Shibata K

References (15)

Title : Brain regions associated with anosognosia for memory disturbance in Alzheimer's disease: a magnetic resonance imaging study - Fujimoto_2017_Neuropsychiatr.Dis.Treat_13_1753
Author(s) : Fujimoto H , Matsuoka T , Kato Y , Shibata K , Nakamura K , Yamada K , Narumoto J
Ref : Neuropsychiatr Dis Treat , 13 :1753 , 2017
Abstract : BACKGROUND AND OBJECTIVE: Patients with Alzheimer's disease (AD) are frequently unaware of their cognitive symptoms and medical diagnosis. The term "anosognosia" is used to indicate a general lack of awareness of one's disease or disorder. The neural substrate underlying anosognosia in AD is unclear. Since anosognosia for memory disturbance might be an initial sign of AD, it is important to determine the neural correlates. This study was designed to investigate the characteristics and neural correlates of anosognosia for memory disturbance in patients with mild AD.
METHODS: The subjects were 49 patients with mild AD who participated in a retrospective cross-sectional study. None of the patients had been treated with cholinesterase inhibitors, memantine, or psychotropic drugs. All patients underwent magnetic resonance imaging (MRI). Anosognosia for memory disturbance was assessed based on the discrepancy between questionnaire scores of patients and their caregivers. Structural MRI data were analyzed to explore the association between anosognosia and brain atrophy, using a voxel-based approach. Statistical parametric mapping software was used to explore neural correlations. In image analysis, multiple regression analysis was performed to examine the relationship between anosognosia score and regional gray matter volume. Age, years of education, and total intracranial volume were entered as covariates.
RESULTS: The anosognosia score for memory disturbance was significantly negatively correlated with gray matter volume in the left superior frontal gyrus. CONCLUSION: The left superior frontal gyrus was involved in anosognosia for memory disturbance, while the medial temporal lobe, which is usually damaged in mild AD, was not associated with anosognosia. The left superior frontal gyrus might be an important region for anosognosia in mild AD.
ESTHER : Fujimoto_2017_Neuropsychiatr.Dis.Treat_13_1753
PubMedSearch : Fujimoto_2017_Neuropsychiatr.Dis.Treat_13_1753
PubMedID: 28740390

Title : Enhanced cytotoxicity with a novel system combining the paclitaxel-2'-ethylcarbonate prodrug and an HSV amplicon with an attenuated replication-competent virus, HF10 as a helper virus - Ishida_2010_Cancer.Lett_288_17
Author(s) : Ishida D , Nawa A , Tanino T , Goshima F , Luo CH , Iwaki M , Kajiyama H , Shibata K , Yamamoto E , Ino K , Tsurumi T , Nishiyama Y , Kikkawa F
Ref : Cancer Letters , 288 :17 , 2010
Abstract : We previously demonstrated that HF10, which is a natural, non-engineered HSV-1, has potent oncolytic activity in the treatment of solid malignant tumors in vitro and in vivo [H. Takakuwa, F. Goshima, N. Nozawa, T. Yoshikawa, H. Kimata, A. Nakao, et al., Oncolytic viral therapy using a spontaneously generated herpes simplex virus type 1 variant for disseminated peritoneal tumor in immunocompetent mice, Arch. Virol. 148 (2003) 813-825; S. Kohno, C. Lou, F. Goshima, Y. Nishiyama, T. Sata, Y. Ono, Herpes simplex virus type 1 mutant HF10 oncolytic viral therapy for bladder cancer, Urology 66 (2005) 1116-1121; D. Watanabe, F. Goshima, I. Mori, Y. Tamada, Y. Matsumoto, Y. Nishiyama, Oncolytic virotherapy for malignant melanoma with herpes simplex virus type 1 mutant HF10, J. Dermatol. Sci. 50 (2008) 185-196; A. Nawa, C. Luo, L. Zhang, Y. Ushijima, D. Ishida, M. Kamakura, et al., Non-engineered, naturally oncolytic herpes simplex virus HSV1 HF10: applications for cancer gene therapy, Curr. Gene. Ther. 8 (2008) 208-221]. Previous reports have also shown that a combination of HF10 and paclitaxel (TAX) was more efficacious than either regimen alone for some types of malignant tumors [S. Shimoyama, F. Goshima, O. Teshigahara, H. Kasuya, Y. Kodera, A. Nakao, et al., Enhanced efficacy of herpes simplex virus mutant HF10 combined with paclitaxel in peritoneal cancer dissemination models, Hepatogastroenterology 54 (2007) 1038-1042]. In this study, we investigated the efficacy of gene-directed enzyme prodrug therapy (GDEPT) using a novel system that combines the paclitaxel-2'-ethylcarbonate prodrug (TAX-2'-Et) and an HSV amplicon expressing rabbit-carboxylesterase (CES) with HF10 as a helper virus. This GDEPT system aims to produce high level of CES at the tumor site, resulting in efficient local conversion of the TAX-2'-Et prodrug into the active drug TAX [A. Nawa, T. Tanino, C. Lou, M. Iwaki, H. Kajiyama, K. Shibata, et al., Gene directed enzyme prodrug therapy for ovarian cancer: could GDEPT become a promising treatment against ovarian cancer?, Anti-Cancer Agents Med Chem 8 (2008) 232-239]. We demonstrated that the green fluorescent protein (GFP) gene, as a trace maker, was more efficiently introduced by the HSV amplicon compared to the expression vector, pHGCX, and that the HSV amplicon system expressed an active CES enzyme that could convert TAX-2'-Et to TAX in Cos7 cells. Furthermore, although the cytotoxicity of this amplicon system was not enhanced in virus-sensitive tumor cells, it was significantly enhanced in low virus-sensitive tumor cells in the presence of the prodrug in a concentration-dependent manner, compared to the control virus alone (p<0.05). These results indicate that the addition of a prodrug converting enzyme may be a feasible approach to further enhance the efficacy of HF10 as a cancer therapeutics in low HF10-sensitive malignancies.
ESTHER : Ishida_2010_Cancer.Lett_288_17
PubMedSearch : Ishida_2010_Cancer.Lett_288_17
PubMedID: 19604626

Title : Gene directed enzyme prodrug therapy for ovarian cancer: could GDEPT become a promising treatment against ovarian cancer? - Nawa_2008_Anticancer.Agents.Med.Chem_8_232
Author(s) : Nawa A , Tanino T , Luo C , Iwaki M , Kajiyama H , Shibata K , Yamamoto E , Ino K , Nishiyama Y , Kikkawa F
Ref : Anticancer Agents Med Chem , 8 :232 , 2008
Abstract : Gene-directed enzyme prodrug therapy (GDEPT) involves the treatment concept of having maximal efficacy and minimal adverse effects. Several GDEPT strategies have been developed combining cytosine deaminase and 5-fluorocytosine, cytochrome P450 2B1 and cyclophosphamide, and carboxylesterase (CES) and irinotecan in experimental models. The active forms of these prodrugs, however, are not a frontline therapy for the treatment of ovarian cancer. It would be beneficial to develop a more effective prodrug-enzyme combination for the treatment of this disease. Paclitaxel (Taxol; TAX) is currently one of the most important anti-cancer drugs in chemotherapy of ovarian cancer. One of TAX prodrugs, 2'-ethylcarbonate-linked paclitaxel (TAX-2'-Et), was generated and examined regarding its pharmacological aspects. The prodrug of TAX-2'-Et converts into active form TAX by carboxylesterase (CES). TAX-2'-Et did not exhibit polarized transport in the Caco-2 cells expressing P-glycoprotein (P-gp) in the absence or presence of verapamil which is a inhibitor of P-gp, suggesting that TAX-2'-Et is not a target of P-gp like TAX and rhodamine123. Moreover, SKOV3/TAX60 cells which are overexpressing P-gp did not also exhibit any change in cellular uptake of TAX-2'-Et regardless of the absence or presence of verapamil. Consequently, the uptake of TAX-2'-Et into the TAX-resistant cells was quantitatively similar to that internalized in the parental SKOV3 cells which are P-gp-negative. In the CES-transfected SKOV3 cells, the EC50 value of TAX (10.6 nM) was approximately 4-fold higher than that of TAX-2'-Et (2.5 nM). We herein provide evidence that TAX-2'-Et could circumvent P-gp-associated cellular efflux of TAX, suggesting that this combination therapy is a potential GDEPT strategy for ovarian cancer in the future. Finally, this review focuses on the development, application and potential of various GDEPTs for treating ovarian cancer, and the scope and progress of new GDEPTs are discussed.
ESTHER : Nawa_2008_Anticancer.Agents.Med.Chem_8_232
PubMedSearch : Nawa_2008_Anticancer.Agents.Med.Chem_8_232
PubMedID: 18288924

Title : Possible involvement of SDF-1alpha\/CXCR4-DPPIV axis in TGF-beta1-induced enhancement of migratory potential in human peritoneal mesothelial cells - Kajiyama_2007_Cell.Tissue.Res_330_221
Author(s) : Kajiyama H , Shibata K , Ino K , Nawa A , Mizutani S , Kikkawa F
Ref : Cell Tissue Research , 330 :221 , 2007
Abstract : We have previously reported that human peritoneal mesothelial cells (HPMCs) express a large amount of dipeptidyl peptidase IV (DPPIV) and that its expression is regulated by a variety of bioactive substances in malignant ascites from ovarian cancer patients. The aim of this study has been to examine the expression and role of the SDF-1alpha/CXCR4-DPPIV axis in HPMCs. We have demonstrated that the expression levels of DPPIV and E-cadherin in HPMCs decrease, following TGF-beta1-induced morphological change, in a time- and concentration-dependent manner. Additionally, we show that both SDF-1alpha (a chemokine and substrate for DPPIV) and its receptor, CXCR4, are expressed on HPMCs, and that their expression levels are upregulated by TGF-beta1 treatment, resulting in an increased migratory potential of HPMCs. Furthermore, the migratory potential of HPMCs is significantly enhanced in the presence of SDF-1alpha or DPPIV-specific inhibitor in the wound-healing assay. These results suggest that DPPIV and SDF-1alpha/CXCR4 play crucial roles in regulating the migratory potential of HPMCs, which may be involved in the re-epithelialization of denuded basement membrane at the site of peritoneal injury.
ESTHER : Kajiyama_2007_Cell.Tissue.Res_330_221
PubMedSearch : Kajiyama_2007_Cell.Tissue.Res_330_221
PubMedID: 17846797

Title : Involvement of DPPIV\/CD26 in epithelial morphology and suppressed invasive ability in ovarian carcinoma cells - Kajiyama_2006_Ann.N.Y.Acad.Sci_1086_233
Author(s) : Kajiyama H , Shibata K , Terauchi M , Ino K , Nawa A , Kikkawa F
Ref : Annals of the New York Academy of Sciences , 1086 :233 , 2006
Abstract : Dipeptidyl peptidase IV (DPPIV) is a multifunctional cell surface aminopeptidase with ubiquitous expression and it has a variety of functional properties in the development of human malignancies. In the present study, we showed the possible correlation between DPPIV/CD26 expression and less migratory potential with decreased MMP-2 expression in ovarian carcinoma cells. Moreover, induction of DPPIV/CD26 resulted in reduced expressions of MMP-2 and mesenchymal markers such as vimentin and SMA, with a less invasive potential and an epithelial morphologic change. This evidence implies that DPPIV/CD26 may play a crucial role in the antimetastatic potential in ovarian carcinoma.
ESTHER : Kajiyama_2006_Ann.N.Y.Acad.Sci_1086_233
PubMedSearch : Kajiyama_2006_Ann.N.Y.Acad.Sci_1086_233
PubMedID: 17185520

Title : Dipeptidyl peptidase IV in tumor progression - Kikkawa_2005_Biochim.Biophys.Acta_1751_45
Author(s) : Kikkawa F , Kajiyama H , Shibata K , Ino K , Nomura S , Mizutani S
Ref : Biochimica & Biophysica Acta , 1751 :45 , 2005
Abstract : Dipeptidyl peptidase IV (DPPIV) is a 110-kDa glycoprotein with ubiquitous expression. Several recent studies have shown that DPPIV affects tumor progression in several human malignancies. We found that ovarian carcinoma cell lines with higher DPPIV expression showed less invasive potential. Furthermore, introduction of DPPIV cDNA into SKOV3 cells (SKDPIV), derived from serous cystadenocarcinoma showing little DPPIV expression, caused a significant decrease in both migration and invasive potential. In addition, nude mice inoculated with SKDPIV cells showed significantly less peritoneal dissemination and longer survival time than those inoculated with parental or vector-transfected cells. We further examined the mechanisms of anti-invasive ability of DPPIV. The expression of E-cadherin was positively correlated with DPPIV expression among five independent ovarian carcinoma cell lines. The SKDPIV cells showed enhanced expression of E-cadherin with a cellular morphological change from a fibroblastic and motile phenotype to an epithelial phenotype compared to parental and MOCK cells. In addition, matrix metalloproteinase 2 (MMP-2) and membrane type 1 matrix metalloprotease (MT1-MMP), which are important markers associated with invasive and metastatic potential, were remarkably reduced in SKDPIV cells. In contrast, tissue inhibitors of matrix metalloproteinases (TIMPs) were enhanced by DPPIV transfection. These findings imply that DPPIV may functionally suppress peritoneal dissemination and progression of ovarian carcinoma by regulating the expression levels of several molecules associated with carcinoma cell invasion and progression.
ESTHER : Kikkawa_2005_Biochim.Biophys.Acta_1751_45
PubMedSearch : Kikkawa_2005_Biochim.Biophys.Acta_1751_45
PubMedID: 16054016

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 : 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 : Functional annotation of a full-length Arabidopsis cDNA collection - Seki_2002_Science_296_141
Author(s) : Seki M , Narusaka M , Kamiya A , Ishida J , Satou M , Sakurai T , Nakajima M , Enju A , Akiyama K , Oono Y , Muramatsu M , Hayashizaki Y , Kawai J , Carninci P , Itoh M , Ishii Y , Arakawa T , Shibata K , Shinagawa A , Shinozaki K
Ref : Science , 296 :141 , 2002
Abstract : Full-length complementary DNAs (cDNAs) are essential for the correct annotation of genomic sequences and for the functional analysis of genes and their products. We isolated 155,144 RIKEN Arabidopsis full-length (RAFL) cDNA clones. The 3'-end expressed sequence tags (ESTs) of 155,144 RAFL cDNAs were clustered into 14,668 nonredundant cDNA groups, about 60% of predicted genes. We also obtained 5' ESTs from 14,034 nonredundant cDNA groups and constructed a promoter database. The sequence database of the RAFL cDNAs is useful for promoter analysis and correct annotation of predicted transcription units and gene products. Furthermore, the full-length cDNAs are useful resources for analyses of the expression profiles, functions, and structures of plant proteins.
ESTHER : Seki_2002_Science_296_141
PubMedSearch : Seki_2002_Science_296_141
PubMedID: 11910074
Gene_locus related to this paper: arath-CXE15

Title : Sensitivity to vecuronium in seropositive and seronegative patients with myasthenia gravis - Itoh_2002_Anesth.Analg_95_109
Author(s) : Itoh H , Shibata K , Nitta S
Ref : Anesthesia & Analgesia , 95 :109 , 2002
Abstract : Patients with myasthenia gravis (MG) are hypersensitive to nondepolarizing neuromuscular blocking drugs. Although antibodies to the acetylcholine receptor (AChR) often are observed in MG patients, 10% to 30% of patients do not show an anti-AChR antibody. Little is known about differences in sensitivity to nondepolarizing neuromuscular blocking drugs between MG patients with and without anti-AChR antibody. Hypothesizing that seronegative patients are as sensitive to vecuronium as seropositive patients, we assessed sensitivity in seropositive and seronegative MG patients and in non-MG patients (n = 8 each). During anesthesia with sevoflurane (2.5%) and nitrous oxide (60%) in oxygen, neuromuscular transmission was monitored by measuring the twitch tension of the adductor pollicis muscle with supramaximal stimulation. After baseline measurements, 10 microg/kg IV dose increments of vecuronium were administered sequentially until blockade exceeded 90%. The degree of blockade and onset time after the initial 10 microg/kg of vecuronium were assessed, and doses required to exceed 90% blockade were recorded. In addition, effective doses of 50% and 95% for vecuronium were calculated from a single data point. Both types of MG patients showed increased sensitivity to vecuronium compared with non-MG patients. IMPLICATIONS: Hypothesizing that seronegative patients are as sensitive to vecuronium as seropositive patients, we assessed sensitivity in seropositive and seronegative myasthenia gravis (MG) patients and in non-MG patients. They were, indeed, both equally sensitive to vecuronium.
ESTHER : Itoh_2002_Anesth.Analg_95_109
PubMedSearch : Itoh_2002_Anesth.Analg_95_109
PubMedID: 12088952

Title : Molecular cloning and functional expression of rat liver cytosolic acetyl-CoA hydrolase - Suematsu_2001_Eur.J.Biochem_268_2700
Author(s) : Suematsu N , Okamoto K , Shibata K , Nakanishi Y , Isohashi F
Ref : European Journal of Biochemistry , 268 :2700 , 2001
Abstract : A cytosolic acetyl-CoA hydrolase (CACH) was purified from rat liver to homogeneity by a new method using Triton X-100 as a stabilizer. We digested the purified enzyme with an endopeptidase and determined the N-terminal amino-acid sequences of the two proteolytic fragments. From the sequence data, we designed probes for RT-PCR, and amplified CACH cDNA from rat liver mRNA. The CACH cDNA contains a 1668-bp ORF encoding a protein of 556 amino-acid residues (62 017 Da). Recombinant expression of the cDNA in insect cells resulted in overproduction of functional acetyl-CoA hydrolase with comparable acyl-CoA chain-length specificity and Michaelis constant for acetyl-CoA to those of the native CACH. Database searching shows no homology to other known proteins, but reveals high similarities to two mouse expressed sequence tags (91% and 93% homology) and human mRNA for KIAA0707 hypothetical protein (50% homology) of unknown function.
ESTHER : Suematsu_2001_Eur.J.Biochem_268_2700
PubMedSearch : Suematsu_2001_Eur.J.Biochem_268_2700
PubMedID: 11322891

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 : Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes - Carninci_2000_Genome.Res_10_1617
Author(s) : Carninci P , Shibata Y , Hayatsu N , Sugahara Y , Shibata K , Itoh M , Konno H , Okazaki Y , Muramatsu M , Hayashizaki Y
Ref : Genome Res , 10 :1617 , 2000
Abstract : In the effort to prepare the mouse full-length cDNA encyclopedia, we previously developed several techniques to prepare and select full-length cDNAs. To increase the number of different cDNAs, we introduce here a strategy to prepare normalized and subtracted cDNA libraries in a single step. The method is based on hybridization of the first-strand, full-length cDNA with several RNA drivers, including starting mRNA as the normalizing driver and run-off transcripts from minilibraries containing highly expressed genes, rearrayed clones, and previously sequenced cDNAs as subtracting drivers. Our method keeps the proportion of full-length cDNAs in the subtracted/normalized library high. Moreover, our method dramatically enhances the discovery of new genes as compared to results obtained by using standard, full-length cDNA libraries. This procedure can be extended to the preparation of full-length cDNA encyclopedias from other organisms.
ESTHER : Carninci_2000_Genome.Res_10_1617
PubMedSearch : Carninci_2000_Genome.Res_10_1617
PubMedID: 11042159
Gene_locus related to this paper: mouse-1plip , mouse-1plrp , mouse-abhd5 , mouse-Abhd8 , mouse-cauxin , mouse-Ces1g , mouse-CPMac , mouse-dpp8 , mouse-hslip , mouse-hyes , mouse-lipli , mouse-LIPN , mouse-pafa , mouse-Ppgb , mouse-q3uuq7 , mouse-Q9DAI6 , mouse-RISC

Title : RIKEN integrated sequence analysis (RISA) system--384-format sequencing pipeline with 384 multicapillary sequencer - Shibata_2000_Genome.Res_10_1757
Author(s) : Shibata K , Itoh M , Aizawa K , Nagaoka S , Sasaki N , Carninci P , Konno H , Akiyama J , Nishi K , Kitsunai T , Tashiro H , Sumi N , Ishii Y , Nakamura S , Hazama M , Nishine T , Harada A , Yamamoto R , Matsumoto H , Sakaguchi S , Ikegami T , Kashiwagi K , Fujiwake S , Inoue K , Togawa Y
Ref : Genome Res , 10 :1757 , 2000
Abstract : The RIKEN high-throughput 384-format sequencing pipeline (RISA system) including a 384-multicapillary sequencer (the so-called RISA sequencer) was developed for the RIKEN mouse encyclopedia project. The RISA system consists of colony picking, template preparation, sequencing reaction, and the sequencing process. A novel high-throughput 384-format capillary sequencer system (RISA sequencer system) was developed for the sequencing process. This system consists of a 384-multicapillary auto sequencer (RISA sequencer), a 384-multicapillary array assembler (CAS), and a 384-multicapillary casting device. The RISA sequencer can simultaneously analyze 384 independent sequencing products. The optical system is a scanning system chosen after careful comparison with an image detection system for the simultaneous detection of the 384-capillary array. This scanning system can be used with any fluorescent-labeled sequencing reaction (chain termination reaction), including transcriptional sequencing based on RNA polymerase, which was originally developed by us, and cycle sequencing based on thermostable DNA polymerase. For long-read sequencing, 380 out of 384 sequences (99.2%) were successfully analyzed and the average read length, with more than 99% accuracy, was 654.4 bp. A single RISA sequencer can analyze 216 kb with >99% accuracy in 2.7 h (90 kb/h). For short-read sequencing to cluster the 3' end and 5' end sequencing by reading 350 bp, 384 samples can be analyzed in 1.5 h. We have also developed a RISA inoculator, RISA filtrator and densitometer, RISA plasmid preparator which can handle throughput of 40,000 samples in 17.5 h, and a high-throughput RISA thermal cycler which has four 384-well sites. The combination of these technologies allowed us to construct the RISA system consisting of 16 RISA sequencers, which can process 50,000 DNA samples per day. One haploid genome shotgun sequence of a higher organism, such as human, mouse, rat, domestic animals, and plants, can be revealed by seven RISA systems within one month.
ESTHER : Shibata_2000_Genome.Res_10_1757
PubMedSearch : Shibata_2000_Genome.Res_10_1757
PubMedID: 11076861
Gene_locus related to this paper: mouse-1plrp , mouse-abhd5 , mouse-Abhd8 , mouse-cauxin , mouse-dpp8 , mouse-hslip , mouse-lipli , mouse-LIPN , mouse-Ppgb , mouse-q3uuq7 , mouse-Q9DAI6