-compound sacrificial layer only in 1 hour followed with the direct deposition of crystallized HA layer, substituting the 20 hours of post-annealing. The FSM of HA was separated successfully from the substrate by means of dissolution of Ba-compound with water. Our novel process can shrink the process time by 19 hours.
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