Okumura K

References (7)

Title : A bio-image sensor for simultaneous detection of multi-neurotransmitters - Lee_2018_Talanta_179_569
Author(s) : Lee YN , Okumura K , Horio T , Iwata T , Takahashi K , Hattori T , Sawada K
Ref : Talanta , 179 :569 , 2018
Abstract : We report here a new bio-image sensor for simultaneous detection of spatial and temporal distribution of multi-neurotransmitters. It consists of multiple enzyme-immobilized membranes on a 128 x 128 pixel array with read-out circuit. Apyrase and acetylcholinesterase (AChE), as selective elements, are used to recognize adenosine 5'-triphosphate (ATP) and acetylcholine (ACh), respectively. To enhance the spatial resolution, hydrogen ion (H(+)) diffusion barrier layers are deposited on top of the bio-image sensor and demonstrated their prevention capability. The results are used to design the space among enzyme-immobilized pixels and the null H(+) sensor to minimize the undesired signal overlap by H(+) diffusion. Using this bio-image sensor, we can obtain H(+) diffusion-independent imaging of concentration gradients of ATP and ACh in real-time. The sensing characteristics, such as sensitivity and detection of limit, are determined experimentally. With the proposed bio-image sensor the possibility exists for customizable monitoring of the activities of various neurochemicals by using different kinds of proton-consuming or generating enzymes.
ESTHER : Lee_2018_Talanta_179_569
PubMedSearch : Lee_2018_Talanta_179_569
PubMedID: 29310276

Title : Complete genome sequence of Melissococcus plutonius DAT561, a strain that shows an unusual growth profile and is representative of an endemic cluster in Japan - Okumura_2012_J.Bacteriol_194_3014
Author(s) : Okumura K , Arai R , Okura M , Kirikae T , Takamatsu D , Osaki M , Miyoshi-Akiyama T
Ref : Journal of Bacteriology , 194 :3014 , 2012
Abstract : We report the complete genome sequence of Melissococcus plutonius DAT561, which is a causative agent of European foulbrood. M. plutonius DAT561 is a representative of nonfastidious strains isolated in Japan. The addition of potassium phosphate was not required for normal growth, unlike for typical M. plutonius strain/isolates.
ESTHER : Okumura_2012_J.Bacteriol_194_3014
PubMedSearch : Okumura_2012_J.Bacteriol_194_3014
PubMedID: 22582373
Gene_locus related to this paper: melpt-f3ybx5

Title : Complete genome sequence of Melissococcus plutonius ATCC 35311 - Okumura_2011_J.Bacteriol_193_4029
Author(s) : Okumura K , Arai R , Okura M , Kirikae T , Takamatsu D , Osaki M , Miyoshi-Akiyama T
Ref : Journal of Bacteriology , 193 :4029 , 2011
Abstract : We report the first completely annotated genome sequence of Melissococcus plutonius ATCC 35311. M. plutonius is a one-genus, one-species bacterium and the etiological agent of European foulbrood of the honeybee. The genome sequence will provide new insights into the molecular mechanisms underlying its pathogenicity.
ESTHER : Okumura_2011_J.Bacteriol_193_4029
PubMedSearch : Okumura_2011_J.Bacteriol_193_4029
PubMedID: 21622755
Gene_locus related to this paper: melpt-f3yc39

Title : Complete genome sequencing and analysis of a Lancefield group G Streptococcus dysgalactiae subsp. equisimilis strain causing streptococcal toxic shock syndrome (STSS) - Shimomura_2011_BMC.Genomics_12_17
Author(s) : Shimomura Y , Okumura K , Murayama SY , Yagi J , Ubukata K , Kirikae T , Miyoshi-Akiyama T
Ref : BMC Genomics , 12 :17 , 2011
Abstract : BACKGROUND: Streptococcus dysgalactiae subsp. equisimilis (SDSE) causes invasive streptococcal infections, including streptococcal toxic shock syndrome (STSS), as does Lancefield group A Streptococcus pyogenes (GAS). We sequenced the entire genome of SDSE strain GGS_124 isolated from a patient with STSS.
RESULTS: We found that GGS_124 consisted of a circular genome of 2,106,340 bp. Comparative analyses among bacterial genomes indicated that GGS_124 was most closely related to GAS. GGS_124 and GAS, but not other streptococci, shared a number of virulence factor genes, including genes encoding streptolysin O, NADase, and streptokinase A, distantly related to SIC (DRS), suggesting the importance of these factors in the development of invasive disease. GGS_124 contained 3 prophages, with one containing a virulence factor gene for streptodornase. All 3 prophages were significantly similar to GAS prophages that carry virulence factor genes, indicating that these prophages had transferred these genes between pathogens. SDSE was found to contain a gene encoding a superantigen, streptococcal exotoxin type G, but lacked several genes present in GAS that encode virulence factors, such as other superantigens, cysteine protease speB, and hyaluronan synthase operon hasABC. Similar to GGS_124, the SDSE strains contained larger numbers of clustered, regularly interspaced, short palindromic repeats (CRISPR) spacers than did GAS, suggesting that horizontal gene transfer via streptococcal phages between SDSE and GAS is somewhat restricted, although they share phage species. CONCLUSION: Genome wide comparisons of SDSE with GAS indicate that SDSE is closely and quantitatively related to GAS. SDSE, however, lacks several virulence factors of GAS, including superantigens, SPE-B and the hasABC operon. CRISPR spacers may limit the horizontal transfer of phage encoded GAS virulence genes into SDSE. These findings may provide clues for dissecting the pathological roles of the virulence factors in SDSE and GAS that cause STSS.
ESTHER : Shimomura_2011_BMC.Genomics_12_17
PubMedSearch : Shimomura_2011_BMC.Genomics_12_17
PubMedID: 21223537
Gene_locus related to this paper: strpy-SPYM18.1727

Title : Increased level of pericardial insulin-like growth factor-1 in patients with left ventricular dysfunction and advanced heart failure - Abe_2006_J.Am.Coll.Cardiol_48_1387
Author(s) : Abe N , Matsunaga T , Kameda K , Tomita H , Fujiwara T , Ishizaka H , Hanada H , Fukui K , Fukuda I , Osanai T , Okumura K
Ref : J Am Coll Cardiol , 48 :1387 , 2006
Abstract : OBJECTIVES: To test the hypothesis that the cardiac insulin-like growth factor-1 (IGF-1) system is up-regulated in the failing heart, we measured the pericardial (cardiac) and plasma (circulating) IGF-1 levels in coronary artery disease patients. BACKGROUND: Local IGF-1 systems are regulated differently from the systemic IGF-1 system. The cardiac IGF-1 system is up-regulated by the increased left ventricular (LV) wall stress. However, it remains unknown how this system is affected in LV dysfunction and heart failure.
METHODS: We measured the plasma and pericardial fluid levels of IGF-1 and brain natriuretic peptide (BNP) in 87 coronary artery disease patients undergoing cardiac surgery, and examined their relationships with LV function and heart failure severity. The expressions of IGF-1 and IGF-1 receptor proteins were examined in endomyocardial biopsies obtained from other patients with normal or impaired LV function.
RESULTS: The pericardial IGF-1 and BNP levels were positively correlated with the plasma BNP level (both p < 0.001). The pericardial IGF-1 level was increased in heart failure patients, whereas the plasma IGF-1 level was rather decreased. The pericardial IGF-1 level was inversely correlated with the LV ejection fraction (p < 0.001), whereas the plasma IGF-1 level was not. Positive immunostaining for IGF-1 and IGF-1 receptor proteins was enhanced in myocardial biopsies from failing hearts compared with those from nonfailing hearts.
CONCLUSIONS: The pericardial IGF-1 level was increased in patients with LV dysfunction and heart failure, whereas the plasma IGF-1 level was decreased. These results may indicate that up-regulation of the cardiac IGF-1 system serves as a compensatory mechanism for LV dysfunction.
ESTHER : Abe_2006_J.Am.Coll.Cardiol_48_1387
PubMedSearch : Abe_2006_J.Am.Coll.Cardiol_48_1387
PubMedID: 17010800

Title : Signal sequence and keyword trap in silico for selection of full-length human cDNAs encoding secretion or membrane proteins from oligo-capped cDNA libraries - Otsuki_2005_DNA.Res_12_117
Author(s) : Otsuki T , Ota T , Nishikawa T , Hayashi K , Suzuki Y , Yamamoto J , Wakamatsu A , Kimura K , Sakamoto K , Hatano N , Kawai Y , Ishii S , Saito K , Kojima S , Sugiyama T , Ono T , Okano K , Yoshikawa Y , Aotsuka S , Sasaki N , Hattori A , Okumura K , Nagai K , Sugano S , Isogai T
Ref : DNA Research , 12 :117 , 2005
Abstract : We have developed an in silico method of selection of human full-length cDNAs encoding secretion or membrane proteins from oligo-capped cDNA libraries. Fullness rates were increased to about 80% by combination of the oligo-capping method and ATGpr, software for prediction of translation start point and the coding potential. Then, using 5'-end single-pass sequences, cDNAs having the signal sequence were selected by PSORT ('signal sequence trap'). We also applied 'secretion or membrane protein-related keyword trap' based on the result of BLAST search against the SWISS-PROT database for the cDNAs which could not be selected by PSORT. Using the above procedures, 789 cDNAs were primarily selected and subjected to full-length sequencing, and 334 of these cDNAs were finally selected as novel. Most of the cDNAs (295 cDNAs: 88.3%) were predicted to encode secretion or membrane proteins. In particular, 165(80.5%) of the 205 cDNAs selected by PSORT were predicted to have signal sequences, while 70 (54.2%) of the 129 cDNAs selected by 'keyword trap' preserved the secretion or membrane protein-related keywords. Many important cDNAs were obtained, including transporters, receptors, and ligands, involved in significant cellular functions. Thus, an efficient method of selecting secretion or membrane protein-encoding cDNAs was developed by combining the above four procedures.
ESTHER : Otsuki_2005_DNA.Res_12_117
PubMedSearch : Otsuki_2005_DNA.Res_12_117
PubMedID: 16303743

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