Matsumoto T

References (20)

Title : Clinical impact of diarrhea during enteral feeding after esophagectomy - Haneda_2023_Int.J.Clin.Oncol__
Author(s) : Haneda R , Hiramatsu Y , Kawata S , Soneda W , Booka E , Murakami T , Matsumoto T , Morita Y , Kikuchi H , Takeuchi H
Ref : Int J Clin Oncol , : , 2023
Abstract : BACKGROUND: Enteral feeding (EF) is recommended to enhance nutritional status after esophagectomy; however, diarrhea is a common complication of EF. We investigated the clinical and prognostic impact of diarrhea during EF after esophagectomy. METHODS: One hundred and fifty-two patients who underwent transthoracic esophagectomy were enrolled. The King's stool chart was used for stool characterization. The short- and long-term outcomes were compared between a non-diarrhea (Group N) and diarrhea group (Group D). RESULTS: A higher dysphagia score (<= 1) was observed more frequently in Group D than in Group N (45.7% vs. 19.8%, p = 0.002). Deterioration of serum total protein, serum albumin, serum cholinesterase, and the prognostic nutritional index after esophagectomy was greater in Group D than in Group N (p = 0.003, 0.004, 0.014, and 0.001, respectively). Patients in Group D had significantly worse overall survival (OS) and recurrence-free survival (RFS) than those in Group N (median survival time (MST): OS, 21.9 vs. 30.6 months, p = 0.001; RFS, 12.4 vs. 27.7 months, p < 0.001). In stratified analysis due to age, although there was no difference in OS with or without diarrhea in young patients (MST: 24.1 months in a diarrhea group vs. 33.6 months in a non-diarrhea group, p = 0.218), patients in a diarrhea group had significantly worse OS than those in a non-diarrhea group in elderly patients (MST: 17.8 months vs. 27.9 months, p < 0.001). CONCLUSIONS: Diarrhea during EF can put elderly patients at risk of postoperative malnutrition and a poor prognosis after esophagectomy.
ESTHER : Haneda_2023_Int.J.Clin.Oncol__
PubMedSearch : Haneda_2023_Int.J.Clin.Oncol__
PubMedID: 37994975

Title : Thioester-Based Coupled Fluorogenic Assays in Microdevice for the Detection of Single-Molecule Enzyme Activities of Esterases with Specified Substrate Recognition - Ukegawa_2023_Adv.Sci.(Weinh)__e2306559
Author(s) : Ukegawa T , Komatsu T , Minoda M , Matsumoto T , Iwasaka T , Mizuno T , Tachibana R , Sakamoto S , Hanaoka K , Kusuhara H , Honda K , Watanabe R , Urano Y
Ref : Adv Sci (Weinh) , :e2306559 , 2023
Abstract : Single-molecule enzyme activity assay is a platform that enables the analysis of enzyme activities at single proteoform level. The limitation of the targetable enzymes is the major drawback of the assay, but the general assay platform is reported to study single-molecule enzyme activities of esterases based on the coupled assay using thioesters as substrate analogues. The coupled assay is realized by developing highly water-soluble thiol-reacting probes based on phosphonate-substituted boron dipyrromethene (BODIPY). The system enables the detection of cholinesterase activities in blood samples at single-molecule level, and it is shown that the dissecting alterations of single-molecule esterase activities can serve as an informative platform for activity-based diagnosis.
ESTHER : Ukegawa_2023_Adv.Sci.(Weinh)__e2306559
PubMedSearch : Ukegawa_2023_Adv.Sci.(Weinh)__e2306559
PubMedID: 38140707

Title : Hemorrhoidectomy for elderly patients aged 75 years or more, before and after studies - Yamamoto_2020_Ann.Med.Surg.(Lond)_55_88
Author(s) : Yamamoto M , Ikeda M , Matsumoto T , Takemoto M , Sumimoto R , Kobayashi T , Ohdan H
Ref : Ann Med Surg (Lond) , 55 :88 , 2020
Abstract : Background: The incidence of hemorrhoids requiring hemorrhoidectomy among the elderly has been increasing. Old age is sometimes considered a contraindication for surgery. The relationship between age and complications of hemorrhoidectomy for elderly patients is not well established. This study aimed to compare the clinicopathological features and postoperative outcomes of hemorrhoidectomy in the elderly (>/=75 years old) and non-elderly patients (<75 years old). Methods: A total of 100 patients who underwent hemorrhoidectomy for hemorrhoids of Goligher classification grades 3 and 4 at our institution between 2014 and 2018 were enrolled. The clinical characteristics were compared between the elderly and non-elderly patients. Pain scores were measured at 6, 12, 24, and 48 h after surgery. The risk factors for postoperative complications were identified. Results: A total of 34 patients were classified as elderly patients. In the elderly group, aspartate aminotransferase levels were higher while the albumin levels and cholinesterase levels were lower and the platelet counts were significantly lower. The blood urea nitrogen levels were higher and estimated glomerular filtration rates and hemoglobin levels were significantly lower in the elderly group. The pain scores significantly decreased at 48 h postoperatively compared to those recorded at 6 h postoperatively in both groups. Multivariate analysis identified Goligher classification grade 4 and high neutrophil to lymphocyte ratio at the indicators of complications. Conclusions: Hemorrhoids due to impairment of liver function and kidney function were dominant in elderly patients. Aging itself was not a risk factor for postoperative complications.
ESTHER : Yamamoto_2020_Ann.Med.Surg.(Lond)_55_88
PubMedSearch : Yamamoto_2020_Ann.Med.Surg.(Lond)_55_88
PubMedID: 32477502

Title : Cholinesterase inhibitor rivastigmine enhances nerve growth factor-induced neurite outgrowth in PC12 cells via sigma-1 and sigma-2 receptors - Terada_2018_PLoS.One_13_e0209250
Author(s) : Terada K , Migita K , Matsushima Y , Sugimoto Y , Kamei C , Matsumoto T , Mori M , Matsunaga K , Takata J , Karube Y
Ref : PLoS ONE , 13 :e0209250 , 2018
Abstract : Rivastigmine (Riv) is a potent and selective cholinesterase (acetylcholinesterase, AChE and butyrylcholinesterase, BuChE) inhibitor developed for the treatment of Alzheimer's disease (AD). To elucidate whether Riv causes neuronal differentiation, we examined its effect on nerve growth factor (NGF)-induced neurite outgrowth in PC12 cells. At concentrations of 0-100 muM, Riv was non-toxic in PC12 cells. Riv caused dose-dependent (10-100 muM) enhancement of NGF-induced neurite outgrowth, which was completely inhibited by the TrkA antagonist GW-441756. By contrast, Riv-mediated enhancement of neurite outgrowth was not blocked by the acetylcholine receptor antagonists, scopolamine and hexamethonium. However, the sigma-1 receptor (Sig-1R) antagonist NE-100 and sigma-2 receptor (Sig-2R) antagonist SM-21 each blocked about half of the Riv-mediated enhancement of NGF-induced neurite outgrowth. Interestingly, the simultaneous application of NE-100 and SM-21 completely blocked the enhancement of NGF-induced neurite outgrowth by Riv. These findings suggest that both Sig-1R and Sig-2R play important roles in NGF-induced neurite outgrowth through TrkA and that Riv may contribute to neuronal repair via Sig-1R and Sig-2R in AD therapy.
ESTHER : Terada_2018_PLoS.One_13_e0209250
PubMedSearch : Terada_2018_PLoS.One_13_e0209250
PubMedID: 30557385

Title : The early diverging ascomycetous budding yeast Saitoella complicata has three histone deacetylases belonging to the Clr6, Hos2, and Rpd3 lineages - Nishida_2014_J.Gen.Appl.Microbiol_60_7
Author(s) : Nishida H , Matsumoto T , Kondo S , Hamamoto M , Yoshikawa H
Ref : J Gen Appl Microbiol , 60 :7 , 2014
Abstract : We sequenced the genomic DNA and the transcribed RNA of the ascomycetous budding yeast Saitoella complicata, which belongs to the earliest lineage (Taphrinomycotina) of ascomycetes. We found 3 protein-coding regions similar to Clr6 of Schizosaccharomyces (a member of Taphrinomycotina). Clr6 has a structure similar to that of Rpd3 and Hos2 of Saccharomyces. These proteins belong to the class 1 histone deacetylase (HDAC) family. The phylogenetic tree showed that the Clr6, Hos2, and Rpd3 lineages are separated in fungal HDACs. Basidiomycetes have 3 proteins belonging to the Clr6, Hos2, and Rpd3 lineages. On the other hand, whereas ascomycetes except for Schizosaccharomyces have the Hos2 and Rpd3 homologs, and lack the Clr6 homolog, Schizosaccharomyces has the Clr6 and Hos2 homologs, and lacks the Rpd3 homolog. Interestingly, Pneumocystis and Saitoella have 3 proteins belonging to the Clr6, Hos2, and Rpd3 lineages. Thus, these fungi are the first ascomycete found to possess all 3 types. Our findings indicated that Taphrinomycotina has conserved the Clr6 protein, suggesting that the ancestor of Dikarya (ascomycetes and basidiomycetes) had 3 proteins belonging to the Clr6, Hos2, and Rpd3 lineages. During ascomycete evolution, Pezizomycotina and Saccharomycotina appear to have lost their Clr6 homologs and Schizosaccharomyces to have lost its Rpd3 homolog.
ESTHER : Nishida_2014_J.Gen.Appl.Microbiol_60_7
PubMedSearch : Nishida_2014_J.Gen.Appl.Microbiol_60_7
PubMedID: 24646756
Gene_locus related to this paper: 9asco-a0a0e9n858 , 9asco-a0a0e9nel9 , 9asco-a0a0e9nf84 , 9asco-a0a0e9ngh8 , 9asco-a0a0e9nl00 , 9asco-a0a0e9nnf5 , 9asco-a0a0e9nrg0 , 9asco-a0a0e9ns69 , saicn-a0a0e9n8s3 , saicn-a0a0e9ntr9

Title : Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics - Sakai_2013_Plant.Cell.Physiol_54_e6
Author(s) : Sakai H , Lee SS , Tanaka T , Numa H , Kim J , Kawahara Y , Wakimoto H , Yang CC , Iwamoto M , Abe T , Yamada Y , Muto A , Inokuchi H , Ikemura T , Matsumoto T , Sasaki T , Itoh T
Ref : Plant Cell Physiol , 54 :e6 , 2013
Abstract : The Rice Annotation Project Database (RAP-DB, http://rapdb.dna.affrc.go.jp/) has been providing a comprehensive set of gene annotations for the genome sequence of rice, Oryza sativa (japonica group) cv. Nipponbare. Since the first release in 2005, RAP-DB has been updated several times along with the genome assembly updates. Here, we present our newest RAP-DB based on the latest genome assembly, Os-Nipponbare-Reference-IRGSP-1.0 (IRGSP-1.0), which was released in 2011. We detected 37,869 loci by mapping transcript and protein sequences of 150 monocot species. To provide plant researchers with highly reliable and up to date rice gene annotations, we have been incorporating literature-based manually curated data, and 1,626 loci currently incorporate literature-based annotation data, including commonly used gene names or gene symbols. Transcriptional activities are shown at the nucleotide level by mapping RNA-Seq reads derived from 27 samples. We also mapped the Illumina reads of a Japanese leading japonica cultivar, Koshihikari, and a Chinese indica cultivar, Guangluai-4, to the genome and show alignments together with the single nucleotide polymorphisms (SNPs) and gene functional annotations through a newly developed browser, Short-Read Assembly Browser (S-RAB). We have developed two satellite databases, Plant Gene Family Database (PGFD) and Integrative Database of Cereal Gene Phylogeny (IDCGP), which display gene family and homologous gene relationships among diverse plant species. RAP-DB and the satellite databases offer simple and user-friendly web interfaces, enabling plant and genome researchers to access the data easily and facilitating a broad range of plant research topics.
ESTHER : Sakai_2013_Plant.Cell.Physiol_54_e6
PubMedSearch : Sakai_2013_Plant.Cell.Physiol_54_e6
PubMedID: 23299411
Gene_locus related to this paper: orysa-Q0JK71 , orysj-q6yse8 , orysa-q6yzk1 , orysj-q2r2z8

Title : Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data - Kawahara_2013_Rice.(N.Y)_6_4
Author(s) : Kawahara Y , de la Bastide M , Hamilton JP , Kanamori H , McCombie WR , Ouyang S , Schwartz DC , Tanaka T , Wu J , Zhou S , Childs KL , Davidson RM , Lin H , Quesada-Ocampo L , Vaillancourt B , Sakai H , Lee SS , Kim J , Numa H , Itoh T , Buell CR , Matsumoto T
Ref : Rice (N Y) , 6 :4 , 2013
Abstract : BACKGROUND: Rice research has been enabled by access to the high quality reference genome sequence generated in 2005 by the International Rice Genome Sequencing Project (IRGSP). To further facilitate genomic-enabled research, we have updated and validated the genome assembly and sequence for the Nipponbare cultivar of Oryza sativa (japonica group). RESULTS: The Nipponbare genome assembly was updated by revising and validating the minimal tiling path of clones with the optical map for rice. Sequencing errors in the revised genome assembly were identified by re-sequencing the genome of two different Nipponbare individuals using the Illumina Genome Analyzer II/IIx platform. A total of 4,886 sequencing errors were identified in 321 Mb of the assembled genome indicating an error rate in the original IRGSP assembly of only 0.15 per 10,000 nucleotides. A small number (five) of insertions/deletions were identified using longer reads generated using the Roche 454 pyrosequencing platform. As the re-sequencing data were generated from two different individuals, we were able to identify a number of allelic differences between the original individual used in the IRGSP effort and the two individuals used in the re-sequencing effort. The revised assembly, termed Os-Nipponbare-Reference-IRGSP-1.0, is now being used in updated releases of the Rice Annotation Project and the Michigan State University Rice Genome Annotation Project, thereby providing a unified set of pseudomolecules for the rice community. CONCLUSIONS: A revised, error-corrected, and validated assembly of the Nipponbare cultivar of rice was generated using optical map data, re-sequencing data, and manual curation that will facilitate on-going and future research in rice. Detection of polymorphisms between three different Nipponbare individuals highlights that allelic differences between individuals should be considered in diversity studies.
ESTHER : Kawahara_2013_Rice.(N.Y)_6_4
PubMedSearch : Kawahara_2013_Rice.(N.Y)_6_4
PubMedID: 24280374
Gene_locus related to this paper: orysa-Q0JK71 , orysj-q6yse8 , orysa-q6yzk1 , orysa-q7xej4 , orysa-q7xem8 , orysa-q7xr64 , orysj-a0a0p0y6l9 , orysj-pla4 , orysj-pla1 , orysj-q2r2z8

Title : Streptomycin alleviates irinotecan-induced delayed-onset diarrhea in rats by a mechanism other than inhibition of beta-glucuronidase activity in intestinal lumen - Kurita_2011_Cancer.Chemother.Pharmacol_67_201
Author(s) : Kurita A , Kado S , Matsumoto T , Asakawa N , Kaneda N , Kato I , Uchida K , Onoue M , Yokokura T
Ref : Cancer Chemother Pharmacol , 67 :201 , 2011
Abstract : Irinotecan hydrochloride (CPT-11) is a useful drug for cancer chemotherapy but sometimes induces severe diarrhea clinically. CPT-11 is mainly activated to SN-38 by carboxylesterase (CES) and then detoxified to SN-38 glucuronide (SN-38G) by UDP-glucuronosyltransferase (UGT) in the liver. SN-38G is excreted via bile and de-conjugated to SN-38 by beta-glucuronidase (beta-GLU) in the intestinal content. In order to clarify the alleviative effect of antibiotics on CPT-11-induced diarrhea, we examined whether penicillin G and streptomycin (SM) alleviate CPT-11-induced delayed-onset diarrhea using three diarrheal models, i.e., Wistar rats with repeated dosing of CPT-11 (60 mg/kg/day i.v. for 4 consecutive days) and Wistar and Gunn rats with a single dosing of CPT-11 (200 and 20 mg/kg i.v., respectively). Gunn rats have an inherited deficiency of UGT1A and cannot conjugate SN-38 to SN-38G. Therefore, onset of CPT-11-induced diarrhea in Gunn rats is not affected by beta-GLU activity. SM alleviated diarrhea in all three diarrheal models. The alleviation of diarrhea by SM in Gunn rats indicated that the effect of SM occurred by a mechanism other than the inhibition of beta-GLU activity. SM decreased CPT-11 and/or SN-38 concentrations in intestinal tissues and alleviated epithelial damage from the ileum to colon. SM did not inhibit beta-GLU activity in the cecal content. SM also inhibited the intestinal absorption of CPT-11 and decreased CES activity and increased UGT activity in the intestinal epithelium. These findings indicated that SM decreased the exposure of CPT-11 and SN-38 to the intestinal epithelium by inhibiting the absorption of CPT-11 from the intestinal lumen and the change of CES and UGT activities in the intestinal epithelium and alleviated delayed-onset diarrhea.
ESTHER : Kurita_2011_Cancer.Chemother.Pharmacol_67_201
PubMedSearch : Kurita_2011_Cancer.Chemother.Pharmacol_67_201
PubMedID: 20354702

Title : Comprehensive sequence analysis of 24,783 barley full-length cDNAs derived from 12 clone libraries - Matsumoto_2011_Plant.Physiol_156_20
Author(s) : Matsumoto T , Tanaka T , Sakai H , Amano N , Kanamori H , Kurita K , Kikuta A , Kamiya K , Yamamoto M , Ikawa H , Fujii N , Hori K , Itoh T , Sato K
Ref : Plant Physiol , 156 :20 , 2011
Abstract : Full-length cDNA (FLcDNA) libraries consisting of 172,000 clones were constructed from a two-row malting barley cultivar (Hordeum vulgare 'Haruna Nijo') under normal and stressed conditions. After sequencing the clones from both ends and clustering the sequences, a total of 24,783 complete sequences were produced. By removing duplicates between these and publicly available sequences, 22,651 representative sequences were obtained: 17,773 were novel barley FLcDNAs, and 1,699 were barley specific. Highly conserved genes were found in the barley FLcDNA sequences for 721 of 881 rice (Oryza sativa) trait genes with 50% or greater identity. These FLcDNA resources from our Haruna Nijo cDNA libraries and the full-length sequences of representative clones will improve our understanding of the biological functions of genes in barley, which is the cereal crop with the fourth highest production in the world, and will provide a powerful tool for annotating the barley genome sequences that will become available in the near future.
ESTHER : Matsumoto_2011_Plant.Physiol_156_20
PubMedSearch : Matsumoto_2011_Plant.Physiol_156_20
PubMedID: 21415278
Gene_locus related to this paper: horvd-f2cta8 , horvd-f2cu28 , horvd-f2cu67 , horvd-f2cvb1 , horvd-f2d2e7 , horvd-f2d3b2 , horvd-f2d8w8 , horvd-f2dam1 , horvd-f2db20 , horvd-f2de38 , horvd-f2dey8 , horvd-f2djs2 , horvd-f2dlw1 , horvd-f2dnj9 , horvd-f2dnr0 , horvd-f2dq60 , horvd-f2dr75 , horvd-f2dvh4 , horvd-f2dwx9 , horvd-f2e2j6 , horvd-f2e3n3 , horvd-f2e504 , horvd-f2eb83 , horvd-f2ebk6 , horvd-f2ec44 , horvd-f2ecv3 , horvd-f2ee51 , horvd-f2eji1 , horvu-cp22 , orysa-q2qx94 , horvd-f2dey9 , horvd-f2djx2 , horvd-f2dln9 , horvd-f2dmr7 , horvd-f2dnv4 , horvd-f2drv9 , horvd-f2ds75 , horvd-f2dsx0 , horvd-f2e0a7 , horvd-f2e0u2 , horvd-f2e5v7 , horvd-f2d4p5 , horvd-m0vg59 , horvd-f2cqv0 , horvd-f2e1j3 , horvd-f2d241 , horvd-f2e8z5 , horvd-m0x298 , horvd-m0y280 , horvd-f2djb2 , horvd-f2dq90 , horvv-f2dwm7 , horvv-f2cwp1 , horvv-a0a287g9l8 , horvv-f2dfe3 , horvv-f2db09 , horvv-f2e0h1

Title : Cloning and expression of carp acetylcholinesterase gene in Pichia pastoris and characterization of the recombinant enzyme - Sato_2009_Protein.Expr.Purif_64_205
Author(s) : Sato R , Matsumoto T , Hidaka N , Imai Y , Abe K , Takahashi S , Yamada RH , Kera Y
Ref : Protein Expr Purif , 64 :205 , 2009
Abstract : The gene encoding acetylcholinesterase (AChE) was cloned from common carp muscle tissue. The full-length cDNA was 2368 bp that contains a coding region of 1902 bp, corresponding to a protein of 634 amino acids. The deduced amino acid sequence showed a significant homology with those of ichthyic AChEs and several common features among them, including T peptide encoded by exon T in the C-terminus. Three yeast expression vectors were constructed and introduced into the yeast Pichia pastoris. The transformant harboring carp AChE gene lacking exon T most effectively produced AChE activity extracellularly. The replacement of the native signal sequence with the yeast alpha-factor prepro signal sequence rather decreased the production. A decrease in cultivation temperature from 30 to 15 degrees C increased the activity production 32.8-fold. The purified recombinant AChE lacking T peptide, eluted as a single peak with a molecular mass of about 230 kDa on the gel filtration chromatography, exhibited the specific activity of 4970 U/mg. On the SDS-PAGE, three proteins with molecular masses of 73, 54, and 22 kDa were observed. These proteins were N-glycosylated, and their N-terminal sequence showed that the latter two were produced from the former probably by proteolytic cleavage at the C-terminal region. Thus, the recombinant AChE is homotrimer of three identical subunits with 73 kDa. The optimal temperature and pH of the recombinant were comparable to those of the native enzyme purified previously, but the values of kinetic parameters and the sensitivities to substrate inhibition and inhibitors were considerably different between them.
ESTHER : Sato_2009_Protein.Expr.Purif_64_205
PubMedSearch : Sato_2009_Protein.Expr.Purif_64_205
PubMedID: 19121395
Gene_locus related to this paper: cypca-ACHE

Title : Liver function tests in patients with bacteremia - Kanai_2008_J.Clin.Lab.Anal_22_66
Author(s) : Kanai S , Honda T , Uehara T , Matsumoto T
Ref : J Clin Lab Anal , 22 :66 , 2008
Abstract : The purpose of this study was to evaluate liver function tests as potential indicators of bacteremia. We examined 156 patients with laboratory-confirmed bacteremia (bacteremia group) and 211 bacteremia-negative patients with bacterial infections (control group). The patients of the two groups had no underlying liver diseases. For patients in the bacteremia group, we analyzed liver function tests results obtained the day when the first positive blood culture was ordered. For those in the control group, the same data were obtained on the day when the first of multiple negative blood cultures was ordered. At t-test analyses, serum levels of gamma-glutamyl transpeptidase (gamma-GT) and alkaline phosphatase (ALP) were significantly higher, and those of albumin, total cholesterol, and cholinesterase were significantly lower in the bacteremia group than in the control group. Multivariate analyses found serum cholinesterase as an independent factor with adjusted odds ratio of 0.319 (per 65 U/L, standard deviation [SD] size). Serum level of C-reactive protein (CRP), on the other hand, showed no significant difference between the two groups. Serum levels of gamma-GT, ALP, albumin, total cholesterol, and cholinesterase more rapidly altered when various bacterial infections accompanied bacteremia. Therefore, they may be useful in detecting sepsis in its early stages.
ESTHER : Kanai_2008_J.Clin.Lab.Anal_22_66
PubMedSearch : Kanai_2008_J.Clin.Lab.Anal_22_66
PubMedID: 18200569

Title : The Rice Annotation Project Database (RAP-DB): 2008 update - Tanaka_2008_Nucleic.Acids.Res_36_D1028
Author(s) : Tanaka T , Antonio BA , Kikuchi S , Matsumoto T , Nagamura Y , Numa H , Sakai H , Wu J , Itoh T , Sasaki T , Aono R , Fujii Y , Habara T , Harada E , Kanno M , Kawahara Y , Kawashima H , Kubooka H , Matsuya A , Nakaoka H , Saichi N , Sanbonmatsu R , Sato Y , Shinso Y , Suzuki M , Takeda J , Tanino M , Todokoro F , Yamaguchi K , Yamamoto N , Yamasaki C , Imanishi T , Okido T , Tada M , Ikeo K , Tateno Y , Gojobori T , Lin YC , Wei FJ , Hsing YI , Zhao Q , Han B , Kramer MR , McCombie RW , Lonsdale D , O'Donovan CC , Whitfield EJ , Apweiler R , Koyanagi KO , Khurana JP , Raghuvanshi S , Singh NK , Tyagi AK , Haberer G , Fujisawa M , Hosokawa S , Ito Y , Ikawa H , Shibata M , Yamamoto M , Bruskiewich RM , Hoen DR , Bureau TE , Namiki N , Ohyanagi H , Sakai Y , Nobushima S , Sakata K , Barrero RA , Souvorov A , Smith-White B , Tatusova T , An S , An G , S OO , Fuks G , Messing J , Christie KR , Lieberherr D , Kim H , Zuccolo A , Wing RA , Nobuta K , Green PJ , Lu C , Meyers BC , Chaparro C , Piegu B , Panaud O , Echeverria M
Ref : Nucleic Acids Research , 36 :D1028 , 2008
Abstract : The Rice Annotation Project Database (RAP-DB) was created to provide the genome sequence assembly of the International Rice Genome Sequencing Project (IRGSP), manually curated annotation of the sequence, and other genomics information that could be useful for comprehensive understanding of the rice biology. Since the last publication of the RAP-DB, the IRGSP genome has been revised and reassembled. In addition, a large number of rice-expressed sequence tags have been released, and functional genomics resources have been produced worldwide. Thus, we have thoroughly updated our genome annotation by manual curation of all the functional descriptions of rice genes. The latest version of the RAP-DB contains a variety of annotation data as follows: clone positions, structures and functions of 31 439 genes validated by cDNAs, RNA genes detected by massively parallel signature sequencing (MPSS) technology and sequence similarity, flanking sequences of mutant lines, transposable elements, etc. Other annotation data such as Gnomon can be displayed along with those of RAP for comparison. We have also developed a new keyword search system to allow the user to access useful information. The RAP-DB is available at: http://rapdb.dna.affrc.go.jp/ and http://rapdb.lab.nig.ac.jp/.
ESTHER : Tanaka_2008_Nucleic.Acids.Res_36_D1028
PubMedSearch : Tanaka_2008_Nucleic.Acids.Res_36_D1028
PubMedID: 18089549
Gene_locus related to this paper: orysa-Q9FW17 , orysa-Q0JK71 , orysa-B9EWJ8 , orysa-Q5N7L1 , orysa-pir7a , orysa-q2qyj1 , orysj-q6yse8 , orysa-q6yzk1 , orysa-Q8S0U8 , orysa-q33aq0 , orysa-Q0J0A4 , orysi-a2z179 , orysi-a2zef2 , orysi-b8a7e6 , orysi-b8a7e7 , orysi-b8bfe5 , orysi-b8bhp9 , orysj-b9fi05 , orysj-b9fkb0 , orysj-cgep , orysj-q0djj0 , orysj-q0dud7 , orysj-q0jaf0 , orysj-q0jga1 , orysj-q5jl22 , orysj-q5jlw7 , orysj-q6h7q9 , orysj-q6yvk6 , orysj-q7f8x1 , orysj-q7xcx3 , orysj-q9fwm6 , orysj-q10j20 , orysj-q10ss2 , orysj-q69uw6 , orysj-q94d71 , orysj-q0iq98 , orysj-b9gbs4 , orysj-b9gbs1 , orysj-pla4 , orysj-pla1

Title : Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana - Itoh_2007_Genome.Res_17_175
Author(s) : Itoh T , Tanaka T , Barrero RA , Yamasaki C , Fujii Y , Hilton PB , Antonio BA , Aono H , Apweiler R , Bruskiewich R , Bureau T , Burr F , Costa de Oliveira A , Fuks G , Habara T , Haberer G , Han B , Harada E , Hiraki AT , Hirochika H , Hoen D , Hokari H , Hosokawa S , Hsing YI , Ikawa H , Ikeo K , Imanishi T , Ito Y , Jaiswal P , Kanno M , Kawahara Y , Kawamura T , Kawashima H , Khurana JP , Kikuchi S , Komatsu S , Koyanagi KO , Kubooka H , Lieberherr D , Lin YC , Lonsdale D , Matsumoto T , Matsuya A , McCombie WR , Messing J , Miyao A , Mulder N , Nagamura Y , Nam J , Namiki N , Numa H , Nurimoto S , O'Donovan C , Ohyanagi H , Okido T , Oota S , Osato N , Palmer LE , Quetier F , Raghuvanshi S , Saichi N , Sakai H , Sakai Y , Sakata K , Sakurai T , Sato F , Sato Y , Schoof H , Seki M , Shibata M , Shimizu Y , Shinozaki K , Shinso Y , Singh NK , Smith-White B , Takeda J , Tanino M , Tatusova T , Thongjuea S , Todokoro F , Tsugane M , Tyagi AK , Vanavichit A , Wang A , Wing RA , Yamaguchi K , Yamamoto M , Yamamoto N , Yu Y , Zhang H , Zhao Q , Higo K , Burr B , Gojobori T , Sasaki T
Ref : Genome Res , 17 :175 , 2007
Abstract : We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions were identified or inferred in 19,969 (70%) of the proteins, and 131 possible npRNAs (including 58 antisense transcripts) were found. Almost 5000 annotated protein-coding genes were found to be disrupted in insertional mutant lines, which will accelerate future experimental validation of the annotations. The rice loci were determined by using cDNA sequences obtained from rice and other representative cereals. Our conservative estimate based on these loci and an extrapolation suggested that the gene number of rice is approximately 32,000, which is smaller than previous estimates. We conducted comparative analyses between rice and Arabidopsis thaliana and found that both genomes possessed several lineage-specific genes, which might account for the observed differences between these species, while they had similar sets of predicted functional domains among the protein sequences. A system to control translational efficiency seems to be conserved across large evolutionary distances. Moreover, the evolutionary process of protein-coding genes was examined. Our results suggest that natural selection may have played a role for duplicated genes in both species, so that duplication was suppressed or favored in a manner that depended on the function of a gene.
ESTHER : Itoh_2007_Genome.Res_17_175
PubMedSearch : Itoh_2007_Genome.Res_17_175
PubMedID: 17210932
Gene_locus related to this paper: orysa-Q7XTC5 , orysa-Q852M6 , orysa-Q8GSE8 , orysa-Q9FYP7 , orysa-Q5ZA26 , orysa-Q5JLP6 , orysa-Q8H5P5 , orysa-Q7F1Y5 , orysa-cbp3 , orysa-cbpx , orysa-Q6YSZ8 , orysa-Q9FW17 , orysa-Q84QZ6 , orysa-Q0JK71 , orysa-B9EWJ8 , orysa-Q6ZDG6 , orysa-Q6ZDG5 , orysa-Q658B2 , orysa-Q5N7L1 , orysa-Q8RYV9 , orysa-Q8H3R3 , orysa-Q5SNH3 , orysa-pir7a , orysa-q2qnj4 , orysa-q2qyj1 , orysa-q2r077 , orysa-Q4VWY7 , orysa-q5smv5 , orysa-q5z901 , orysa-Q5ZBI5 , orysa-q6atz0 , orysa-q6i5q3 , orysa-q6j657 , orysa-q6k4q2 , orysj-q6yse8 , orysa-q6yy42 , orysa-q6yzk1 , orysa-q6z8b1 , orysa-q6z995 , orysa-q6zjq6 , orysa-q7x7y5 , orysa-Q7XC50 , orysa-q7xr62 , orysa-q7xr63 , orysa-q7xsg1 , orysa-q7xsq2 , orysa-q7xts6 , orysa-q7xv53 , orysa-Q8LQS5 , orysa-Q8RZ79 , orysa-Q8S0U8 , orysa-Q8W3C6 , orysa-Q9LHX5 , orysa-q53m20 , orysa-q53nd8 , orysa-q60e79 , orysa-q67iz2 , orysa-q67iz3 , orysa-q67iz7 , orysa-q67iz8 , orysa-q67j02 , orysa-q67j05 , orysa-q67j09 , orysa-q67j10 , orysa-q67tr6 , orysa-q67tv0 , orysa-q69j38 , orysa-q69y21 , orysa-q75hy1 , orysa-q75hy2 , orysa-Q0J0A4 , orysa-q651a8 , orysa-q652g4 , orysa-q688m8 , orysa-Q6H8G1 , orysi-a2z179 , orysi-a2zef2 , orysi-b8a7e6 , orysi-b8a7e7 , orysi-b8bfe5 , orysi-b8bhp9 , orysj-b9fi05 , orysj-q0djj0 , orysj-q0jaf0 , orysj-q0jga1 , orysj-q0jhi5 , orysj-q5jl22 , orysj-q5jlw7 , orysj-q6h7q9 , orysj-q6yvk6 , orysj-q7f8x1 , orysj-q7xcx3 , orysj-q9fwm6 , orysj-q10j20 , orysj-q10ss2 , orysj-q69uw6 , orysj-q94d71 , orysj-q0iq98 , orysj-b9gbs4 , orysj-b9gbs1

Title : Enhancement of Activity of Lipase-Displaying Yeast Cells and Their Application to Optical Resolution of (R,S)-1-Benzyloxy-3-Chloro-2-Propyl Monosuccinate - Nakamura_2006_Biotechnol.Prog_22_998
Author(s) : Nakamura Y , Matsumoto T , Nomoto F , Ueda M , Fukuda H , Kondo A
Ref : Biotechnol Prog , 22 :998 , 2006
Abstract : Rhizopus oryzae lipase (ROL) was displayed on the cell surface of Saccharomyces cerevisiae via the Flo1 N-terminal region (1100 amino acids), which corresponds to a flocculation functional domain. The activity of lipase-displaying yeast whole-cell biocatalysts was enhanced 7.3-fold by incubation of the yeast cells at 20 degrees C in distilled water for 8 days after 8 day cultivation. The amount of lipase molecules present in cell wall and intracellular fractions was found to be increased 4.5- and 1.8-fold, respectively, by incubation, which proves that ROL molecules are expressed during incubation. The ROL-displaying yeast whole-cell biocatalyst with enhanced activity was successfully catalyzed by optical resolution of the pharmaceutical precursor (R,S)-1-benzyloxy-3-chloro-2-propyl monosuccinate. Moreover, it showed stable activity through at least eight reaction cycles. These results demonstrate that ROL-displaying yeast cells with enhanced activity by incubation in distilled water are very effective in industrial bioconversion processes.
ESTHER : Nakamura_2006_Biotechnol.Prog_22_998
PubMedSearch : Nakamura_2006_Biotechnol.Prog_22_998
PubMedID: 16889376

Title : A fine physical map of the rice chromosome 5 - Cheng_2005_Mol.Genet.Genomics_274_337
Author(s) : Cheng CH , Chung MC , Liu SM , Chen SK , Kao FY , Lin SJ , Hsiao SH , Tseng IC , Hsing YI , Wu HP , Chen CS , Shaw JF , Wu J , Matsumoto T , Sasaki T , Chen HH , Chow TY
Ref : Mol Genet Genomics , 274 :337 , 2005
Abstract : A fine physical map of the rice (Oryza sativa spp. Japonica var. Nipponbare) chromosome 5 with bacterial artificial chromosome (BAC) and PI-derived artificial chromosome (PAC) clones was constructed through integration of 280 sequenced BAC/PAC clones and 232 sequence tagged site/expressed sequence tag markers with the use of fingerprinted contig data of the Nipponbare genome. This map consists of five contigs covering 99% of the estimated chromosome size (30.08 Mb). The four physical gaps were estimated at 30 and 20 kb for gaps 1-3 and gap 4, respectively. We have submitted 42.2-Mb sequences with 29.8 Mb of nonoverlapping sequences to public databases. BAC clones corresponding to telomere and centromere regions were confirmed by BAC-fluorescence in situ hybridization (FISH) on a pachytene chromosome. The genetically centromeric region at 54.6 cM was covered by a minimum tiling path spanning 2.1 Mb with no physical gaps. The precise position of the centromere was revealed by using three overlapping BAC/PACs for approximately 150 kb. In addition, FISH results revealed uneven chromatin condensation around the centromeric region at the pachytene stage. This map is of use for positional cloning and further characterization of the rice functional genomics.
ESTHER : Cheng_2005_Mol.Genet.Genomics_274_337
PubMedSearch : Cheng_2005_Mol.Genet.Genomics_274_337
PubMedID: 16261349
Gene_locus related to this paper: orysa-gid1 , orysa-q6f358 , orysj-PLA7

Title : Construction of yeast strains with high cell surface lipase activity by using novel display systems based on the Flo1p flocculation functional domain - Matsumoto_2002_Appl.Environ.Microbiol_68_4517
Author(s) : Matsumoto T , Fukuda H , Ueda M , Tanaka A , Kondo A
Ref : Applied Environmental Microbiology , 68 :4517 , 2002
Abstract : We constructed a novel cell-surface display system, using as a new type of cell-wall anchor 3,297 or 4,341 bp of the 3' region of the FLO1 gene (FS or FL gene, respectively), which encodes the flocculation functional domain of Flo1p. In this system, the N terminus of the target protein was fused to the FS or FL protein and the fusion proteins were expressed under the control of the inducible promoter UPR-ICL (5' upstream region of the isocitrate lyase of Candida tropicalis). Using this new system, recombinant lipase with a pro sequence from Rhizopus oryzae (rProROL), which has its active site near the C terminus, was displayed on the cell surface. Cell-surface display of the FSProROL and FLProROL fusion proteins was confirmed by immunofluorescence microscopy and immunoblotting. Lipase activity reached 145 IU/liter (61.3 IU/g [dry cell weight]) on the surface of the yeast cells, which successfully catalyzed the methanolysis reaction. Using these whole-cell biocatalysts, methylesters synthesized from triglyceride and methanol reached 78.3% after 72 h of reaction. To our knowledge, this is the first example of cell-surface display of lipase with high activity. Interestingly, the yeast cells displaying the FLProROL protein showed strong flocculation, even though the glycosylphosphatidylinositol anchor attachment signal and cell-membrane-anchoring region of Flo1p had been deleted from this gene. The cell-surface display system based on FL thus endows the yeast strain with both novel enzyme display and strong flocculation ability.
ESTHER : Matsumoto_2002_Appl.Environ.Microbiol_68_4517
PubMedSearch : Matsumoto_2002_Appl.Environ.Microbiol_68_4517
PubMedID: 12200308

Title : The genome sequence and structure of rice chromosome 1 - Sasaki_2002_Nature_420_312
Author(s) : Sasaki T , Matsumoto T , Yamamoto K , Sakata K , Baba T , Katayose Y , Wu J , Niimura Y , Cheng Z , Nagamura Y , Antonio BA , Kanamori H , Hosokawa S , Masukawa M , Arikawa K , Chiden Y , Hayashi M , Okamoto M , Ando T , Aoki H , Arita K , Hamada M , Harada C , Hijishita S , Honda M , Ichikawa Y , Idonuma A , Iijima M , Ikeda M , Ikeno M , Ito S , Ito T , Ito Y , Iwabuchi A , Kamiya K , Karasawa W , Katagiri S , Kikuta A , Kobayashi N , Kono I , Machita K , Maehara T , Mizuno H , Mizubayashi T , Mukai Y , Nagasaki H , Nakashima M , Nakama Y , Nakamichi Y , Nakamura M , Namiki N , Negishi M , Ohta I , Ono N , Saji S , Sakai K , Shibata M , Shimokawa T , Shomura A , Song J , Takazaki Y , Terasawa K , Tsuji K , Waki K , Yamagata H , Yamane H , Yoshiki S , Yoshihara R , Yukawa K , Zhong H , Iwama H , Endo T , Ito H , Hahn JH , Kim HI , Eun MY , Yano M , Jiang J , Gojobori T
Ref : Nature , 420 :312 , 2002
Abstract : The rice species Oryza sativa is considered to be a model plant because of its small genome size, extensive genetic map, relative ease of transformation and synteny with other cereal crops. Here we report the essentially complete sequence of chromosome 1, the longest chromosome in the rice genome. We summarize characteristics of the chromosome structure and the biological insight gained from the sequence. The analysis of 43.3 megabases (Mb) of non-overlapping sequence reveals 6,756 protein coding genes, of which 3,161 show homology to proteins of Arabidopsis thaliana, another model plant. About 30% (2,073) of the genes have been functionally categorized. Rice chromosome 1 is (G + C)-rich, especially in its coding regions, and is characterized by several gene families that are dispersed or arranged in tandem repeats. Comparison with a draft sequence indicates the importance of a high-quality finished sequence.
ESTHER : Sasaki_2002_Nature_420_312
PubMedSearch : Sasaki_2002_Nature_420_312
PubMedID: 12447438
Gene_locus related to this paper: orysa-Q9S7P1 , orysa-Q9FYP7 , orysa-Q5ZBH3 , orysa-Q5NA74 , orysa-Q5ZA26 , orysa-Q5JLP6 , orysa-Q94D81 , orysa-cbp , orysa-Q5VQE5 , orysa-Q8RZ95 , orysa-Q9AWW1 , orysa-Q9AS70 , orysa-Q0JK71 , orysa-Q8S1D9 , orysa-Q5N8V4 , orysa-Q943F9 , orysa-B9EWJ8 , orysa-Q5N8H1 , orysa-Q5NAI4 , orysa-Q94DP8 , orysa-Q658B2 , orysa-Q5JMQ8 , orysa-Q5QMD9 , orysa-Q5N7L1 , orysa-Q5N7J6 , orysa-Q8RYV9 , orysa-Q5SNH3 , orysa-Q94DD0 , orysa-Q8W0F0 , orysa-pir7a , orysa-pir7b , orysa-Q4VWY7 , orysa-q5jlm9 , orysa-q5na00 , orysa-q5nbu1 , orysa-Q5QLC0 , orysa-q5vnp5 , orysa-Q5VP27 , orysa-Q5ZAM8 , orysa-Q5ZBI5 , orysa-q5zc23 , orysa-Q5ZCR3 , orysa-Q8L562 , orysa-Q8L570 , orysa-Q8LQS5 , orysa-Q8RZ40 , orysa-Q8RZ79 , orysa-Q8S0U8 , orysa-Q8S0V0 , orysa-Q8S125 , orysa-Q9LHX5 , orysa-Q94E46 , orysa-Q656F2 , orysi-a2wn01 , orysi-b8a7e6 , orysi-b8a7e7 , orysj-b9eya5 , orysj-q5jl22 , orysj-q5jlw7 , orysj-q94d71

Title : Pretreatment of immobilized Candida antarctica lipase for biodiesel fuel production from plant oil - Samukawa_2000_J.Biosci.Bioeng_90_180
Author(s) : Samukawa T , Kaieda M , Matsumoto T , Ban K , Kondo A , Shimada Y , Noda H , Fukuda H
Ref : J Biosci Bioeng , 90 :180 , 2000
Abstract : The effects of the pretreatment of immobilized Candida antarctica lipase enzyme (Novozym 435) on methanolysis for biodiesel fuel production were investigated. Methanolysis progressed much faster when Novozym 435 was preincubated in methyl oleate for 0.5 h and subsequently in soybean oil for 12 h. The initial reaction rate of methanolysis catalyzed by both the non-treated and preincubated enzyme decreased significantly with increasing water content. The initial reaction rate increased with increasing methanol content, showed a maximum, and thereafter decreased when the methanol content was increased further. The variation of the initial reaction rate with the methanol content was therefore analyzed using a Michaelis-Menten-type equation with substrate inhibition. Based on this equation, a procedure for the stepwise addition of methanol to the reaction mixture so as to maintain the desired methanol content was determined. When preincubated Novozym 435 was used, the ME content reached over 97% within 3.5 h by stepwise addition of 0.33 molar equivalent of methanol at 0.25-0.4 h intervals.
ESTHER : Samukawa_2000_J.Biosci.Bioeng_90_180
PubMedSearch : Samukawa_2000_J.Biosci.Bioeng_90_180
PubMedID: 16232839
Gene_locus related to this paper: canar-LipB

Title : Biodiesel fuel production from plant oil catalyzed by Rhizopus oryzae lipase in a water-containing system without an organic solvent - Kaieda_1999_J.Biosci.Bioeng_88_627
Author(s) : Kaieda M , Samukawa T , Matsumoto T , Ban K , Kondo A , Shimada Y , Noda H , Nomoto F , Ohtsuka K , Izumoto E , Fukuda H
Ref : J Biosci Bioeng , 88 :627 , 1999
Abstract : A new enzymatic method of synthesizing methyl esters from plant oil and methanol in a solvent-free reaction system was developed. It is anticipated that such plant oil methyl esters can be used as a biodiesel fuel in the future. Lipase from Rhizopus oryzae efficiently catalyzed the methanolysis of soybean oil in the presence of 4-30 wt% water in the starting materials; however the lipase was nearly inactive in the absence of water. The methyl ester (ME) content in the reaction mixture reached 80-90 wt% by stepwise additions of methanol to the reaction mixture. The kinetics of the reaction appears to be in accordance with the successive reaction mechanism. That is, the oil is first hydrolyzed to free fatty acids and partial glycerides, and the fatty acids produced are then esterified with methanol. Although R. oryzae lipase is considered to exhibit 1(3)-regiospecificity, a certain amount of 1,3-diglyceride was obtained during the methanolysis and hydrolysis of soybean oil by R. oryzae lipase solution. Therefore, the high ME content in the reaction mixture is probably attributable to the acyl migration from the sn-2 position to the sn-1 or sn-3 position in partial glycerides.
ESTHER : Kaieda_1999_J.Biosci.Bioeng_88_627
PubMedSearch : Kaieda_1999_J.Biosci.Bioeng_88_627
PubMedID: 16232675

Title : The neurotrophic effects of ebiratide, an analog of ACTH4-9, on cultured septal cells and aged rats - Matsumoto_1995_J.Neur.Transm_100_1
Author(s) : Matsumoto T , Tsuda S , Nakamura S
Ref : Journal of Neural Transmission General Section , 100 :1 , 1995
Abstract : The neurotrophic effects of ebiratide, an ACTH4-9 analog, have been examined using both fetal rat septal cultures and aged rats. The 5-day treatment with ebiratide (10-100 pmol/ml) partially prevented neuronal degeneration that occurred in the cultures in which cells were sparsely plated. Ebiratide (10 pmol/ ml) increased choline acetyltransferase (ChAT) and acetylcholinesterase (AChE) activities up to 1.5 and 1.2 times the respective control values in the sub-confluent cultures. AChE cytochemistry of the cultures has shown that ebiratide increased the stained area per cell. Ebiratide subcutaneously administered by constant infusion (10 nmol/body/hr) for 4 weeks elevated ChAT activities in the septum (35% over control), neocortex (79%) and hippocampus (89%) of aged rats. Thus, the present study indicates that ebiratide shares neurotrophic properties which may prove beneficial in the therapy for CNS degenerative disorders, especially Alzheimer's disease.
ESTHER : Matsumoto_1995_J.Neur.Transm_100_1
PubMedSearch : Matsumoto_1995_J.Neur.Transm_100_1
PubMedID: 8748659