Fukuda S

References (16)

Title : Intermittent fasting prompted recovery from dextran sulfate sodium-induced colitis in mice - Okada_2017_J.Clin.Biochem.Nutr_61_100
Author(s) : Okada T , Otsubo T , Hagiwara T , Inazuka F , Kobayashi E , Fukuda S , Inoue T , Higuchi K , Kawamura YI , Dohi T
Ref : J Clinical Biochemistry Nutr , 61 :100 , 2017
Abstract : Fasting-refeeding in mice induces transient hyperproliferation of colonic epithelial cells, which is dependent on the lactate produced as a metabolite of commensal bacteria. We attempted to manipulate colonic epithelial cell turnover with intermittent fasting to prompt recovery from acute colitis. Acute colitis was induced in C57BL/6 mice by administration of dextran sulfate sodium in the drinking water for 5 days. From day 6, mice were fasted for 36 h and refed normal bait, glucose powder, or lactylated high-amylose starch. On day 9, colon tissues were subjected to analysis of histology and cytokine expression. The effect of lactate on the proliferation of colonocytes was assessed by enema in vivo and primary culture in vitro. Intermittent fasting resulted in restored colonic crypts and less expression of interleukin-1beta and interleukin-17 in the colon than in mice fed ad libitum. Administration of lactate in the colon at refeeding time by enema or by feeding lactylated high-amylose starch increased the number of regenerating crypts. Addition of lactate but not butyrate or acetate supported colony formation of colonocytes in vitro. In conclusion, intermittent fasting in the resolution phase of acute colitis resulted in better recovery of epithelial cells and reduced inflammation.
ESTHER : Okada_2017_J.Clin.Biochem.Nutr_61_100
PubMedSearch : Okada_2017_J.Clin.Biochem.Nutr_61_100
PubMedID: 28955126

Title : Discovery and preclinical profile of teneligliptin (3-[(2S,4S)-4-[4-(3-methyl-1-phenyl-1H-pyrazol-5-yl)piperazin-1-yl]pyrrolidin-2-y lcarbonyl]thiazolidine): a highly potent, selective, long-lasting and orally active dipeptidyl peptidase IV inhibitor for the treatment of type 2 diabetes - Yoshida_2012_Bioorg.Med.Chem_20_5705
Author(s) : Yoshida T , Akahoshi F , Sakashita H , Kitajima H , Nakamura M , Sonda S , Takeuchi M , Tanaka Y , Ueda N , Sekiguchi S , Ishige T , Shima K , Nabeno M , Abe Y , Anabuki J , Soejima A , Yoshida K , Takashina Y , Ishii S , Kiuchi S , Fukuda S , Tsutsumiuchi R , Kosaka K , Murozono T , Nakamaru Y , Utsumi H , Masutomi N , Kishida H , Miyaguchi I , Hayashi Y
Ref : Bioorganic & Medicinal Chemistry , 20 :5705 , 2012
Abstract : Dipeptidyl peptidase IV (DPP-4) inhibition is suitable mechanism for once daily oral dosing regimen because of its low risk of hypoglycemia. We explored linked bicyclic heteroarylpiperazines substituted at the gamma-position of the proline structure in the course of the investigation of l-prolylthiazolidines. The efforts led to the discovery of a highly potent, selective, long-lasting and orally active DPP-4 inhibitor, 3-[(2S,4S)-4-[4-(3-methyl-1-phenyl-1H-pyrazol-5-yl)piperazin-1-yl]pyrrolidin-2-yl carbonyl]thiazolidine (8 g), which has a unique structure characterized by five consecutive rings. An X-ray co-crystal structure of 8 g in DPP-4 demonstrated that the key interaction between the phenyl ring on the pyrazole and the S(2) extensive subsite of DPP-4 not only boosted potency, but also increased selectivity. Compound 8 g, at 0.03 mg/kg or higher doses, significantly inhibited the increase of plasma glucose levels after an oral glucose load in Zucker fatty rats. Compound 8 g (teneligliptin) has been approved for the treatment of type 2 diabetes in Japan.
ESTHER : Yoshida_2012_Bioorg.Med.Chem_20_5705
PubMedSearch : Yoshida_2012_Bioorg.Med.Chem_20_5705
PubMedID: 22959556
Gene_locus related to this paper: human-DPP4

Title : The cyanine Dye NK-4 improves scopolamine-induced memory impairments in mice - Uchida_2012_Biol.Pharm.Bull_35_1831
Author(s) : Uchida S , Endo S , Akita K , Ohta T , Fukuda S
Ref : Biol Pharm Bull , 35 :1831 , 2012
Abstract : The aim of this study is to evaluate the effects of NK-4, a kind of cyanine dye, on cholinergic memory deficits in mice. We examined whether NK-4 could reverse scopolamine-induced amnesia in mice since NK-4 displays a potent and selective inhibitory effect on acetylcholinesterase (AChE) in vitro. Intraperitoneal administration of NK-4 significantly reversed scopolamine-induced cognitive impairments in mice in the Y maze and the passive avoidance tests, and NK-4 also improved spatial learning ability in the Morris water maze test. Despite NK-4 displaying remarkable AChE inhibitory activity in vitro, we could not detect a significant reduction of AChE activity in brain homogenates of NK-4-treated mice. Although the mechanism through which NK-4 reverses cognitive impairments in scopolamine-treated mice remains unclear, these data suggest that NK-4 may have potential as a therapeutic agent for the treatment of dementia.
ESTHER : Uchida_2012_Biol.Pharm.Bull_35_1831
PubMedSearch : Uchida_2012_Biol.Pharm.Bull_35_1831
PubMedID: 23037173

Title : Complete genome sequences of rat and mouse segmented filamentous bacteria, a potent inducer of th17 cell differentiation - Prakash_2011_Cell.Host.Microbe_10_273
Author(s) : Prakash T , Oshima K , Morita H , Fukuda S , Imaoka A , Kumar N , Sharma VK , Kim SW , Takahashi M , Saitou N , Taylor TD , Ohno H , Umesaki Y , Hattori M
Ref : Cell Host Microbe , 10 :273 , 2011
Abstract : Segmented filamentous bacteria (SFB) are noncultivable commensals inhabiting the gut of various vertebrate species and have been shown to induce Th17 cells in mice. We present the complete genome sequences of both rat and mouse SFB isolated from SFB-monocolonized hosts. The rat and mouse SFB genomes each harbor a single circular chromosome of 1.52 and 1.59 Mb encoding 1346 and 1420 protein-coding genes, respectively. The overall nucleotide identity between the two genomes is 86%, and the substitution rate was estimated to be similar to that of the free-living E. coli. SFB genomes encode typical genes for anaerobic fermentation and spore and flagella formation, but lack most of the amino acid biosynthesis enzymes, reminiscent of pathogenic Clostridia, exhibiting large dependency on the host. However, SFB lack most of the clostridial virulence-related genes. Comparative analysis with clostridial genomes suggested possible mechanisms for host responses and specific adaptations in the intestine.
ESTHER : Prakash_2011_Cell.Host.Microbe_10_273
PubMedSearch : Prakash_2011_Cell.Host.Microbe_10_273
PubMedID: 21925114
Gene_locus related to this paper: 9clot-g2ifk0

Title : Bifidobacteria can protect from enteropathogenic infection through production of acetate - Fukuda_2011_Nature_469_543
Author(s) : Fukuda S , Toh H , Hase K , Oshima K , Nakanishi Y , Yoshimura K , Tobe T , Clarke JM , Topping DL , Suzuki T , Taylor TD , Itoh K , Kikuchi J , Morita H , Hattori M , Ohno H
Ref : Nature , 469 :543 , 2011
Abstract : The human gut is colonized with a wide variety of microorganisms, including species, such as those belonging to the bacterial genus Bifidobacterium, that have beneficial effects on human physiology and pathology. Among the most distinctive benefits of bifidobacteria are modulation of host defence responses and protection against infectious diseases. Nevertheless, the molecular mechanisms underlying these effects have barely been elucidated. To investigate these mechanisms, we used mice associated with certain bifidobacterial strains and a simplified model of lethal infection with enterohaemorrhagic Escherichia coli O157:H7, together with an integrated 'omics' approach. Here we show that genes encoding an ATP-binding-cassette-type carbohydrate transporter present in certain bifidobacteria contribute to protecting mice against death induced by E. coli O157:H7. We found that this effect can be attributed, at least in part, to increased production of acetate and that translocation of the E. coli O157:H7 Shiga toxin from the gut lumen to the blood was inhibited. We propose that acetate produced by protective bifidobacteria improves intestinal defence mediated by epithelial cells and thereby protects the host against lethal infection.
ESTHER : Fukuda_2011_Nature_469_543
PubMedSearch : Fukuda_2011_Nature_469_543
PubMedID: 21270894
Gene_locus related to this paper: bifli-c2gxu7 , biflo-BL0073 , biflo-BL0336 , biflo-BL0581 , biflo-BL0582 , biflo-BL0682 , biflo-BL0787 , biflo-BL0807 , biflo-BL1109 , biflo-BL1514 , biflo-PAP , biflo-PTRB , bifln-c2gtr2

Title : Microinjection of propofol into the perifornical area induces sedation with decreasing cortical acetylcholine release in rats - Gamou_2010_Anesth.Analg_111_395
Author(s) : Gamou S , Fukuda S , Ogura M , Sakamoto H , Morita S
Ref : Anesthesia & Analgesia , 111 :395 , 2010
Abstract : BACKGROUND: Among many neurotransmitter systems in the central nervous system, the cholinergic system has been shown to contribute to propofol's sedative/anesthetic effects, because it has been shown that cholinesterase inhibitor reverses the level of propofol-induced unconsciousness in humans. It has been reported that intraperitoneal injection of propofol induced sedative/anesthetic actions and decreased the release of acetylcholine (Ach) from the rat cortex. However, the sites of action of propofol in the cholinergic pathway and its related pathways remain unresolved. We studied whether microinjection of propofol into the nuclei in the cholinergic pathway and its related pathways may induce sedation and decrease Ach from the cortex. METHODS: Thirty-seven male Wistar rats weighing 270 to 320 g were used. Almost 5 days before the experiments, 23 rats anesthetized with pentobarbital (50 mg/kg) were outfitted with an electroencephalogram (EEG) socket, a microdialysis cannula in the cortex, and an intraperitoneal tube or a microinjection tube into the basal forebrain (BF), the perifornical area (Pef), or the striatum. The Ach effluxes in the somatosensory cortex were detected using in vivo intracerebral microdialysis in freely moving rats. Once basal levels of Ach were stabilized, samples were collected every 20 minutes and measured by high-performance liquid chromatography. In the intraperitoneal group, propofol was cumulatively administered (10, 30, and 100 mg/kg) into the peritoneal cavity. In the microinjection groups, propofol (40 ng in 0.2 microL) was administered into the BF, the Pef, or the striatum (control), and the cortical changes in Ach efflux and EEG were observed for 2 hours. In another 14 rats, the sedative/anesthetic score was obtained after intraperitoneal, Pef, or striatal injection of propofol. The placement of the tip of the microdialysis probe and the microinjection tube was confirmed by histological examination. RESULTS: Intraperitoneal injection of propofol dose-dependently decreased the Ach efflux and induced light sedative to moderate anesthetic states. Loss of righting reflex was observed with significant increases in the relative alpha-power band at 100 mg/kg propofol. Microinjection of propofol into the BF significantly decreased the cortical Ach efflux to -40.2% + or - 19.9% at 40 to 60 minutes. However, there was no difference in the total Ach efflux for 2 hours between BF and control groups. In contrast, microinjection of propofol into the Pef immediately decreased the Ach efflux at 0 to 20 min and maximally to -59.3 + or - 20.4 at 100 to 120 minutes. The total Ach efflux in the Pef microinjection group was significantly less than that in the control group. The same dose of propofol injected into the Pef induced light to deep sedation. There was no significant change in the relative EEG power band between BF or Pef and control groups. CONCLUSION: The nuclei in the Pef are, at least in part, responsible for the sedative action of propofol in rats.
ESTHER : Gamou_2010_Anesth.Analg_111_395
PubMedSearch : Gamou_2010_Anesth.Analg_111_395
PubMedID: 20495137

Title : Comparative genome analysis of Lactobacillus reuteri and Lactobacillus fermentum reveal a genomic island for reuterin and cobalamin production - Morita_2008_DNA.Res_15_151
Author(s) : Morita H , Toh H , Fukuda S , Horikawa H , Oshima K , Suzuki T , Murakami M , Hisamatsu S , Kato Y , Takizawa T , Fukuoka H , Yoshimura T , Itoh K , O'Sullivan DJ , McKay LL , Ohno H , Kikuchi J , Masaoka T , Hattori M
Ref : DNA Research , 15 :151 , 2008
Abstract : Lactobacillus reuteri is a heterofermentative lactic acid bacterium that naturally inhabits the gut of humans and other animals. The probiotic effects of L. reuteri have been proposed to be largely associated with the production of the broad-spectrum antimicrobial compound reuterin during anaerobic metabolism of glycerol. We determined the complete genome sequences of the reuterin-producing L. reuteri JCM 1112(T) and its closely related species Lactobacillus fermentum IFO 3956. Both are in the same phylogenetic group within the genus Lactobacillus. Comparative genome analysis revealed that L. reuteri JCM 1112(T) has a unique cluster of 58 genes for the biosynthesis of reuterin and cobalamin (vitamin B(12)). The 58-gene cluster has a lower GC content and is apparently inserted into the conserved region, suggesting that the cluster represents a genomic island acquired from an anomalous source. Two-dimensional nuclear magnetic resonance (2D-NMR) with (13)C(3)-glycerol demonstrated that L. reuteri JCM 1112(T) could convert glycerol to reuterin in vivo, substantiating the potential of L. reuteri JCM 1112(T) to produce reuterin in the intestine. Given that glycerol is shown to be naturally present in feces, the acquired ability to produce reuterin and cobalamin is an adaptive evolutionary response that likely contributes to the probiotic properties of L. reuteri.
ESTHER : Morita_2008_DNA.Res_15_151
PubMedSearch : Morita_2008_DNA.Res_15_151
PubMedID: 18487258
Gene_locus related to this paper: lacfe-c0wz89 , lacre-a5vi88 , lacre-b3xl59 , lacre-b3xl60 , lacre-b3xlh0 , lacre-b3xps7 , lacre-q4jle7 , lacre-q4jlf2 , lacre-q4jll5 , lacre-q6wu85 , lacrj-b2g622

Title : [Role of orexin in the cholinergic ascending arousal system--orexin-induced arousal from anesthesia] - Fukuda_2007_Masui_56_19
Author(s) : Fukuda S , Zhu Z , Morita S
Ref : Masui , 56 :19 , 2007
Abstract : The cholinergic ascending arousal pathway is one of the most powerful cortical activation systems. The origins of this system is from the pedunculopontine tegmentum (PPTg) and laterodorsal tegmentum (LDT), which relay their signals to the posterior hypothalamus, the basal forebrain and then the cerebral cortex. The cholinergic activation by selective agonists or cholinesterase inhibitors has been shown to produce cortical activation and induce awareness from anesthesia. Orexin neurons are localized in the lateral to posterior hypothalamus. In this review, we presented the antagonistic action of orexin-A to isoflurane anesthesia in terms of the cortical release of acetylcholine and EEG arousal. Microinjection of orexin-A into the basal forebrain induced the increases in acetylcholine release and EEG arousal through orexin-1 receptors. Furthermore, electrical stimulation of the PPTg induced the increases in acetylcholine release and EEG arousal under isoflurane anesthesia, and SB334867, an orexin-1 receptor antagonist, attenuated these arousal responses. These findings suggest that the orexinergic system may contribute to the arousal from anesthesia through the cholinergic ascending arousal pathway.
ESTHER : Fukuda_2007_Masui_56_19
PubMedSearch : Fukuda_2007_Masui_56_19
PubMedID: 17243642

Title : The transcriptional landscape of the mammalian genome - Carninci_2005_Science_309_1559
Author(s) : Carninci P , Kasukawa T , Katayama S , Gough J , Frith MC , Maeda N , Oyama R , Ravasi T , Lenhard B , Wells C , Kodzius R , Shimokawa K , Bajic VB , Brenner SE , Batalov S , Forrest AR , Zavolan M , Davis MJ , Wilming LG , Aidinis V , Allen JE , Ambesi-Impiombato A , Apweiler R , Aturaliya RN , Bailey TL , Bansal M , Baxter L , Beisel KW , Bersano T , Bono H , Chalk AM , Chiu KP , Choudhary V , Christoffels A , Clutterbuck DR , Crowe ML , Dalla E , Dalrymple BP , de Bono B , Della Gatta G , di Bernardo D , Down T , Engstrom P , Fagiolini M , Faulkner G , Fletcher CF , Fukushima T , Furuno M , Futaki S , Gariboldi M , Georgii-Hemming P , Gingeras TR , Gojobori T , Green RE , Gustincich S , Harbers M , Hayashi Y , Hensch TK , Hirokawa N , Hill D , Huminiecki L , Iacono M , Ikeo K , Iwama A , Ishikawa T , Jakt M , Kanapin A , Katoh M , Kawasawa Y , Kelso J , Kitamura H , Kitano H , Kollias G , Krishnan SP , Kruger A , Kummerfeld SK , Kurochkin IV , Lareau LF , Lazarevic D , Lipovich L , Liu J , Liuni S , McWilliam S , Madan Babu M , Madera M , Marchionni L , Matsuda H , Matsuzawa S , Miki H , Mignone F , Miyake S , Morris K , Mottagui-Tabar S , Mulder N , Nakano N , Nakauchi H , Ng P , Nilsson R , Nishiguchi S , Nishikawa S , Nori F , Ohara O , Okazaki Y , Orlando V , Pang KC , Pavan WJ , Pavesi G , Pesole G , Petrovsky N , Piazza S , Reed J , Reid JF , Ring BZ , Ringwald M , Rost B , Ruan Y , Salzberg SL , Sandelin A , Schneider C , Schonbach C , Sekiguchi K , Semple CA , Seno S , Sessa L , Sheng Y , Shibata Y , Shimada H , Shimada K , Silva D , Sinclair B , Sperling S , Stupka E , Sugiura K , Sultana R , Takenaka Y , Taki K , Tammoja K , Tan SL , Tang S , Taylor MS , Tegner J , Teichmann SA , Ueda HR , van Nimwegen E , Verardo R , Wei CL , Yagi K , Yamanishi H , Zabarovsky E , Zhu S , Zimmer A , Hide W , Bult C , Grimmond SM , Teasdale RD , Liu ET , Brusic V , Quackenbush J , Wahlestedt C , Mattick JS , Hume DA , Kai C , Sasaki D , Tomaru Y , Fukuda S , Kanamori-Katayama M , Suzuki M , Aoki J , Arakawa T , Iida J , Imamura K , Itoh M , Kato T , Kawaji H , Kawagashira N , Kawashima T , Kojima M , Kondo S , Konno H , Nakano K , Ninomiya N , Nishio T , Okada M , Plessy C , Shibata K , Shiraki T , Suzuki S , Tagami M , Waki K , Watahiki A , Okamura-Oho Y , Suzuki H , Kawai J , Hayashizaki Y
Ref : Science , 309 :1559 , 2005
Abstract : This study describes comprehensive polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome. We identify the 5' and 3' boundaries of 181,047 transcripts with extensive variation in transcripts arising from alternative promoter usage, splicing, and polyadenylation. There are 16,247 new mouse protein-coding transcripts, including 5154 encoding previously unidentified proteins. Genomic mapping of the transcriptome reveals transcriptional forests, with overlapping transcription on both strands, separated by deserts in which few transcripts are observed. The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development.
ESTHER : Carninci_2005_Science_309_1559
PubMedSearch : Carninci_2005_Science_309_1559
PubMedID: 16141072
Gene_locus related to this paper: mouse-abhd1 , mouse-abhd3 , mouse-abhd4 , mouse-acot4 , mouse-adcl4 , mouse-DGLB , mouse-ephx3 , mouse-Kansl3 , mouse-lipli , mouse-LIPN , mouse-Ppgb , mouse-q3uuq7 , mouse-srac1 , mouse-Tex30 , mouse-tmco4 , mouse-tmm53 , mouse-f172a

Title : Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice - Kikuchi_2003_Science_301_376
Author(s) : Kikuchi S , Satoh K , Nagata T , Kawagashira N , Doi K , Kishimoto N , Yazaki J , Ishikawa M , Yamada H , Ooka H , Hotta I , Kojima K , Namiki T , Ohneda E , Yahagi W , Suzuki K , Li CJ , Ohtsuki K , Shishiki T , Otomo Y , Murakami K , Iida Y , Sugano S , Fujimura T , Suzuki Y , Tsunoda Y , Kurosaki T , Kodama T , Masuda H , Kobayashi M , Xie Q , Lu M , Narikawa R , Sugiyama A , Mizuno K , Yokomizo S , Niikura J , Ikeda R , Ishibiki J , Kawamata M , Yoshimura A , Miura J , Kusumegi T , Oka M , Ryu R , Ueda M , Matsubara K , Kawai J , Carninci P , Adachi J , Aizawa K , Arakawa T , Fukuda S , Hara A , Hashizume W , Hayatsu N , Imotani K , Ishii Y , Itoh M , Kagawa I , Kondo S , Konno H , Miyazaki A , Osato N , Ota Y , Saito R , Sasaki D , Sato K , Shibata K , Shinagawa A , Shiraki T , Yoshino M , Hayashizaki Y , Yasunishi A
Ref : Science , 301 :376 , 2003
Abstract : We collected and completely sequenced 28,469 full-length complementary DNA clones from Oryza sativa L. ssp. japonica cv. Nipponbare. Through homology searches of publicly available sequence data, we assigned tentative protein functions to 21,596 clones (75.86%). Mapping of the cDNA clones to genomic DNA revealed that there are 19,000 to 20,500 transcription units in the rice genome. Protein informatics analysis against the InterPro database revealed the existence of proteins presented in rice but not in Arabidopsis. Sixty-four percent of our cDNAs are homologous to Arabidopsis proteins.
ESTHER : Kikuchi_2003_Science_301_376
PubMedSearch : Kikuchi_2003_Science_301_376
PubMedID: 12869764
Gene_locus related to this paper: orysa-Q852M6 , orysa-Q8GSE8 , orysa-Q9FYP7 , orysa-Q5JLP6 , orysa-Q8H5P5 , orysa-Q7F1Y5 , orysa-cbp3 , orysa-Q6YSZ8 , orysa-Q8S5X5 , orysa-Q8LIG3 , orysa-Q7F1B1 , orysa-Q9FW17 , orysa-Q337C3 , orysa-Q84QZ6 , orysa-Q84QY7 , orysa-Q6ZDG5 , orysa-Q658B2 , orysa-Q8H3R3 , orysa-Q5SNH3 , orysa-q2qnj4 , orysa-q2qyi1 , orysa-Q4VWY7 , orysa-q5smv5 , orysa-q5z901 , orysa-Q5ZBI5 , orysa-q6atz0 , orysa-q6i5q3 , orysj-q6yse8 , orysa-q6z8b1 , orysa-q6z995 , orysa-q7x7y5 , orysa-q7xkj9 , orysa-q7xr63 , orysa-q7xsq2 , orysa-q7xts6 , orysa-Q8LQS5 , orysa-Q8W3C6 , orysa-q53m20 , orysa-q67iz3 , orysa-q67j02 , orysa-q67j05 , orysa-q67j09 , orysa-q67j10 , orysa-q67tv0 , orysa-q67uz1 , orysa-q69xr2 , orysa-q69y21 , orysa-q75hy2 , orysa-q75i01 , orysa-q688m8 , orysa-q688m9 , orysa-Q6H8G1 , orysi-b8a7e7 , orysi-b8bfe5 , orysj-cgep , orysj-q0djj0 , orysj-q0jaf0 , orysj-q5jl22 , orysj-q6h7q9 , orysj-q6yvk6 , orysj-q7f8x1 , orysj-q10j20 , orysj-q10ss2 , orysj-q69uw6

Title : 6-Alpha-glucosyltransferase and 3-alpha-isomaltosyltransferase from Bacillus globisporus N75 - Aga_2003_J.Biosci.Bioeng_95_215
Author(s) : Aga H , Nishimoto T , Kuniyoshi M , Maruta K , Yamashita H , Higashiyama T , Nakada T , Kubota M , Fukuda S , Kurimoto M , Tsujisaka Y
Ref : J Biosci Bioeng , 95 :215 , 2003
Abstract : A bacterial strain, Bacillus globisporus N75, produced two glycosyltransferases, 6-alpha-glucosyltransferase (6GT) and 3-alpha-isomaltosyltransferase (IMT), jointly catalyzing formation of cyclo-->6)-alpha-D-Glcp-(1-->3)-alpha-D-Glcp-(1-->6)-alpha-D-Glcp-(1-->3)-alpha-D -Glcp-(1--> (CTS) from alpha-1,4-glucan. The N75 enzymes produced CTS from dextrin in a 43.8% yield at the reaction temperature of 50 degrees C, which was 10 degrees C higher than a critical temperature of CTS-forming by the enzymes from B. globisporus C11. The optimum temperatures for 6GT and IMT reactions were 55 degrees C and 50 degrees C, respectively. The thermal stability of both enzymes was 45 degrees C under the condition at pH 6.0 for 60 min. The genes for 6GT and IMT were cloned from the genomic DNA of N75. The amino acid sequences deduced from the 6GT and IMT genes showed 82% and 85% identities, respectively, to the sequences of the enzymes from C11. CTS yield was decreased by high concentrations of the substrate. It was found that the reaction yield was improved by adding cyclomaltodextrin glucanotransferase (CGTase). We demonstrated mass-production of CTS from starch by using the N75 enzymes and CGTase.
ESTHER : Aga_2003_J.Biosci.Bioeng_95_215
PubMedSearch : Aga_2003_J.Biosci.Bioeng_95_215
PubMedID: 16233396

Title : Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs - Okazaki_2002_Nature_420_563
Author(s) : Okazaki Y , Furuno M , Kasukawa T , Adachi J , Bono H , Kondo S , Nikaido I , Osato N , Saito R , Suzuki H , Yamanaka I , Kiyosawa H , Yagi K , Tomaru Y , Hasegawa Y , Nogami A , Schonbach C , Gojobori T , Baldarelli R , Hill DP , Bult C , Hume DA , Quackenbush J , Schriml LM , Kanapin A , Matsuda H , Batalov S , Beisel KW , Blake JA , Bradt D , Brusic V , Chothia C , Corbani LE , Cousins S , Dalla E , Dragani TA , Fletcher CF , Forrest A , Frazer KS , Gaasterland T , Gariboldi M , Gissi C , Godzik A , Gough J , Grimmond S , Gustincich S , Hirokawa N , Jackson IJ , Jarvis ED , Kanai A , Kawaji H , Kawasawa Y , Kedzierski RM , King BL , Konagaya A , Kurochkin IV , Lee Y , Lenhard B , Lyons PA , Maglott DR , Maltais L , Marchionni L , McKenzie L , Miki H , Nagashima T , Numata K , Okido T , Pavan WJ , Pertea G , Pesole G , Petrovsky N , Pillai R , Pontius JU , Qi D , Ramachandran S , Ravasi T , Reed JC , Reed DJ , Reid J , Ring BZ , Ringwald M , Sandelin A , Schneider C , Semple CA , Setou M , Shimada K , Sultana R , Takenaka Y , Taylor MS , Teasdale RD , Tomita M , Verardo R , Wagner L , Wahlestedt C , Wang Y , Watanabe Y , Wells C , Wilming LG , Wynshaw-Boris A , Yanagisawa M , Yang I , Yang L , Yuan Z , Zavolan M , Zhu Y , Zimmer A , Carninci P , Hayatsu N , Hirozane-Kishikawa T , Konno H , Nakamura M , Sakazume N , Sato K , Shiraki T , Waki K , Kawai J , Aizawa K , Arakawa T , Fukuda S , Hara A , Hashizume W , Imotani K , Ishii Y , Itoh M , Kagawa I , Miyazaki A , Sakai K , Sasaki D , Shibata K , Shinagawa A , Yasunishi A , Yoshino M , Waterston R , Lander ES , Rogers J , Birney E , Hayashizaki Y
Ref : Nature , 420 :563 , 2002
Abstract : Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones. Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences. These are clustered into 33,409 'transcriptional units', contributing 90.1% of a newly established mouse transcriptome database. Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome. 41% of all transcriptional units showed evidence of alternative splicing. In protein-coding transcripts, 79% of splice variations altered the protein product. Whole-transcriptome analyses resulted in the identification of 2,431 sense-antisense pairs. The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.
ESTHER : Okazaki_2002_Nature_420_563
PubMedSearch : Okazaki_2002_Nature_420_563
PubMedID: 12466851
Gene_locus related to this paper: mouse-1lipg , mouse-1llip , mouse-1plrp , mouse-3neur , mouse-ABH15 , mouse-abhd4 , mouse-abhd5 , mouse-Abhd8 , mouse-Abhd11 , mouse-abhda , mouse-acot4 , mouse-adcl4 , mouse-AI607300 , mouse-BAAT , mouse-bphl , mouse-C87498 , mouse-Ldah , mouse-Ces1d , mouse-Ces2e , mouse-CMBL , mouse-DGLB , mouse-dpp9 , mouse-ES10 , mouse-F135A , mouse-FASN , mouse-hslip , mouse-hyes , mouse-Kansl3 , mouse-LIPH , mouse-LIPK , mouse-lipli , mouse-LIPM , mouse-lypla1 , mouse-lypla2 , mouse-MEST , mouse-MGLL , mouse-ndr4 , mouse-OVCA2 , mouse-pafa , mouse-pcp , mouse-ppce , mouse-Ppgb , mouse-PPME1 , mouse-q3uuq7 , mouse-Q8BLF1 , mouse-ACOT6 , mouse-Q8C1A9 , mouse-Q9DAI6 , mouse-Q80UX8 , mouse-Q8BGG9 , mouse-Q8C167 , mouse-rbbp9 , mouse-SERHL , mouse-tssp

Title : Cloning and sequencing of the genes encoding cyclic tetrasaccharide-synthesizing enzymes from Bacillus globisporus C11 - Aga_2002_Biosci.Biotechnol.Biochem_66_1057
Author(s) : Aga H , Maruta K , Yamamoto T , Kubota M , Fukuda S , Kurimoto M , Tsujisaka Y
Ref : Biosci Biotechnol Biochem , 66 :1057 , 2002
Abstract : The genes for isomaltosyltransferase (CtsY) and 6-glucosyltransferase (CtsZ), involved in synthesis of a cyclic tetrasaccharide from alpha-glucan, have been cloned from the genome of Bacillus globisporus C11. The amino-acid sequence deduced from the ctsY gene is composed of 1093 residues having a signal sequence of 29 residues in its N-terminus. The ctsZ gene encodes a protein consisting of 1284 residues with a signal sequence of 35 residues. Both of the gene products show similarities to alpha-glucosidases belonging to glycoside hydrolase family 31 and conserve two aspartic acids corresponding to the putative catalytic residues of these enzymes. The two genes are linked together, forming ctsYZ. The DNA sequence of 16,515 bp analyzed in this study contains four open reading frames (ORFs) upstream of ctsYZ and one ORF downstream. The first six ORFs, including ctsYZ, form a gene cluster, ctsUVWXYZ. The amino-acid sequences deduced from ctsUV are similar in to a sequence permease and a sugar-binding protein for the sugar transport system from Thermococcus sp. B1001. The third ctsW encodes a protein similar to CtsY, suggested to be another isomaltosyltransferase preferring panose to high-molecular-mass substrates.
ESTHER : Aga_2002_Biosci.Biotechnol.Biochem_66_1057
PubMedSearch : Aga_2002_Biosci.Biotechnol.Biochem_66_1057
PubMedID: 12092816
Gene_locus related to this paper: bacgo-CTSX

Title : Genetic polymorphisms and lung cancer susceptibility: a review - Kiyohara_2002_Lung.Cancer_37_241
Author(s) : Kiyohara C , Otsu A , Shirakawa T , Fukuda S , Hopkin JM
Ref : Lung Cancer , 37 :241 , 2002
Abstract : Lung cancer is a major cause of cancer-related death in the developed countries and the overall survival rate has still an extremely poor. Cigarette smoking is an established risk factor for lung cancer although a possible role for genetic susceptibility in the development of lung cancer has been inferred from familial clustering of the disease and segregation analyzes. Everyone may have a unique combination of polymorphic traits that modify genetic susceptibility and response to drugs, chemicals and carcinogens. Developments in molecular biology have led to growing interest in investigation of biological markers, which may increase predisposition to lung carcinogenesis. Therefore, the high-risk genotype of an individual could be determined easily. As there are the great number of carcinogen-activating and -detoxifying enzymes, the variation in their expression and the complexity of exposures to tobacco carcinogens, the existence of multiple alleles at loci of those enzymes may result in differential susceptibilities of individuals. This review summarize data addressing the relationships of lung cancer to markers of genetic susceptibility genes, including metabolic polymorphisms other than well-investigated cytochrome P450s or glutathione S-transferases, DNA repair genes and the p53 tumor suppressor gene. Among genetic polymorphisms reviewed here, myeloperoxidase gene (a G to A mutation) and microsomal epoxide hydrolase exon 4 polymorphism (substitution of Arg for His) were significantly associated with lung cancer risk. As lung cancer is a multifactorial disease, an improved understanding of the interplay of environmental and genetic polymorphisms at multiple loci may help identify individuals who are at increased risk for lung cancer. Hopefully, in the future we will be able to screen for lung cancer susceptibility by using specific biomarkers.
ESTHER : Kiyohara_2002_Lung.Cancer_37_241
PubMedSearch : Kiyohara_2002_Lung.Cancer_37_241
PubMedID: 12234692

Title : Functional annotation of a full-length mouse cDNA collection - Kawai_2001_Nature_409_685
Author(s) : Kawai J , Shinagawa A , Shibata K , Yoshino M , Itoh M , Ishii Y , Arakawa T , Hara A , Fukunishi Y , Konno H , Adachi J , Fukuda S , Aizawa K , Izawa M , Nishi K , Kiyosawa H , Kondo S , Yamanaka I , Saito T , Okazaki Y , Gojobori T , Bono H , Kasukawa T , Saito R , Kadota K , Matsuda H , Ashburner M , Batalov S , Casavant T , Fleischmann W , Gaasterland T , Gissi C , King B , Kochiwa H , Kuehl P , Lewis S , Matsuo Y , Nikaido I , Pesole G , Quackenbush J , Schriml LM , Staubli F , Suzuki R , Tomita M , Wagner L , Washio T , Sakai K , Okido T , Furuno M , Aono H , Baldarelli R , Barsh G , Blake J , Boffelli D , Bojunga N , Carninci P , de Bonaldo MF , Brownstein MJ , Bult C , Fletcher C , Fujita M , Gariboldi M , Gustincich S , Hill D , Hofmann M , Hume DA , Kamiya M , Lee NH , Lyons P , Marchionni L , Mashima J , Mazzarelli J , Mombaerts P , Nordone P , Ring B , Ringwald M , Rodriguez I , Sakamoto N , Sasaki H , Sato K , Schonbach C , Seya T , Shibata Y , Storch KF , Suzuki H , Toyo-oka K , Wang KH , Weitz C , Whittaker C , Wilming L , Wynshaw-Boris A , Yoshida K , Hasegawa Y , Kawaji H , Kohtsuki S , Hayashizaki Y
Ref : Nature , 409 :685 , 2001
Abstract : The RIKEN Mouse Gene Encyclopaedia Project, a systematic approach to determining the full coding potential of the mouse genome, involves collection and sequencing of full-length complementary DNAs and physical mapping of the corresponding genes to the mouse genome. We organized an international functional annotation meeting (FANTOM) to annotate the first 21,076 cDNAs to be analysed in this project. Here we describe the first RIKEN clone collection, which is one of the largest described for any organism. Analysis of these cDNAs extends known gene families and identifies new ones.
ESTHER : Kawai_2001_Nature_409_685
PubMedSearch : Kawai_2001_Nature_409_685
PubMedID: 11217851
Gene_locus related to this paper: mouse-1lipg , mouse-1plip , mouse-1plrp , mouse-ABH15 , mouse-abhd5 , mouse-ABHD6 , mouse-Abhd8 , mouse-aryla , mouse-bphl , mouse-cauxin , mouse-Ces1g , mouse-CPMac , mouse-dpp8 , mouse-EPHX1 , mouse-ES10 , mouse-hslip , mouse-hyes , mouse-ABHD2 , mouse-lcat , mouse-lipli , mouse-LIPN , mouse-lypla1 , mouse-lypla2 , mouse-OVCA2 , mouse-pafa , mouse-pcp , mouse-Ppgb , mouse-PPME1 , mouse-ppt , mouse-q3uuq7 , mouse-Q9DAI6 , mouse-Q80UX8 , mouse-RISC , mouse-SERHL , mouse-SPG21 , mouse-Tex30

Title : Interferon-gamma enhances megakaryocyte colony-stimulating activity in murine bone marrow cells - Tsuji-Takayama_1996_J.Interferon.Cytokine.Res_16_701
Author(s) : Tsuji-Takayama K , Tahata H , Harashima A , Nishida Y , Izumi N , Fukuda S , Ohta T , Kurimoto M
Ref : J Interferon Cytokine Res , 16 :701 , 1996
Abstract : We have demonstrated previously that interferon-gamma (IFN-gamma) accelerates platelet recovery in mice with 5-FU induced-marrow aplasia in vivo. However, the mechanism for the regulation of megakaryocyte development induced by IFN-gamma in bone marrow cells in vivo remains unknown. To further study the effects of IFN-gamma on megakaryocyte development, various steps during IFN-gamma-mediated accelerated differentiation of the megakaryocytes were investigated in serum-free cultures of murine bone marrow cells in vitro. IFN-gamma markedly induced acetylcholine esterase (AChE) activity, a marker of murine megakaryocytic cells, accompanied by increased colony formation of the megakaryocyte lineage. A prominent increase in megakaryocyte number was observed after IFN-gamma treatment. All of these effects were dependent on the presence of IL-3, and, therefore, these results suggest that IFN-gamma acts as a megakaryocyte potentiator (Meg-POT). However, IFN-gamma did not enhance megakaryocyte maturation with respect to increase in cell size. The effects of IFN-gamma on megakaryocyte maturation were similar to those observed after treatment with higher doses of IL-3 alone. Meg-POT is defined as a factor that induces megakaryocyte maturation. Since IFN-gamma enhanced IL-3-dependent megakaryocyte colony formation and proliferation rather than megakaryocyte maturation, the effects on megakaryocyte development, which were induced by IFN-gamma treatment, seem to be different from the effects of a Meg-POT. We, therefore, propose a new function for IFN-gamma as an enhancer of megakaryocyte colony-stimulating factor activity. The effect of IFN-gamma in vitro appears to correlate well with the acceleration of platelet recovery in vivo.
ESTHER : Tsuji-Takayama_1996_J.Interferon.Cytokine.Res_16_701
PubMedSearch : Tsuji-Takayama_1996_J.Interferon.Cytokine.Res_16_701
PubMedID: 8887054