Itoh T

References (29)

Title : Comparative analysis of stilbene and benzofuran neolignan derivatives as acetylcholinesterase inhibitors with neuroprotective and anti-inflammatory activities - Nagumo_2019_Bioorg.Med.Chem.Lett_29_2475
Author(s) : Nagumo M , Ninomiya M , Oshima N , Itoh T , Tanaka K , Nishina A , Koketsu M
Ref : Bioorganic & Medicinal Chemistry Lett , 29 :2475 , 2019
Abstract : Stilbenes and benzofuran neolignans are important groups of plant phenolics therefore they play a significant role in plants and human health. The objective of this study was to investigate the structure-activity relationships of naturally occurring stilbene and benzofuran neolignan derivatives as acetylcholinesterase inhibitors. A series of these compounds were prepared and assessed for their inhibition on acetylcholinesterase activity. delta-Viniferin, pterostilbene trans-dehydrodimer, pallidol, grossamide, and boehmenan exerted acetylcholinesterase inhibitory potential. The several oligomeric compounds protected against cell damage resulting from t-BHP exposure and inhibited lipopolysaccharide/interferon-gamma (LPS/IFNgamma)-induced NO production in vitro. Our findings highlight the great potential of pterostilbene trans-dehydrodimer, pallidol, and boehmenan as multifunctional nutraceuticals for management of neurodegenerative diseases.
ESTHER : Nagumo_2019_Bioorg.Med.Chem.Lett_29_2475
PubMedSearch : Nagumo_2019_Bioorg.Med.Chem.Lett_29_2475
PubMedID: 31350127

Title : A novel role for CD26\/dipeptidyl peptidase IV as a therapeutic target - Ohnuma_2018_Front.Biosci.(Landmark.Ed)_23_1754
Author(s) : Ohnuma K , Hatano R , Komiya E , Otsuka H , Itoh T , Iwao N , Kaneko Y , Yamada T , Dang NH , Morimoto C
Ref : Front Biosci (Landmark Ed) , 23 :1754 , 2018
Abstract : CD26 is a 110 kDa surface glycoprotein with intrinsic dipeptidyl peptidase IV activity that is expressed on numerous cell types and has a multitude of biological functions. The role of CD26 in immune regulation has been extensively characterized, with recent findings elucidating its linkage with signaling pathways and structures involved in T-lymphocyte activation as well as antigen presenting cell-T-cell interaction. In this paper, we will review emerging data on CD26-mediated immune regulation suggesting that CD26 may be an appropriate therapeutic target for the treatment of selected immune disorders as well as Middle East respiratory syndrome coronavirus. Moreover, we have had a long-standing interest in the role of CD26 in cancer biology and its suitability as a novel therapeutic target in selected neoplasms. We reported robust in vivo data on the anti-tumor activity of anti-CD26 monoclonal antibody in mouse xenograft models. We herein review significant novel findings and the early clinical development of a CD26-targeted therapy in selected immune disorders and cancers, advances that can lead to a more hopeful future for patients with these intractable diseases.
ESTHER : Ohnuma_2018_Front.Biosci.(Landmark.Ed)_23_1754
PubMedSearch : Ohnuma_2018_Front.Biosci.(Landmark.Ed)_23_1754
PubMedID: 29772527

Title : Complete genome sequence and expression profile of the commercial lytic enzyme producer Lysobacter enzymogenes M497-1 - Takami_2017_DNA.Res_24_169
Author(s) : Takami H , Toyoda A , Uchiyama I , Itoh T , Takaki Y , Arai W , Nishi S , Kawai M , Shin-Ya K , Ikeda H
Ref : DNA Research , 24 :169 , 2017
Abstract : Lysobacter enzymogenes M497-1 is a producer of commercialized achromopeptidase and is expected to harbour genes encoding various other antimicrobial enzymes. Here, we present the complete sequence of the genome of M497-1 and the expression profiles of the genes for various antimicrobial enzymes. Of the 117 peptidase-encoding genes found in the 6.1-Mb genome of M497-1, 15 genes (aside from the gene encoding the achromopeptidase) were expressed at a level higher than that of the average ribosomal protein genes in the 24-h culture. Thus, the strain was found more valuable than hitherto considered. In addition, M497-1 harbours 98 genes involved in the biosynthesis of various natural products, 16 of which are M497-1-specific across 4 Lysobacter species. A gene cluster starting at LEN_2603 through LEN_2673 among the 98 genes closely resembled the lysobactin biosynthesis gene cluster of Lysobacter sp. ATCC 53042. It is likely that M497-1 may produce lysobactin or related antibacterial compounds. Furthermore, comparative genomic analysis of M497-1 and four other Lysobacter species revealed that their core genome structure comprises 3,737 orthologous groups. Our findings are expected to advance further biotechnological application of Lysobacter spp. as a promising source of natural bioactive compounds.
ESTHER : Takami_2017_DNA.Res_24_169
PubMedSearch : Takami_2017_DNA.Res_24_169
PubMedID: 28065880
Gene_locus related to this paper: lysen-a0a1j1ebl3 , lysen-a0a1j1e5b0 , lysen-a0a0s2dfs0

Title : Exploration of DPP-IV inhibitors with a novel scaffold by multistep in silico screening - Uchida_2017_J.Mol.Graph.Model_79_254
Author(s) : Uchida T , Wakasugi M , Kitamura T , Yamamoto T , Asakura M , Fujiwara R , Itoh T , Fujii H , Hirono S
Ref : J Mol Graph Model , 79 :254 , 2017
Abstract : Dipeptidyl peptidase-IV (DPP-IV), an enzyme that degrades incretins-hormones that promote insulin secretion-is a therapeutic target for type 2 diabetes, with a number of its inhibitors having been launched as therapies for diabetes. Since adverse effects of these inhibitors have recently been reported, the development of novel DPP-IV inhibitors with higher efficacy and safety is required. We, therefore, screened for novel DPP-IV inhibitors using the combination of an in silico drug discovery technique and a DPP-IV assay system. We initially selected seven candidate compounds as DPP-IV inhibitors from a database consisting of four million compounds by a multistep in silico screening procedure combining pharmacophore-based screening, docking calculation and the analysis of three-dimensional quantitative structure-activity relationship. We then measured the inhibitory activity of the selected compounds and identified a hit compound. In addition, we discuss the structure-activity relationship between the binding mode model and inhibitory activity of the hit compound.
ESTHER : Uchida_2017_J.Mol.Graph.Model_79_254
PubMedSearch : Uchida_2017_J.Mol.Graph.Model_79_254
PubMedID: 29274572

Title : The genomic basis of parasitism in the Strongyloides clade of nematodes - Hunt_2016_Nat.Genet_48_299
Author(s) : Hunt VL , Tsai IJ , Coghlan A , Reid AJ , Holroyd N , Foth BJ , Tracey A , Cotton JA , Stanley EJ , Beasley H , Bennett HM , Brooks K , Harsha B , Kajitani R , Kulkarni A , Harbecke D , Nagayasu E , Nichol S , Ogura Y , Quail MA , Randle N , Xia D , Brattig NW , Soblik H , Ribeiro DM , Sanchez-Flores A , Hayashi T , Itoh T , Denver DR , Grant W , Stoltzfus JD , Lok JB , Murayama H , Wastling J , Streit A , Kikuchi T , Viney M , Berriman M
Ref : Nat Genet , 48 :299 , 2016
Abstract : Soil-transmitted nematodes, including the Strongyloides genus, cause one of the most prevalent neglected tropical diseases. Here we compare the genomes of four Strongyloides species, including the human pathogen Strongyloides stercoralis, and their close relatives that are facultatively parasitic (Parastrongyloides trichosuri) and free-living (Rhabditophanes sp. KR3021). A significant paralogous expansion of key gene families-families encoding astacin-like and SCP/TAPS proteins-is associated with the evolution of parasitism in this clade. Exploiting the unique Strongyloides life cycle, we compare the transcriptomes of the parasitic and free-living stages and find that these same gene families are upregulated in the parasitic stages, underscoring their role in nematode parasitism.
ESTHER : Hunt_2016_Nat.Genet_48_299
PubMedSearch : Hunt_2016_Nat.Genet_48_299
PubMedID: 26829753
Gene_locus related to this paper: 9bila-a0a1i8c9u2 , 9bila-a0a1i8cf76 , 9bila-a0a1i8d2w3 , 9bila-a0a1i8ce18 , 9bila-a0a1i8cmc7

Title : The power of single molecule real-time sequencing technology in the de novo assembly of a eukaryotic genome - Sakai_2015_Sci.Rep_5_16780
Author(s) : Sakai H , Naito K , Ogiso-Tanaka E , Takahashi Y , Iseki K , Muto C , Satou K , Teruya K , Shiroma A , Shimoji M , Hirano T , Itoh T , Kaga A , Tomooka N
Ref : Sci Rep , 5 :16780 , 2015
Abstract : Second-generation sequencers (SGS) have been game-changing, achieving cost-effective whole genome sequencing in many non-model organisms. However, a large portion of the genomes still remains unassembled. We reconstructed azuki bean (Vigna angularis) genome using single molecule real-time (SMRT) sequencing technology and achieved the best contiguity and coverage among currently assembled legume crops. The SMRT-based assembly produced 100 times longer contigs with 100 times smaller amount of gaps compared to the SGS-based assemblies. A detailed comparison between the assemblies revealed that the SMRT-based assembly enabled a more comprehensive gene annotation than the SGS-based assemblies where thousands of genes were missing or fragmented. A chromosome-scale assembly was generated based on the high-density genetic map, covering 86% of the azuki bean genome. We demonstrated that SMRT technology, though still needed support of SGS data, achieved a near-complete assembly of a eukaryotic genome.
ESTHER : Sakai_2015_Sci.Rep_5_16780
PubMedSearch : Sakai_2015_Sci.Rep_5_16780
PubMedID: 26616024
Gene_locus related to this paper: phaan-a0a0s3rce3 , phaan-a0a0s3tc53 , vigrr-a0a1s3v914 , phaan-a0a0s3s998 , phaan-a0a0s3siv8 , phaan-a0a0l9uys5 , phaan-a0a0s3rp07 , phaan-a0a0s3rbq0 , phaan-a0a0s3smk7 , phaan-a0a0s3slm9 , phaan-a0a0l9uc60 , phaan-a0a0l9ucr8

Title : Electrochemical enzymatic biosensor with long-term stability using hybrid mesoporous membrane - Itoh_2014_Analyst_139_4654
Author(s) : Itoh T , Shimomura T , Hayashi A , Yamaguchi A , Teramae N , Ono M , Tsunoda T , Mizukami F , Stucky GD , Hanaoka TA
Ref : Analyst , 139 :4654 , 2014
Abstract : An acetylcholinesterase-immobilized sensor unit was successfully prepared by encapsulating the enzyme within hybrid mesoporous silica membranes (F127-MST). Through a novel combination with tetracyanoquinodimethane, both acetylcholine and organophosphorus pesticides were successfully detected with high sensitivity. Furthermore, we manufactured the working prototype of an enzyme sensor with this sensor unit for detecting dichlorvos, aldicarb and parathion. At present, the detection limit in this working prototype either equaled or surpassed that of others. Also, we have the advantage of increased stability of the enzyme against the outer environment by encapsulation of the enzymes into a silica nanospace. Consequently, acetylcholinesterase immobilized in F127-MST is a practical sensor with high sensitivity, reusability, and storage stability.
ESTHER : Itoh_2014_Analyst_139_4654
PubMedSearch : Itoh_2014_Analyst_139_4654
PubMedID: 25050480

Title : Acute effects of a sarin-like organophosphorus agent, bis(isopropyl methyl)phosphonate, on cardiovascular parameters in anaesthetized, artificially ventilated rats - Watanabe_2013_Toxicol.Appl.Pharmacol_272_61
Author(s) : Watanabe Y , Itoh T , Shiraishi H , Maeno Y , Arima Y , Torikoshi A , Namera A , Makita R , Yoshizumi M , Nagao M
Ref : Toxicol Appl Pharmacol , 272 :61 , 2013
Abstract : The organophosphorus compound sarin irreversibly inhibits acetylcholinesterase. We examined the acute cardiovascular effects of a sarin-like organophosphorus agent, bis(isopropyl methyl)phosphonate (BIMP), in anaesthetized, artificially ventilated rats. Intravenous administration of BIMP (0.8mg/kg; the LD50 value) induced a long-lasting increase in blood pressure and tended to increase heart rate. In rats pretreated with the non-selective muscarinic-receptor antagonist atropine, BIMP significantly increased both heart rate and blood pressure. In atropine-treated rats, hexamethonium (antagonist of ganglionic nicotinic receptors) greatly attenuated the BIMP-induced increase in blood pressure without changing the BIMP-induced increase in heart rate. In rats treated with atropine plus hexamethonium, intravenous phentolamine (non-selective alpha-adrenergic receptor antagonist) plus propranolol (non-selective beta-adrenergic receptor antagonist) completely blocked the BIMP-induced increases in blood pressure and heart rate. In atropine-treated rats, the reversible acetylcholinesterase inhibitor neostigmine (1mg/kg) induced a transient increase in blood pressure, but had no effect on heart rate. These results suggest that in anaesthetized rats, BIMP induces powerful stimulation of sympathetic as well as parasympathetic nerves and thereby modulates heart rate and blood pressure. They may also indicate that an action independent of acetylcholinesterase inhibition contributes to the acute cardiovascular responses induced by BIMP.
ESTHER : Watanabe_2013_Toxicol.Appl.Pharmacol_272_61
PubMedSearch : Watanabe_2013_Toxicol.Appl.Pharmacol_272_61
PubMedID: 23769715

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, 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 : Identification of a key prenyltransferase involved in biosynthesis of the most abundant fungal meroterpenoids derived from 3,5-dimethylorsellinic acid - Itoh_2012_Chembiochem_13_1132
Author(s) : Itoh T , Tokunaga K , Radhakrishnan EK , Fujii I , Abe I , Ebizuka Y , Kushiro T
Ref : Chembiochem , 13 :1132 , 2012
Abstract : Destroying aromaticity: A novel prenyltransferase (Trt2) involved in fungal meroterpenoid biosynthesis was shown to catalyze an unusual aromatic addition reaction onto a fully substituted aromatic ring. The prenylated product serves as a key intermediate in the biosynthesis of the most abundant series of meroterpenoids in fungi.
ESTHER : Itoh_2012_Chembiochem_13_1132
PubMedSearch : Itoh_2012_Chembiochem_13_1132
PubMedID: 22549923
Gene_locus related to this paper: asptn-trt4

Title : Terretonin biosynthesis requires methylation as essential step for cyclization -
Author(s) : Matsuda Y , Awakawa T , Itoh T , Wakimoto T , Kushiro T , Fujii I , Ebizuka Y , Abe I
Ref : Chembiochem , 13 :1738 , 2012
PubMedID: 22782788
Gene_locus related to this paper: asptn-trt4

Title : A deeply branching thermophilic bacterium with an ancient acetyl-CoA pathway dominates a subsurface ecosystem - Takami_2012_PLoS.One_7_e30559
Author(s) : Takami H , Noguchi H , Takaki Y , Uchiyama I , Toyoda A , Nishi S , Chee GJ , Arai W , Nunoura T , Itoh T , Hattori M , Takai K
Ref : PLoS ONE , 7 :e30559 , 2012
Abstract : A nearly complete genome sequence of Candidatus 'Acetothermum autotrophicum', a presently uncultivated bacterium in candidate division OP1, was revealed by metagenomic analysis of a subsurface thermophilic microbial mat community. Phylogenetic analysis based on the concatenated sequences of proteins common among 367 prokaryotes suggests that Ca. 'A. autotrophicum' is one of the earliest diverging bacterial lineages. It possesses a folate-dependent Wood-Ljungdahl (acetyl-CoA) pathway of CO(2) fixation, is predicted to have an acetogenic lifestyle, and possesses the newly discovered archaeal-autotrophic type of bifunctional fructose 1,6-bisphosphate aldolase/phosphatase. A phylogenetic analysis of the core gene cluster of the acethyl-CoA pathway, shared by acetogens, methanogens, some sulfur- and iron-reducers and dechlorinators, supports the hypothesis that the core gene cluster of Ca. 'A. autotrophicum' is a particularly ancient bacterial pathway. The habitat, physiology and phylogenetic position of Ca. 'A. autotrophicum' support the view that the first bacterial and archaeal lineages were H(2)-dependent acetogens and methanogenes living in hydrothermal environments.
ESTHER : Takami_2012_PLoS.One_7_e30559
PubMedSearch : Takami_2012_PLoS.One_7_e30559
PubMedID: 22303444
Gene_locus related to this paper: 9bact-h5srl9 , 9chlr-h5sfm8

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 : Linker-oriented design of binaphthol derivatives for optical resolution using lipase-catalyzed reaction - Taniguchi_2008_J.Org.Chem_73_3875
Author(s) : Taniguchi T , Fukuba TA , Nakatsuka S , Hayase S , Kawatsura M , Uno H , Itoh T
Ref : J Org Chem , 73 :3875 , 2008
Abstract : Candida antarctica lipase B (CAL-B) is one the most frequently used enzymes in organic synthesis for the preparation of optically active alcohols. However, it has not been used for the optical resolution of (+/-)-2,2'-binaphthol. We established an efficient linker-oriented design of 2,2'-binaphthol derivatives that is appropriate for optical resolution using CAL-B-catalyzed hydrolysis reaction. Methyl 4-(1-(6-bromo-2-methoxymethoxynaphthalen-1-yl)-6-bromonaphthalen-2-yloxy)butanoat e was hydrolyzed by CAL-B to afford a corresponding acid with excellent enantioselectivity ( E > 200). Two types of optically active binaphthol derivatives, 1-(2-hydroxy-6-(naphthalen-1-yl)naphthalen-1-yl)-6-(naphthalen-1-yl)naphthalen-2- ol and 6-butyl-1-(6-butyl-2-hydroxynaphthalen-1-yl)naphthalen-2-ol, were prepared by this chemo-enzymatic reaction protocol and were used as chiral templates for symmetric reactions.
ESTHER : Taniguchi_2008_J.Org.Chem_73_3875
PubMedSearch : Taniguchi_2008_J.Org.Chem_73_3875
PubMedID: 18426238

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: and
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 : Human chromosome 11 DNA sequence and analysis including novel gene identification - Taylor_2006_Nature_440_497
Author(s) : Taylor TD , Noguchi H , Totoki Y , Toyoda A , Kuroki Y , Dewar K , Lloyd C , Itoh T , Takeda T , Kim DW , She X , Barlow KF , Bloom T , Bruford E , Chang JL , Cuomo CA , Eichler E , Fitzgerald MG , Jaffe DB , LaButti K , Nicol R , Park HS , Seaman C , Sougnez C , Yang X , Zimmer AR , Zody MC , Birren BW , Nusbaum C , Fujiyama A , Hattori M , Rogers J , Lander ES , Sakaki Y
Ref : Nature , 440 :497 , 2006
Abstract : Chromosome 11, although average in size, is one of the most gene- and disease-rich chromosomes in the human genome. Initial gene annotation indicates an average gene density of 11.6 genes per megabase, including 1,524 protein-coding genes, some of which were identified using novel methods, and 765 pseudogenes. One-quarter of the protein-coding genes shows overlap with other genes. Of the 856 olfactory receptor genes in the human genome, more than 40% are located in 28 single- and multi-gene clusters along this chromosome. Out of the 171 disorders currently attributed to the chromosome, 86 remain for which the underlying molecular basis is not yet known, including several mendelian traits, cancer and susceptibility loci. The high-quality data presented here--nearly 134.5 million base pairs representing 99.8% coverage of the euchromatic sequence--provide scientists with a solid foundation for understanding the genetic basis of these disorders and other biological phenomena.
ESTHER : Taylor_2006_Nature_440_497
PubMedSearch : Taylor_2006_Nature_440_497
PubMedID: 16554811
Gene_locus related to this paper: human-PRCP

Title : Increased enantioselectivity and remarkable acceleration of lipase-catalyzed transesterification by using an imidazolium PEG-alkyl sulfate ionic liquid - Itoh_2006_Chemistry_12_9228
Author(s) : Itoh T , Matsushita Y , Abe Y , Han SH , Wada S , Hayase S , Kawatsura M , Takai S , Morimoto M , Hirose Y
Ref : Chemistry , 12 :9228 , 2006
Abstract : Several types of imidazolium salt ionic liquids were prepared derived from poly(oxyethylene)alkyl sulfate and used as an additive or coating material for lipase-catalyzed transesterification in an organic solvent. A remarkably increased enantioselectivity was obtained when the salt was added at 3-10 mol % versus substrate in the Burkholderia cepacia lipase (lipase PS-C)-catalyzed transesterification of 1-phenylethanol by using vinyl acetate in diisopropyl ether or a hexane solvent system. In particular, a remarkable acceleration was accomplished by the ionic liquid coating with lipase PS in an iPr(2)O solvent system while maintaining excellent enantioselectivity; it reached approximately 500- to 1000-fold acceleration for some substrates with excellent enantioselectivity. A similar acceleration was also observed for IL 1-coated Candida rugosa lipase. MALDI-TOF mass spectrometry experiments of the ionic-liquid-coated lipase PS suggest that ionic liquid binds with lipase protein.
ESTHER : Itoh_2006_Chemistry_12_9228
PubMedSearch : Itoh_2006_Chemistry_12_9228
PubMedID: 17029309

Title : Characterization of secretory intestinal transport of the lactone form of CPT-11 - Takemoto_2006_Cancer.Chemother.Pharmacol_57_129
Author(s) : Takemoto I , Itagaki S , Chiba M , Itoh T , Hirano T , Iseki K
Ref : Cancer Chemother Pharmacol , 57 :129 , 2006
Abstract : PURPOSE: It has been reported that a significant portion of the lactone form of 7-ethyl-10-(4-[1-piperidino]-1-piperidino)-carbonyloxy-camptothecin (CPT-11) is excreted into the gastrointestinal lumen via the intestinal membrane and that carboxylesterase activity, which converts CPT-11 to SN-38, was detected in the intestine. It is possible that a reduction in the excretion of CPT-11 lactone into the gastrointestinal lumen induces the gastrointestinal toxicity. The purpose of this study was to investigate the characteristics of transporter(s) that contribute to the jejunal efflux of the lactone form of CPT-11.
METHODS: The serosal-to-mucosal permeation rate of CPT-11 lactone was investigated in everted sac studies.
RESULTS: The secretory transport required metabolic energy and was diminished by sulfobromophthalein (BSP) and 1-naphthol, inhibitors of the ME3277 transport system. However, inhibitors of breast cancer resistance protein (Bcrp), multidrug resistance-associated protein 2 (Mrp2) and P-glycoprotein (P-gp) did not affect the secretion of CPT-11 lactone.
CONCLUSIONS: The results suggest that a specific transport system, which is identical to the ME3277 transport system, plays a major role in the secretion of CPT-11 lactone.
ESTHER : Takemoto_2006_Cancer.Chemother.Pharmacol_57_129
PubMedSearch : Takemoto_2006_Cancer.Chemother.Pharmacol_57_129
PubMedID: 16003561

Title : The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information - Ohyanagi_2006_Nucleic.Acids.Res_34_D741
Author(s) : Ohyanagi H , Tanaka T , Sakai H , Shigemoto Y , Yamaguchi K , Habara T , Fujii Y , Antonio BA , Nagamura Y , Imanishi T , Ikeo K , Itoh T , Gojobori T , Sasaki T
Ref : Nucleic Acids Research , 34 :D741 , 2006
Abstract : With the completion of the rice genome sequencing, a standardized annotation is necessary so that the information from the genome sequence can be fully utilized in understanding the biology of rice and other cereal crops. An annotation jamboree was held in Japan with the aim of annotating and manually curating all the genes in the rice genome. Here we present the Rice Annotation Project Database (RAP-DB), which has been developed to provide access to the annotation data. The RAP-DB has two different types of annotation viewers, BLAST and BLAT search, and other useful features. By connecting the annotations to other rice genomics data, such as full-length cDNAs and Tos17 mutant lines, the RAP-DB serves as a hub for rice genomics. All of the resources can be accessed through
ESTHER : Ohyanagi_2006_Nucleic.Acids.Res_34_D741
PubMedSearch : Ohyanagi_2006_Nucleic.Acids.Res_34_D741
PubMedID: 16381971
Gene_locus related to this paper: orysa-Q9FW17 , orysa-Q0JK71 , orysa-B9EWJ8 , orysa-Q5N7L1 , orysa-Q5N7J6 , orysa-pir7a , orysa-q2qyi1 , orysa-q2qyj1 , orysa-q2rbb3 , orysj-q6yse8 , orysa-q6yzk1 , orysa-Q8S0U8 , orysa-Q84ZY8 , orysa-Q0J0A4 , orysi-a2z179 , orysi-a2zef2 , orysi-b8a7e6 , orysi-b8a7e7 , orysi-b8bfe5 , orysi-b8bhp9 , orysj-b9fi05 , orysj-q0d4u5 , 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 : DNA sequence and analysis of human chromosome 18 - Nusbaum_2005_Nature_437_551
Author(s) : Nusbaum C , Zody MC , Borowsky ML , Kamal M , Kodira CD , Taylor TD , Whittaker CA , Chang JL , Cuomo CA , Dewar K , Fitzgerald MG , Yang X , Abouelleil A , Allen NR , Anderson S , Bloom T , Bugalter B , Butler J , Cook A , Decaprio D , Engels R , Garber M , Gnirke A , Hafez N , Hall JL , Norman CH , Itoh T , Jaffe DB , Kuroki Y , Lehoczky J , Lui A , Macdonald P , Mauceli E , Mikkelsen TS , Naylor JW , Nicol R , Nguyen C , Noguchi H , O'Leary SB , O'Neill K , Piqani B , Smith CL , Talamas JA , Topham K , Totoki Y , Toyoda A , Wain HM , Young SK , Zeng Q , Zimmer AR , Fujiyama A , Hattori M , Birren BW , Sakaki Y , Lander ES
Ref : Nature , 437 :551 , 2005
Abstract : Chromosome 18 appears to have the lowest gene density of any human chromosome and is one of only three chromosomes for which trisomic individuals survive to term. There are also a number of genetic disorders stemming from chromosome 18 trisomy and aneuploidy. Here we report the finished sequence and gene annotation of human chromosome 18, which will allow a better understanding of the normal and disease biology of this chromosome. Despite the low density of protein-coding genes on chromosome 18, we find that the proportion of non-protein-coding sequences evolutionarily conserved among mammals is close to the genome-wide average. Extending this analysis to the entire human genome, we find that the density of conserved non-protein-coding sequences is largely uncorrelated with gene density. This has important implications for the nature and roles of non-protein-coding sequence elements.
ESTHER : Nusbaum_2005_Nature_437_551
PubMedSearch : Nusbaum_2005_Nature_437_551
PubMedID: 16177791
Gene_locus related to this paper: human-LIPG

Title : Complete sequencing and characterization of 21,243 full-length human cDNAs - Ota_2004_Nat.Genet_36_40
Author(s) : Ota T , Suzuki Y , Nishikawa T , Otsuki T , Sugiyama T , Irie R , Wakamatsu A , Hayashi K , Sato H , Nagai K , Kimura K , Makita H , Sekine M , Obayashi M , Nishi T , Shibahara T , Tanaka T , Ishii S , Yamamoto J , Saito K , Kawai Y , Isono Y , Nakamura Y , Nagahari K , Murakami K , Yasuda T , Iwayanagi T , Wagatsuma M , Shiratori A , Sudo H , Hosoiri T , Kaku Y , Kodaira H , Kondo H , Sugawara M , Takahashi M , Kanda K , Yokoi T , Furuya T , Kikkawa E , Omura Y , Abe K , Kamihara K , Katsuta N , Sato K , Tanikawa M , Yamazaki M , Ninomiya K , Ishibashi T , Yamashita H , Murakawa K , Fujimori K , Tanai H , Kimata M , Watanabe M , Hiraoka S , Chiba Y , Ishida S , Ono Y , Takiguchi S , Watanabe S , Yosida M , Hotuta T , Kusano J , Kanehori K , Takahashi-Fujii A , Hara H , Tanase TO , Nomura Y , Togiya S , Komai F , Hara R , Takeuchi K , Arita M , Imose N , Musashino K , Yuuki H , Oshima A , Sasaki N , Aotsuka S , Yoshikawa Y , Matsunawa H , Ichihara T , Shiohata N , Sano S , Moriya S , Momiyama H , Satoh N , Takami S , Terashima Y , Suzuki O , Nakagawa S , Senoh A , Mizoguchi H , Goto Y , Shimizu F , Wakebe H , Hishigaki H , Watanabe T , Sugiyama A , Takemoto M , Kawakami B , Watanabe K , Kumagai A , Itakura S , Fukuzumi Y , Fujimori Y , Komiyama M , Tashiro H , Tanigami A , Fujiwara T , Ono T , Yamada K , Fujii Y , Ozaki K , Hirao M , Ohmori Y , Kawabata A , Hikiji T , Kobatake N , Inagaki H , Ikema Y , Okamoto S , Okitani R , Kawakami T , Noguchi S , Itoh T , Shigeta K , Senba T , Matsumura K , Nakajima Y , Mizuno T , Morinaga M , Sasaki M , Togashi T , Oyama M , Hata H , Komatsu T , Mizushima-Sugano J , Satoh T , Shirai Y , Takahashi Y , Nakagawa K , Okumura K , Nagase T , Nomura N , Kikuchi H , Masuho Y , Yamashita R , Nakai K , Yada T , Ohara O , Isogai T , Sugano S
Ref : Nat Genet , 36 :40 , 2004
Abstract : As a base for human transcriptome and functional genomics, we created the "full-length long Japan" (FLJ) collection of sequenced human cDNAs. We determined the entire sequence of 21,243 selected clones and found that 14,490 cDNAs (10,897 clusters) were unique to the FLJ collection. About half of them (5,416) seemed to be protein-coding. Of those, 1,999 clusters had not been predicted by computational methods. The distribution of GC content of nonpredicted cDNAs had a peak at approximately 58% compared with a peak at approximately 42%for predicted cDNAs. Thus, there seems to be a slight bias against GC-rich transcripts in current gene prediction procedures. The rest of the cDNAs unique to the FLJ collection (5,481) contained no obvious open reading frames (ORFs) and thus are candidate noncoding RNAs. About one-fourth of them (1,378) showed a clear pattern of splicing. The distribution of GC content of noncoding cDNAs was narrow and had a peak at approximately 42%, relatively low compared with that of protein-coding cDNAs.
ESTHER : Ota_2004_Nat.Genet_36_40
PubMedSearch : Ota_2004_Nat.Genet_36_40
PubMedID: 14702039
Gene_locus related to this paper: human-ABHD1 , human-ABHD4 , human-ABHD12 , human-ABHD16A , human-ACOT1 , human-LDAH , human-ABHD18 , human-CES1 , human-CES4A , human-CES5A , human-CPVL , human-DAGLB , human-EPHX2 , human-KANSL3 , human-LIPA , human-LPL , human-MEST , human-NDRG1 , human-NLGN1 , human-NLGN4X , human-PRCP , human-PRSS16 , human-SERAC1 , human-TMEM53

Title : Lipase-catalyzed direct and regioselective acylation of flavonoid glucoside for mechanistic investigation of stable plant pigments - Nakajima_1999_J.Biosci.Bioeng_87_105
Author(s) : Nakajima N , Ishihara K , Itoh T , Furuya T , Hamada H
Ref : J Biosci Bioeng , 87 :105 , 1999
Abstract : One-step and regioselective acylation of flavonoid glucosides was achieved by lipase-catalyzed transesterification in dry organic media. For example, isoquercitrin (quercetin 3-O-glucoside), one of the flavonol monoglucosides, was converted efficiently to the corresponding aromatic acid ester (isoquercitrin 6''-O-cinnamate) by a lipase with vinyl cinnamate as an acyl donor. The method described, which is the first allowing the direct synthesis of aromatic acid esters of flavonoid glucosides, can be applied to the acylation of other glucosides, including naringin, rutin, callistephin, and chrysanthemin.
ESTHER : Nakajima_1999_J.Biosci.Bioeng_87_105
PubMedSearch : Nakajima_1999_J.Biosci.Bioeng_87_105
PubMedID: 16232434

Title : Construction of a contiguous 874-kb sequence of the Escherichia coli -K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features - Yamamoto_1997_DNA.Res_4_91
Author(s) : Yamamoto Y , Aiba H , Baba T , Hayashi K , Inada T , Isono K , Itoh T , Kimura S , Kitagawa M , Makino K , Miki T , Mitsuhashi N , Mizobuchi K , Mori H , Nakade S , Nakamura Y , Nashimoto H , Oshima T , Oyama S , Saito N , Sampei G , Satoh Y , Sivasundaram S , Tagami H , Horiuchi T , et al.
Ref : DNA Research , 4 :91 , 1997
Abstract : The contiguous 874.423 base pair sequence corresponding to the 50.0-68.8 min region on the genetic map of the Escherichia coli K-12 (W3110) was constructed by the determination of DNA sequences in the 50.0-57.9 min region (360 kb) and two large (100 kb in all) and five short gaps in the 57.9-68.8 min region whose sequences had been registered in the DNA databases. We analyzed its sequence features and found that this region contained at least 894 potential open reading frames (ORFs), of which 346 (38.7%) were previously reported, 158 (17.7%) were homologous to other known genes, 232 (26.0%) were identical or similar to hypothetical genes registered in databases, and the remaining 158 (17.7%) showed no significant similarity to any other genes. A homology search of the ORFs also identified several new gene clusters. Those include two clusters of fimbrial genes, a gene cluster of three genes encoding homologues of the human long chain fatty acid degradation enzyme complex in the mitochondrial membrane, a cluster of at least nine genes involved in the utilization of ethanolamine, a cluster of the secondary set of 11 hyc genes participating in the formate hydrogenlyase reaction and a cluster of five genes coding for the homologues of degradation enzymes for aromatic hydrocarbons in Pseudomonas putida. We also noted a variety of novel genes, including two ORFs, which were homologous to the putative genes encoding xanthine dehydrogenase in the fly and a protein responsible for axonal guidance and outgrowth of the rat, mouse and nematode. An isoleucine tRNA gene, designated ileY, was also newly identified at 60.0 min.
ESTHER : Yamamoto_1997_DNA.Res_4_91
PubMedSearch : Yamamoto_1997_DNA.Res_4_91
PubMedID: 9205837
Gene_locus related to this paper: ecoli-YFBB , ecoli-YfhR

Title : A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map - Oshima_1996_DNA.Res_3_137
Author(s) : Oshima T , Aiba H , Baba T , Fujita K , Hayashi K , Honjo A , Ikemoto K , Inada T , Itoh T , Kajihara M , Kanai K , Kashimoto K , Kimura S , Kitagawa M , Makino K , Masuda S , Miki T , Mizobuchi K , Mori H , Motomura K , Nakamura Y , Nashimoto H , Nishio Y , Saito N , Horiuchi T , et al.
Ref : DNA Research , 3 :137 , 1996
Abstract : The 718,122 base pair sequence of the Escherichia coli K-12 genome corresponding to the region from 12.7 to 28.0 minutes on the genetic map is described. This region contains at least 681 potential open reading frames, of which 277 (41%) have been previously identified, 147 (22%) are homologous to other known genes, 139 (20%) are identical or similar to the hypothetical genes registered in databases, and the remaining 118 (17%) do not show a significant similarity to any other gene. In this region, we assigned a cluster of cit genes encoding multienzyme citrate lyase, two clusters of fimbrial genes and a set of lysogenic phage genes encoding integrase, excisionase and repressor in the e14 genetic element. In addition, a new valine tRNA gene, designated valZ, and a family of long directly repeated sequences, LDR-A, -B and -C, were found.
ESTHER : Oshima_1996_DNA.Res_3_137
PubMedSearch : Oshima_1996_DNA.Res_3_137
PubMedID: 8905232
Gene_locus related to this paper: ecoli-rutD , ecoli-fes , ecoli-ybff , ecoli-ycfp

Title : A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 28.0-40.1 min region on the linkage map - Aiba_1996_DNA.Res_3_363
Author(s) : Aiba H , Baba T , Hayashi K , Inada T , Isono K , Itoh T , Kasai H , Kashimoto K , Kimura S , Kitakawa M , Kitagawa M , Makino K , Miki T , Mizobuchi K , Mori H , Mori T , Motomura K , Nakade S , Nakamura Y , Nashimoto H , Nishio Y , Oshima T , Saito N , Sampei G , Horiuchi T , et al.
Ref : DNA Research , 3 :363 , 1996
Abstract : The 569,750 base pair sequence corresponding to the 28.0-40.1 min region on the genetic map of Escherichia coli K-12 (W3110) was determined. This region includes the replication terminus region and contained at least 549 potential open reading frames. Among them, 160 (29%) were previously reported, 174 (32%) were homologous to other known genes, 102 (18%) were identical or similar to hypothetical genes registered in databases, and the remaining 113 (21%) did not show a significant similarity to any other gene. Of interest was the finding of a large number of genes and gene clusters in and near the replication termination region which had been thought to be genetically silent. Those included a cluster of genes for fatty acid beta-oxidation, the third copy of the pot (spermidine/putrescine transport system) gene cluster, the second dpp (dipeptide transport system) operon, the second dsm (anaerobic dimethyl sulfoxide reductase) operon, a cluster of fim (fimbrial) genes and a DNA helicase-like gene with a high molecular weight. In addition, we found the dnaC- and dnaT-like genes in the cryptic prophage, Rac, and a number of genes originated probably from plasmids.
ESTHER : Aiba_1996_DNA.Res_3_363
PubMedSearch : Aiba_1996_DNA.Res_3_363
PubMedID: 9097039
Gene_locus related to this paper: ecoli-ycjy

Title : MKC-231, a choline uptake enhancer, ameliorates working memory deficits and decreased hippocampal acetylcholine induced by ethylcholine aziridinium ion in mice - Murai_1994_J.Neur.Transm_98_1
Author(s) : Murai S , Saito H , Abe E , Masuda Y , Odashima J , Itoh T
Ref : Journal of Neural Transmission General Section , 98 :1 , 1994
Abstract : The effects of acute and chronic administration of MKC-231, a new choline uptake enhancer, and two other nootropic agents, linopiridine (Dup 996) and tetrahydroaminoacridine (THA) on working memory deficits and decreased hippocampal acetylcholine (ACh) content were studied in a delayed non-matching to sample task, using a T-maze, in ethylcholine aziridinium ion (AF64A)-treated mice. Treatment with AF64A (3.5 nmol, i.c.v.) produced memory deficits and decreased hippocampal ACh content. In acute behavioral experiments, MKC-231 and THA had no significant effect on AF64A-induced memory deficits at any doses tested (0.3, 1.0 and 3.0 mg/kg), whereas Dup 996, at a dose of 1.0 mg/kg, significantly improved memory deficits. In chronic experiments, MKC-231 improved memory deficit at all doses tested (0.3, 1.0, or 3.0 mg/kg p.o., once daily for 11 days) and Dup 996 did so only at a dose of 3.0 mg/kg, whereas THA did not improve memory deficit at any doses tested. In acute neurochemical experiments, MKC-231 and THA did not reverse the AF64A-induced hippocampal ACh depletion. Dup 996, however, further decreased hippocampal ACh content compared to that in the AF64A-treated group. In chronic experiments, MKC-231 significantly reversed hippocampal ACh depletion at doses of 0.3 and 1.0 mg/kg, whereas neither Dup 996 nor THA reversed hippocampal ACh depletion at any doses tested. These results indicate that MKC-231 improved the AF64A-induced working memory deficit and hippocampal ACh depletion, probably by recovering reduced high-affinity choline uptake and ACh release.
ESTHER : Murai_1994_J.Neur.Transm_98_1
PubMedSearch : Murai_1994_J.Neur.Transm_98_1
PubMedID: 7710736

Title : Isoelectric focusing studies of human red cell esterase D: evidence for polymorphic occurrence of a new allele EsD7 in Japanese - Nishigaki_1984_Hum.Genet_66_92
Author(s) : Nishigaki I , Itoh T
Ref : Hum Genet , 66 :92 , 1984
Abstract : The isoelectric focusing study of esterase D in Japanese revealed evidence of a new polymorphic allele (EsD7) which is difficult to find by conventional starch gel electrophoresis only. A comparison with the occurrence of a subdivision of EsD2 in Caucasians (EsD5) suggests a remarkable difference in allele distribution of esterase D among races. Quantitative analysis showed a relatively low value of enzyme activity for this new allele. It is therefore emphasized that in addition to conventional electrophoresis, enzyme assay and further detection by isoelectric focusing are essential in analyzing the esterase D system.
ESTHER : Nishigaki_1984_Hum.Genet_66_92
PubMedSearch : Nishigaki_1984_Hum.Genet_66_92
PubMedID: 6698561