Nakamura Y

References (73)

Title : A Complex of Type I Platelet-Activating Factor Acetylhydrolase (PAF-AH) Catalytic Subunits Switches from alpha1\/alpha2 Heterodimer to alpha2\/alpha2 Homodimer during Adipocyte Differentiation of 3T3-L1 Cells - Nakamura_2023_Biol.Pharm.Bull_46_257
Author(s) : Nakamura Y , Kihara-Negishi F , Tanigawa K , Kiriya M , Kadowaki Y , Imagawa H , Nakanishi H , Watanabe S , Maruyama K , Karasawa K
Ref : Biol Pharm Bull , 46 :257 , 2023
Abstract : Platelet-activating factor acetylhydrolase (PAF-AH) hydrolyzes an acetyl ester at the sn-2 position of platelet-activating factor (PAF), thereby mediating a variety of biological functions. PAF-AH is found in three isoforms: Type I PAF-AH (PAF-AH I) and Type II PAF-AH (PAF-AH II) are intracellular enzymes whereas plasma PAF-AH is characterized by association with lipoprotein in plasma. PAF-AH I forms a tetramer constituted by two catalytic subunits (alpha1 and alpha2) with beta regulatory subunits. We recently showed that a deficiency of PAF-AH I catalytic subunits in male mice caused an increase of body weight, food intake, and white adipose tissue (WAT) weight. In this study, we examined whether the expression of this enzyme was altered in the differentiation of 3T3-L1 preadipocytes into adipocytes. The amount of PAF-AH I alpha1 subunit protein was significantly reduced in 3T3-L1 differentiation, while the amount of the PAF-AH I alpha2 subunit was not changed. Immunoprecipitation analysis of 3T3-L1 differentiation showed that the complex of PAF-AH I catalytic subunits was changed from alpha1/alpha2 heterodimer to alpha2/alpha2 homodimer. Our findings suggest that changes in PAF-AH I catalytic subunits are involved in adipocyte differentiation of 3T3-L1 and obesity in mice.
ESTHER : Nakamura_2023_Biol.Pharm.Bull_46_257
PubMedSearch : Nakamura_2023_Biol.Pharm.Bull_46_257
PubMedID: 36724953

Title : Two-step nationwide epidemiological survey of myasthenia gravis in Japan 2018 - Yoshikawa_2022_PLoS.One_17_e0274161
Author(s) : Yoshikawa H , Adachi Y , Nakamura Y , Kuriyama N , Murai H , Nomura Y , Sakai Y , Iwasa K , Furukawa Y , Kuwabara S , Matsui M
Ref : PLoS ONE , 17 :e0274161 , 2022
Abstract : OBJECTIVE: To study the updated prevalence and clinical features of myasthenia gravis (MG) in Japan during 2017. METHODS: We sent survey sheets to the randomly selected medical departments (number = 7,545). First, we asked the number of MG patients who visited medical departments from January 1, 2017, to December 31, 2017. Then, we sent the second survey sheet to the medical departments that answered the first survey to obtain the clinical information of patients who received MG diagnosis between January 1, 2015, and December 31, 2017. RESULTS: The received answer to the first survey were 2,708 (recovery rate: 35.9%). After all, the prevalence of the 100,000 population was estimated as 23.1 (95%CI: 20.5-25.6). As a result of the second survey, we obtained 1,464 case records. After checking the duplications and lacking data, we utilized 1,195 data for further analysis. The median [interquartile range (IQR)] from the onset age of total patients was 59 (43-70) years old. The male-female ratio was 1: 1.15. The onset age [median (IQR)] for female patients was 58 (40-72) years old, and that for male patients was 60 (49-69) years old (Wilcoxon-Mann-Whitney test, p = 0.0299). We divided patients into four categories: 1) anti-acetylcholine receptor antibody (AChRAb) (+) thymoma (Tm) (-), 2) AChRAb(+)Tm(+), 3) anti-muscle-specific kinase antibody (MuSKAb) (+), and AChRAb(-)MuSKAb(-) (double negative; DN). The onset age [median (IQR)] of AChRAb(+)Tm(-) was 64 (48-73) years old, and AChRb(+)Tm(+) was 55 (45-66), MuSKAb(+) was 49 (36-64), DN was 47 (35-60) year old. The multivariate logistic regression analysis using sex, initial symptoms, repetitive nerve stimulation test (RNST), and edrophonium test revealed that sex, ocular symptoms, bulbar symptoms, and RNST were factors to distinguish each category. The myasthenia gravis activities of daily living profile at the severest state were significantly higher in MuSKAb(+). MuSKAb(+) frequently received prednisolone, tacrolimus plasmapheresis, and intravenous immunoglobulin; however, they received less acetylcholine esterase inhibitor. 99.2% of AChRAb(+)Tm(+) and 15.4% of AChRAb(+)Tm(-) received thymectomy. MuSKAb(+) did not receive thymectomy, and only 5.7% of DN received thymectomy. The prognosis was favorable in all categories. CONCLUSION: Our result revealed that the prevalence of Japanese MG doubled from the previous study using the same survey method in 2006. We also found that the onset age shifted to the elderly, and the male-female ratio reached almost even. Classification in four categories; AChRAb(+)Tm(-), AChRAb(+)Tm(+), MuSKAb(+), and DN, well describe the specific clinical features of each category and differences in therapeutic approaches.
ESTHER : Yoshikawa_2022_PLoS.One_17_e0274161
PubMedSearch : Yoshikawa_2022_PLoS.One_17_e0274161
PubMedID: 36129914

Title : Increase in Cellular Lysophosphatidylserine Content Exacerbates Inflammatory Responses in LPS-Activated Microglia - Minamihata_2021_Neurochem.Res__
Author(s) : Minamihata T , Takano K , Nakamura Y , Seto R , Moriyama M
Ref : Neurochem Res , : , 2021
Abstract : Mutations in alpha/beta-hydrolase domain containing (ABHD) 12 gene, which encodes lysophosphatidylserine (LysoPS) lipase, cause the neurodegenerative disease PHARC (Polyneuropathy, Hearing loss, Ataxia, Retinitis pigmentosa, Cataract). Since ABHD12 is expressed by microglia in the central nervous system and is localized to the endoplasmic reticulum, accumulation of intracellular LysoPS by ABHD12 mutations is assumed to be one of the pathological mechanisms associated with microglial activation in PHARC. However, the role of microglia in the PHARC brain and the relationship between microglial function and cellular LysoPS content remains unclear. Therefore, we explored the influence of cellular LysoPS content in microglial inflammatory responses. We evaluated the effects of inhibitors of cellular LysoPS metabolism, KC01 and DO-264, on inflammatory responses using a lipopolysaccharide (LPS)-stimulated mouse microglial cell line, BV-2 and primary microglia. Treatment of DO-264, an inhibitor of cellular LysoPS degradation, enhanced LPS-induced phagocytosis concomitant with the increase in cellular LysoPS content in BV-2 cells. On the other hand, treatment with KC01, an agent had been developed as an inhibitor of LysoPS synthase, reduced phagocytosis without affecting cellular LysoPS content. Such effects of both inhibitors on phagocytosis were also confirmed using primary microglia. KC01 treatment decreased nitric oxide (NO) production, accompanied by a reduction in inducible NO synthase expression in BV-2 microglia. KC01 also suppressed LPS-induced generation of intracellular reactive oxygen species and cytokines such as interleukin-6. Our results suggest that increase in cellular LysoPS levels can exacerbate microglial inflammatory responses. Treatment to prevent the increase in cellular LysoPS in microglia may have therapeutic potential for PHARC.
ESTHER : Minamihata_2021_Neurochem.Res__
PubMedSearch : Minamihata_2021_Neurochem.Res__
PubMedID: 34383250
Gene_locus related to this paper: human-ABHD12B

Title : Sorting nexin 27 rescues neuroligin 2 from lysosomal degradation to control inhibitory synapse number - Binda_2019_Biochem.J_476_293
Author(s) : Binda CS , Nakamura Y , Henley JM , Wilkinson KA
Ref : Biochemical Journal , 476 :293 , 2019
Abstract : Retromer is an evolutionarily conserved endosomal trafficking complex that mediates the retrieval of cargo proteins from a degradative pathway for sorting back to the cell surface. To promote cargo recycling, the core retromer trimer of VPS (vacuolar protein sorting)26, VPS29 and VPS35 recognises cargo either directly, or through an adaptor protein, the most well characterised of which is the PDZ [postsynaptic density 95 (PSD95), disk large, zona occludens] domain-containing sorting nexin SNX27. Neuroligins (NLGs) are postsynaptic trans-synaptic scaffold proteins that function in the clustering of postsynaptic proteins to maintain synaptic stability. Here, we show that each of the NLGs (NLG1-3) bind to SNX27 in a direct PDZ ligand-dependent manner. Depletion of SNX27 from neurons leads to a decrease in levels of each NLG protein and, for NLG2, this occurs as a result of enhanced lysosomal degradation. Notably, while depletion of the core retromer component VPS35 leads to a decrease in NLG1 and NLG3 levels, NLG2 is unaffected, suggesting that, for this cargo, SNX27 acts independently of retromer. Consistent with loss of SNX27 leading to enhanced lysosomal degradation of NLG2, knockdown of SNX27 results in fewer NLG2 clusters in cultured neurons, and loss of SNX27 or VPS35 reduces the size and number of gephyrin clusters. Together, these data indicate that NLGs are SNX27-retromer cargoes and suggest that SNX27-retromer controls inhibitory synapse number, at least in part through trafficking of NLG2.
ESTHER : Binda_2019_Biochem.J_476_293
PubMedSearch : Binda_2019_Biochem.J_476_293
PubMedID: 30602588

Title : Efficacy, Safety, and Tolerability of Switching from Oral Cholinesterase Inhibitors to Rivastigmine Transdermal Patch with 1-Step Titration in Patients with Mild to Moderate Alzheimer's Disease: A 24-Week, Open-Label, Multicenter Study in Japan - Ueda_2019_Dement.Geriatr.Cogn.Dis.Extra_9_302
Author(s) : Ueda K , Katayama S , Arai T , Furuta N , Ikebe S , Ishida Y , Kanaya K , Ouma S , Sakurai H , Sugitani M , Takahashi M , Tanaka T , Tsuno N , Wakutani Y , Shekhawat A , Das Gupta A , Kiyose K , Toriyama K , Nakamura Y
Ref : Dement Geriatr Cogn Dis Extra , 9 :302 , 2019
Abstract : Background: Few studies have investigated treatment options for patients with Alzheimer's disease (AD) showing a poor response to oral cholinesterase inhibitors (ChEIs) in Japan. Objective: To investigate the efficacy and safety of switching from oral ChEIs to rivastigmine transdermal patch in patients with AD. Methods: In this multicenter, open-label, phase IV study in outpatient clinics in Japan, patients with mild-moderate AD who had a poor response to or experienced difficulty in continuing donepezil or galantamine were switched to rivastigmine transdermal patch (5 cm(2); loaded dose 9 mg, delivery rate 4.6 mg/24 h) with a 1-step titration in week 4 (10 cm(2); loaded dose 18 mg, delivery rate 9.5 mg/24 h), which was continued for 4 weeks in the titration period and 16 weeks in a maintenance period. The primary endpoint was the change in Mini-Mental State Examination (MMSE) total score from baseline to week 24. Results: A total of 118 patients were enrolled and switched to rivastigmine, of which 102 completed the 24-week study. The MMSE total score was essentially unchanged during the study, with a least-square mean change (SD) of -0.35 (2.64) at week 24 (p = 0.1750). Exploratory analysis with a mixed-effect model comparing changes in MMSE between the pre- and post-switch periods suggested that switching to rivastigmine prevented a worsening of MMSE. Application site skin reactions/irritations occurred in 30.5% of patients overall, in 22.0% in the 8-week titration period, and in 10.2% in the 16-week maintenance period. Conclusion: Within-class switching from an oral ChEI to rivastigmine transdermal patch might be an efficacious and tolerable option for AD patients showing a poor or limited response to a prior oral ChEI.
ESTHER : Ueda_2019_Dement.Geriatr.Cogn.Dis.Extra_9_302
PubMedSearch : Ueda_2019_Dement.Geriatr.Cogn.Dis.Extra_9_302
PubMedID: 31572426

Title : DPP4 Inhibition Ameliorates Cardiac Function by Blocking the Cleavage of HMGB1 in Diabetic Mice After Myocardial Infarction - Sato_2017_Int.Heart.J_58_778
Author(s) : Sato A , Suzuki S , Watanabe S , Shimizu T , Nakamura Y , Misaka T , Yokokawa T , Shishido T , Saitoh SI , Ishida T , Kubota I , Takeishi Y
Ref : Int Heart J , 58 :778 , 2017
Abstract : High mobility group box 1 (HMGB1), a ubiquitous DNA-binding protein, promotes angiogenesis and tissue repair, resulting in restored cardiac function after myocardial infarction (MI). Although dipeptidyl peptidase 4 (DPP4) degrades certain peptides, it remains unclear as to whether HMGB1 is a substrate of DPP4 and whether DPP4 inhibition prevents the cleavage of HMGB1.In transgenic mice with cardiac-specific overexpression of HMGB1 (TG) and wild-type mice (WT), a diabetic state was induced by streptozotocin, and MI was created by ligation of the left anterior descending coronary artery. To inhibit DPP4 activity, a DPP4 inhibitor anagliptin was used. The plasma levels of HMGB1, infarct size, echocardiographic data, angiogenesis, and vascular endothelial growth factor (VEGF) expression in the peri-infarct area were compared among non-diabetic MI WT/TG, diabetic MI WT/TG, and anagliptin-treated diabetic MI WT/TG mice.DPP4 activity was increased in the diabetic state and blocked by anagliptin administration. The HMGB1 plasma levels were reduced in the diabetic TG compared with the non-diabetic TG mice, but DPP4 inhibition with anagliptin increased HMGB1 plasma levels in the diabetic TG mice. The infarct area was significantly larger in the diabetic TG than in the non-diabetic TG mice, and it was reduced by DPP4 inhibition. Cardiac function, angiogenesis, and VEGF expression were impaired in the diabetic TG mice, but they were ameliorated by the DPP4 inhibition to levels similar to those found in the non-diabetic TG mice.The DPP4 inhibitor ameliorated cardiac function by inhibiting the inactivation of HMGB1 in diabetic mice after MI.
ESTHER : Sato_2017_Int.Heart.J_58_778
PubMedSearch : Sato_2017_Int.Heart.J_58_778
PubMedID: 28966327

Title : Preliminary evidence that rivastigmine-induced inhibition of serum butyrylcholinesterase activity improves behavioral symptoms in Japanese patients with Alzheimer's disease - Bando_2017_Geriatr.Gerontol.Int_17_1306
Author(s) : Bando N , Nakamura Y
Ref : Geriatr Gerontol Int , 17 :1306 , 2017
Abstract : AIM: To investigate whether the inhibitory rate of serum butyrylcholinesterase (BuChE) activity in Japanese patients with Alzheimer's disease is correlated with cognitive function, behavioral symptoms and caregiver burden. METHODS: A total of 61 patients with mild to moderately severe Alzheimer's disease who were not undergoing cholinesterase enzyme inhibitor/memantine combinatorial treatment received a rivastigmine (18 mg) patch for 24 weeks. The rate of inhibition of BuChE was correlated with scores obtained on cognitive (Mini-Mental State Examination), behavioral (the Japanese version of the modified Crichton Geriatric Behavioral Rating Scale [CGBRS] and Vitality Index [VI]) and burden (the Japanese version of Zarit Burden Inventory [ZBI]) scales; and the Clinical Global Impression of Change scale. RESULTS: The serum BuChE activity showed a significant decrease after 24 weeks compared with baseline (P < 0.001). Overall, significant effects were found in the Mini-Mental State Examination score, VI score and modified CGBRS score. We then divided patient groups into a high inhibitory rate (>/=40%) group and a low inhibitory rate (<40%) group; there were significant improvements in the Mini-Mental State Examination score, VI score and modified CGBRS score in both groups. However, favorable results were seen in cooperation, restlessness and leisure on modified CGBRS subscales in the high inhibitory rate group (P < 0.001, P = 0.007, P < 0.001, respectively), and rehabilitation and other activities on VI subscales in the high inhibitory rate group (P = 0.005) compared with those in the low inhibitory rate group. CONCLUSIONS: Demonstrable significant improvements in behavioral symptoms, such as low cooperation, restlessness or low activities in patients with Alzheimer's disease, were achieved on inhibition of BuChE at a rate of 40% or more. Geriatr Gerontol Int 2017; 17: 1306-1312.
ESTHER : Bando_2017_Geriatr.Gerontol.Int_17_1306
PubMedSearch : Bando_2017_Geriatr.Gerontol.Int_17_1306
PubMedID: 27546156

Title : Draft Sequencing of the Heterozygous Diploid Genome of Satsuma (Citrus unshiu Marc.) Using a Hybrid Assembly Approach - Shimizu_2017_Front.Genet_8_180
Author(s) : Shimizu T , Tanizawa Y , Mochizuki T , Nagasaki H , Yoshioka T , Toyoda A , Fujiyama A , Kaminuma E , Nakamura Y
Ref : Front Genet , 8 :180 , 2017
Abstract : Satsuma (Citrus unshiu Marc.) is one of the most abundantly produced mandarin varieties of citrus, known for its seedless fruit production and as a breeding parent of citrus. De novo assembly of the heterozygous diploid genome of Satsuma ("Miyagawa Wase") was conducted by a hybrid assembly approach using short-read sequences, three mate-pair libraries, and a long-read sequence of PacBio by the PLATANUS assembler. The assembled sequence, with a total size of 359.7 Mb at the N50 length of 386,404 bp, consisted of 20,876 scaffolds. Pseudomolecules of Satsuma constructed by aligning the scaffolds to three genetic maps showed genome-wide synteny to the genomes of Clementine, pummelo, and sweet orange. Gene prediction by modeling with MAKER-P proposed 29,024 genes and 37,970 mRNA; additionally, gene prediction analysis found candidates for novel genes in several biosynthesis pathways for gibberellin and violaxanthin catabolism. BUSCO scores for the assembled scaffold and predicted transcripts, and another analysis by BAC end sequence mapping indicated the assembled genome consistency was close to those of the haploid Clementine, pummel, and sweet orange genomes. The number of repeat elements and long terminal repeat retrotransposon were comparable to those of the seven citrus genomes; this suggested no significant failure in the assembly at the repeat region. A resequencing application using the assembled sequence confirmed that both kunenbo-A and Satsuma are offsprings of Kishu, and Satsuma is a back-crossed offspring of Kishu. These results illustrated the performance of the hybrid assembly approach and its ability to construct an accurate heterozygous diploid genome.
ESTHER : Shimizu_2017_Front.Genet_8_180
PubMedSearch : Shimizu_2017_Front.Genet_8_180
PubMedID: 29259619
Gene_locus related to this paper: citsi-a0a067e7f4 , 9rosi-v4u6v9 , citsi-a0a067dhb0 , citsi-a0a067f614 , citun-a0a2h5ny34 , citsi-a0a067f6y7 , citcl-v4syg1

Title : Lipoprotein-associated phospholipase A2 is related to risk of subclinical atherosclerosis but is not supported by Mendelian randomization analysis in a general Japanese population - Ueshima_2016_Atherosclerosis_246_141
Author(s) : Ueshima H , Kadowaki T , Hisamatsu T , Fujiyoshi A , Miura K , Ohkubo T , Sekikawa A , Kadota A , Kadowaki S , Nakamura Y , Miyagawa N , Okamura T , Kita Y , Takashima N , Kashiwagi A , Maegawa H , Horie M , Yamamoto T , Kimura T , Kita T
Ref : Atherosclerosis , 246 :141 , 2016
Abstract : OBJECTIVE: Lipoprotein-associated phospholipase A2 (Lp-PLA2) is an enzyme predominantly bound to low-density lipoprotein (LDL). Lp-PLA2 is recognized as playing a key role in inflammatory processes and the development of atherosclerosis. This study aimed to investigate whether Lp-PLA2 is related to subclinical atherosclerosis, independently from traditional risk factors, in a general Japanese population by analyses of both the observational study and Mendelian randomization using V279F polymorphism. METHODS AND
RESULTS: We cross-sectionally examined community-based sample of 929 Japanese men aged 40-79 years, without statin treatment, who were randomly selected from the resident registration. Multiple regression analyses of Lp-PLA2 activity and concentration were undertaken separately for men aged 40-49 years and 50-79 years, to clarify interactions of age and Lp-PLA2. Lp-PLA2 activity for men aged 50-79 years was significantly and positively related to intima-media thickness (IMT) (P = 0.013) and plaque index (P = 0.008) independent of traditional risk factors including small LDL particles, but not to coronary artery calcification (CAC) score. Associations with Lp-PLA2 concentration were qualitatively similar to those of activity. Corresponding relationships were not observed in men aged 40-49 years. Mendelian randomization analyses based on V279F genotype did not show any significant associations with subclinical atherosclerosis, although the homozygote and heterozygote of V279F showed low Lp-PLA2 activity and concentration.
CONCLUSIONS: Lp-PLA2 activity in Japanese men aged 50-79 years was associated significantly and positively with IMT and plaque in the carotid artery but Mendelian randomization did not support that Lp-PLA2 is a causative factor for subclinical atherosclerosis.
ESTHER : Ueshima_2016_Atherosclerosis_246_141
PubMedSearch : Ueshima_2016_Atherosclerosis_246_141
PubMedID: 26775119

Title : Complete genome sequence of cyanobacterium Nostoc sp. NIES-3756, a potentially useful strain for phytochrome-based bioengineering - Hirose_2016_J.Biotechnol_218_51
Author(s) : Hirose Y , Fujisawa T , Ohtsubo Y , Katayama M , Misawa N , Wakazuki S , Shimura Y , Nakamura Y , Kawachi M , Yoshikawa H , Eki T , Kanesaki Y
Ref : J Biotechnol , 218 :51 , 2016
Abstract : To explore the diverse photoreceptors of cyanobacteria, we isolated Nostoc sp. strain NIES-3756 from soil at Mimomi-Park, Chiba, Japan, and determined its complete genome sequence. The Genome consists of one chromosome and two plasmids (total 6,987,571 bp containing no gaps). The NIES-3756 strain carries 7 phytochrome and 12 cyanobacteriochrome genes, which will facilitate the studies of phytochrome-based bioengineering.
ESTHER : Hirose_2016_J.Biotechnol_218_51
PubMedSearch : Hirose_2016_J.Biotechnol_218_51
PubMedID: 26656223
Gene_locus related to this paper: 9noso-a0a0s3pjx6

Title : Complete genome sequence of cyanobacterium Fischerella sp. NIES-3754, providing thermoresistant optogenetic tools - Hirose_2016_J.Biotechnol_220_45
Author(s) : Hirose Y , Fujisawa T , Ohtsubo Y , Katayama M , Misawa N , Wakazuki S , Shimura Y , Nakamura Y , Kawachi M , Yoshikawa H , Eki T , Kanesaki Y
Ref : J Biotechnol , 220 :45 , 2016
Abstract : Cyanobacterial phytochrome-class photosensors are recently emerging optogenetic tools. We isolated Fischerella sp. strain NIES-3754 from hotspring at Suwa-shrine, Suwa, Nagano, Japan. We determined complete genome sequence of the NIES-3754 strain, which is composed of one chromosome and two putative replicons (total 5,826,863bp containing no gaps). We identified photosensor genes of 5 phytochromes and 9 cyanobacteriochromes, which will facilitate optogenetics of thermophile.
ESTHER : Hirose_2016_J.Biotechnol_220_45
PubMedSearch : Hirose_2016_J.Biotechnol_220_45
PubMedID: 26784989
Gene_locus related to this paper: 9cyan-a0a0s3tkv2

Title : Complete Genome Sequence of Aurantimicrobium minutum Type Strain KNCT, a Planktonic Ultramicrobacterium Isolated from River Water - Nakai_2016_Genome.Announc_4_e00616
Author(s) : Nakai R , Fujisawa T , Nakamura Y , Nishide H , Uchiyama I , Baba T , Toyoda A , Fujiyama A , Naganuma T , Niki H
Ref : Genome Announc , 4 : , 2016
Abstract : Aurantimicrobium minutum type strain KNC(T) is a planktonic ultramicrobacterium isolated from river water in western Japan. Strain KNC(T) has an extremely small, streamlined genome of 1,622,386 bp comprising 1,575 protein-coding sequences. The genome annotation suggests that strain KNC(T) has an actinorhodopsin-based photometabolism.
ESTHER : Nakai_2016_Genome.Announc_4_e00616
PubMedSearch : Nakai_2016_Genome.Announc_4_e00616
PubMedID: 27365350
Gene_locus related to this paper: 9mico-a0a173lyl3

Title : A 24-Week, Randomized, Controlled Study to Evaluate the Tolerability, Safety and Efficacy of 2 Different Titration Schemes of the Rivastigmine Patch in Japanese Patients with Mild to Moderate Alzheimer's Disease - Nakamura_2015_Dement.Geriatr.Cogn.Dis.Extra_5_361
Author(s) : Nakamura Y , Strohmaier C , Tamura K , Kataoka N , Nakano M , Oda S , Nishimura K , Homma A
Ref : Dement Geriatr Cogn Dis Extra , 5 :361 , 2015
Abstract : AIM: To investigate whether 1-step titration of the rivastigmine patch (initiated at 5 cm(2) and titrated to 10 cm(2) after 4 weeks) is well tolerated in Japanese patients with Alzheimer's disease (AD) as compared to 3-step titration (initiated at 2.5 cm(2) and titrated by 2.5 cm(2) every 4 weeks to 10 cm(2)).
METHODS: A 24-week, multicenter, randomized, double-blind study was conducted in Japan between July 2012 and May 2014. Patients with mild to moderate AD aged 50-85 years were randomized 1:1 to 1-step or 3-step titration of the rivastigmine once-daily patch. The primary endpoint was the proportion of patients with adverse events leading to discontinuation.
RESULTS: Of 216 patients randomized, 215 (1-step, n = 107; 3-step, n = 108) were included in the safety analysis. The primary endpoint outcome was 15.0% in the 1-step group and 18.5% in the 3-step group. The observed treatment difference was -3.6% (95% confidence interval: -17.0, 9.6), falling within the prespecified acceptance range. CONCLUSION: The tolerability of two different titration schemes was similar in Japanese patients with AD.
ESTHER : Nakamura_2015_Dement.Geriatr.Cogn.Dis.Extra_5_361
PubMedSearch : Nakamura_2015_Dement.Geriatr.Cogn.Dis.Extra_5_361
PubMedID: 26557135

Title : Klebsormidium flaccidum genome reveals primary factors for plant terrestrial adaptation - Hori_2014_Nat.Commun_5_3978
Author(s) : Hori K , Maruyama F , Fujisawa T , Togashi T , Yamamoto N , Seo M , Sato S , Yamada T , Mori H , Tajima N , Moriyama T , Ikeuchi M , Watanabe M , Wada H , Kobayashi K , Saito M , Masuda T , Sasaki-Sekimoto Y , Mashiguchi K , Awai K , Shimojima M , Masuda S , Iwai M , Nobusawa T , Narise T , Kondo S , Saito H , Sato R , Murakawa M , Ihara Y , Oshima-Yamada Y , Ohtaka K , Satoh M , Sonobe K , Ishii M , Ohtani R , Kanamori-Sato M , Honoki R , Miyazaki D , Mochizuki H , Umetsu J , Higashi K , Shibata D , Kamiya Y , Sato N , Nakamura Y , Tabata S , Ida S , Kurokawa K , Ohta H
Ref : Nat Commun , 5 :3978 , 2014
Abstract : The colonization of land by plants was a key event in the evolution of life. Here we report the draft genome sequence of the filamentous terrestrial alga Klebsormidium flaccidum (Division Charophyta, Order Klebsormidiales) to elucidate the early transition step from aquatic algae to land plants. Comparison of the genome sequence with that of other algae and land plants demonstrate that K. flaccidum acquired many genes specific to land plants. We demonstrate that K. flaccidum indeed produces several plant hormones and homologues of some of the signalling intermediates required for hormone actions in higher plants. The K. flaccidum genome also encodes a primitive system to protect against the harmful effects of high-intensity light. The presence of these plant-related systems in K. flaccidum suggests that, during evolution, this alga acquired the fundamental machinery required for adaptation to terrestrial environments.
ESTHER : Hori_2014_Nat.Commun_5_3978
PubMedSearch : Hori_2014_Nat.Commun_5_3978
PubMedID: 24865297
Gene_locus related to this paper: kleni-a0a1y1i5c5 , kleni-a0a1y1i3f9 , kleni-a0a1y1hnk2 , kleni-a0a1y1hsz2 , kleni-a0a1y1hva2 , kleni-a0a1y1i2g3 , kleni-a0a1y1i4h5 , kleni-a0a1y1i9h9

Title : Primary cultures of rat cortical microglia treated with nicotine increases in the expression of excitatory amino acid transporter 1 (GLAST) via the activation of the alpha7 nicotinic acetylcholine receptor - Morioka_2014_Neurosci_258_374
Author(s) : Morioka N , Tokuhara M , Nakamura Y , Idenoshita Y , Harano S , Zhang FF , Hisaoka-Nakashima K , Nakata Y
Ref : Neuroscience , 258 :374 , 2014
Abstract : Although the clearance of glutamate from the synapse under physiological conditions is performed by astrocytic glutamate transporters, their expression might be diminished under pathological conditions. Microglia glutamate transporters, however, might serve as a back-up system when astrocytic glutamate uptake is impaired, and could have a prominent neuroprotective function under pathological conditions. In the current study, the effect of nicotine, well known as a neuroprotective molecule, on the function of glutamate transporters in cultured rat cortical microglia was examined. Reverse transcription polymerase chain reaction and pharmacological approaches demonstrated that, glutamate/aspartate transporter (GLAST), not glutamate transporter 1 (GLT-1), is the major functional glutamate transporter in cultured cortical microglia. Furthermore, the alpha7 subunit was demonstrated to be the key subunit comprising nicotinic acetylcholine (nACh) receptors in these cells. Treatment of cortical microglia with nicotine led to a significant increase of GLAST mRNA expression and (14)C-glutamate uptake in a concentration- and time-dependent manner, which were markedly inhibited by pretreatment with methyllycaconitine, a selective alpha7 nACh receptor antagonist. The nicotine-induced expression of GLAST mRNA and protein is mediated through an inositol trisphosphate (IP3) and Ca(2+)/calmodulin-dependent protein kinase II (CaMKII) depend intracellular pathway, since pretreatment with either xestospongin C, an IP3 receptor antagonist, or KN-93, a CaMKII inhibitor, blocked GLAST expression. Together, these findings indicate that activation of nACh receptors, specifically those expressing the alpha7 subunit, on cortical microglia could be a key mechanism of the neuroprotective effect of nACh receptor ligands such as nicotine.
ESTHER : Morioka_2014_Neurosci_258_374
PubMedSearch : Morioka_2014_Neurosci_258_374
PubMedID: 24300109

Title : Draft Genome Sequence of Weissella oryzae SG25T, Isolated from Fermented Rice Grains - Tanizawa_2014_Genome.Announc_2_e00667
Author(s) : Tanizawa Y , Fujisawa T , Mochizuki T , Kaminuma E , Suzuki Y , Nakamura Y , Tohno M
Ref : Genome Announc , 2 : , 2014
Abstract : Weissella oryzae was originally isolated from fermented rice grains. Here we report the draft genome sequence of the type strain of W. oryzae. This first report on the genomic sequence of this species may help identify the mechanisms underlying bacterial adaptation to the ecological niche of fermented rice grains.
ESTHER : Tanizawa_2014_Genome.Announc_2_e00667
PubMedSearch : Tanizawa_2014_Genome.Announc_2_e00667
PubMedID: 25013139
Gene_locus related to this paper: 9lact-a0a069d1e3

Title : Draft Genome Sequence of Lactobacillus oryzae Strain SG293T - Tanizawa_2014_Genome.Announc_2_e00861
Author(s) : Tanizawa Y , Fujisawa T , Mochizuki T , Kaminuma E , Nakamura Y , Tohno M
Ref : Genome Announc , 2 : , 2014
Abstract : We report the 1.86-Mb draft genome and annotation of Lactobacillus oryzae SG293(T) isolated from fermented rice grains. This genome information may provide further insights into the mechanisms underlying the fermentation of rice grains.
ESTHER : Tanizawa_2014_Genome.Announc_2_e00861
PubMedSearch : Tanizawa_2014_Genome.Announc_2_e00861
PubMedID: 25169865
Gene_locus related to this paper: 9laco-a0a081bkd2 , 9laco-a0a081bga0

Title : Serum butyrylcholinesterase and the risk of future type 2 diabetes: the Kansai Healthcare Study - Sato_2014_Clin.Endocrinol.(Oxf)_80_362
Author(s) : Sato KK , Hayashi T , Maeda I , Koh H , Harita N , Uehara S , Onishi Y , Oue K , Nakamura Y , Endo G , Kambe H , Fukuda K
Ref : Clinical Endocrinology (Oxf) , 80 :362 , 2014
Abstract : OBJECTIVE: Butyrylcholinesterase is synthesized in the liver. The serum butyrylcholinesterase level has been cross-sectionally reported to be higher in patients with diabetes, hyperlipidaemia, obesity and fatty liver than in those without them. It is not known whether serum butyrylcholinesterase is associated with the risk of future type 2 diabetes. DESIGN: A prospective cohort study. PARTICIPANTS: A total of 8470 Japanese men aged 40-55 years without type 2 diabetes at baseline. MEASUREMENTS: Type 2 diabetes was diagnosed if a fasting plasma glucose (FPG) level was >/=7.0 mmol/l, if a HbA1 c level was >/=6.5% or if participants were taking oral hypoglycaemic medication or insulin.
RESULTS: During the 42 227 person-years of follow-up, 868 cases had developed type 2 diabetes. Serum butyrylcholinesterase was significantly positively correlated with body mass index (BMI), FPG, alanine aminotransferase (ALT), gamma-glutamyltransferase (GGT) and triglycerides (TG), whereas negatively with high-density lipoprotein (HDL) cholesterol. In Cox proportional hazards models, after adjusting for age, BMI, FPG, alcohol consumption, smoking habit, walk to work, regular leisure-time physical activity and family history of diabetes, the highest quartile (398-806 IU/l) of serum butyrylcholinesterase increased the risk of type 2 diabetes compared with the lowest quartile (56-311 IU/l) [hazard ratio (HR) 1.41 (95% confidence interval (CI), 1.14-1.74)]. After further adjusting for ALT and GGT, this association remained [HR 1.40 (95% CI, 1.13-1.73)]. Furthermore, this association was significant independent of TG and HDL cholesterol.
CONCLUSIONS: Elevated serum butyrylcholinesterase was independently associated with an increased risk of future type 2 diabetes.
ESTHER : Sato_2014_Clin.Endocrinol.(Oxf)_80_362
PubMedSearch : Sato_2014_Clin.Endocrinol.(Oxf)_80_362
PubMedID: 23418907

Title : Comparative genomic characterization of three Streptococcus parauberis strains in fish pathogen, as assessed by wide-genome analyses - Nho_2013_PLoS.One_8_e80395
Author(s) : Nho SW , Hikima J , Park SB , Jang HB , Cha IS , Yasuike M , Nakamura Y , Fujiwara A , Sano M , Kanai K , Kondo H , Hirono I , Takeyama H , Aoki T , Jung TS
Ref : PLoS ONE , 8 :e80395 , 2013
Abstract : Streptococcus parauberis, which is the main causative agent of streptococcosis among olive flounder (Paralichthys olivaceus) in northeast Asia, can be distinctly divided into two groups (type I and type II) by an agglutination test. Here, the whole genome sequences of two Japanese strains (KRS-02083 and KRS-02109) were determined and compared with the previously determined genome of a Korean strain (KCTC 11537). The genomes of S. parauberis are intermediate in size and have lower GC contents than those of other streptococci. We annotated 2,236 and 2,048 genes in KRS-02083 and KRS-02109, respectively. Our results revealed that the three S. parauberis strains contain different genomic insertions and deletions. In particular, the genomes of Korean and Japanese strains encode different factors for sugar utilization; the former encodes the phosphotransferase system (PTS) for sorbose, whereas the latter encodes proteins for lactose hydrolysis, respectively. And the KRS-02109 strain, specifically, was the type II strain found to be able to resist phage infection through the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system and which might contribute valuably to serologically distribution. Thus, our genome-wide association study shows that polymorphisms can affect pathogen responses, providing insight into biological/biochemical pathways and phylogenetic diversity.
ESTHER : Nho_2013_PLoS.One_8_e80395
PubMedSearch : Nho_2013_PLoS.One_8_e80395
PubMedID: 24260382
Gene_locus related to this paper: 9stre-f1yze3

Title : Draft Genome Sequence of Agarivorans albus Strain MKT 106T, an Agarolytic Marine Bacterium - Yasuike_2013_Genome.Announc_1_e00367
Author(s) : Yasuike M , Nakamura Y , Kai W , Fujiwara A , Fukui Y , Satomi M , Sano M
Ref : Genome Announc , 1 :e00367 , 2013
Abstract : Agarivorans albus is a Gram-negative, strictly aerobic, and agar-hydrolyzing marine bacterium. We present the draft genome sequence of the A. albus strain MKT 106(T), which is composed of 67 contigs (>500 bp) totaling 4,734,285 bp and containing 4,397 coding DNA sequences (CDSs), four rRNAs, and 64 tRNA sequences.
ESTHER : Yasuike_2013_Genome.Announc_1_e00367
PubMedSearch : Yasuike_2013_Genome.Announc_1_e00367
PubMedID: 23868120
Gene_locus related to this paper: agaal-r9psh6 , agaal-r9pnu7 , agaal-r9ptw5 , agaal-r9pkj2 , agaal-r9ptp8

Title : Proteomics identified nuclear N-myc downstream-regulated gene 1 as a prognostic tissue biomarker candidate in renal cell carcinoma - Hosoya_2013_Biochim.Biophys.Acta_1834_2630
Author(s) : Hosoya N , Sakumoto M , Nakamura Y , Narisawa T , Bilim V , Motoyama T , Tomita Y , Kondo T
Ref : Biochimica & Biophysica Acta , 1834 :2630 , 2013
Abstract : The aim of this study was to identify proteins with aberrant expression in clear cell renal cell carcinoma (ccRCC), and elucidate their clinical utilities. The protein expression profiles of primary ccRCC tumor tissues and neighboring non-tumor tissues were obtained from 9 patients by two-dimensional difference gel electrophoresis and mass spectrometry. Comparative analysis of 3771 protein spots led to the identification of 73 proteins that were expressed at aberrant levels in tumor tissues compared with non-tumor tissues. Among these 73 proteins, we further focused on N-myc downstream-regulated gene 1 protein (NDRG1). NDRG1 expression is regulated by members of myc family as well as by p53, HIF1A, and SGK1. The biological and clinical significance of NDRG1 is controversial for various malignancies and no detailed studies on NDRG1 have been reported in ccRCC until our study. For the 82 newly enrolled ccRCC patients, immunohistochemical analysis revealed a significant association between nuclear NDRG1 and favorable prognosis (p<0.05). Multivariate analysis demonstrated the role of NDRG1 as an independent factor of progression-free survival (p=0.01). Subsequent in vitro gene suppression assay demonstrated that NDRG1 silencing significantly enhanced cell proliferation and invasion of RCC cells. The cytotoxic effects of NDRG1 up-regulation induced by an iron chelator were also confirmed. These findings suggest that nuclear NDRG1 has tumor suppressive effects, and the NDRG1 expression may have clinical values in ccRCC. Nuclear NDRG1 may provide additional insights on molecular backgrounds of ccRCC progression, and contribute to the development of novel therapeutic strategy.
ESTHER : Hosoya_2013_Biochim.Biophys.Acta_1834_2630
PubMedSearch : Hosoya_2013_Biochim.Biophys.Acta_1834_2630
PubMedID: 23999030

Title : Ethanol- and acetaldehyde-induced cholinergic imbalance in the hippocampus of Aldh2-knockout mice does not affect nerve growth factor or brain-derived neurotrophic factor - Jamal_2013_Brain.Res_1539_41
Author(s) : Jamal M , Ameno K , Ruby M , Miki T , Tanaka N , Nakamura Y , Kinoshita H
Ref : Brain Research , 1539 :41 , 2013
Abstract : Neurotrophins, including nerve growth factor (NGF) and brain-derived neurotrophic factor (BDNF), play an important role in the maintenance of cholinergic-neuron function. The objective of this study was to investigate whether ethanol (EtOH)- and acetaldehyde (AcH)- induced cholinergic effects would cause neurotrophic alterations in the hippocampus of mice. We used Aldh2 knockout (Aldh2-KO) mice, a model of aldehyde dehydrogenase 2 (ALDH2)-deficiency in humans, to examine the effects of acute administration of EtOH and the role of AcH. Hippocampal slices were collected and the mRNA and protein levels of choline acetyltransferase (ChAT), acetylcholinesterase (AChE), NGF and BDNF were analyzed 30min after the i.p. administration of EtOH (0.5, 1.0, or 2.0g/kg). We show that treatment with 2.0g/kg of EtOH decreased ChAT mRNA and protein levels in Aldh2-KO mice but not in wild-type (WT) mice, which suggests a role for AcH in the mechanism of action of EtOH. The administration of 2.0g/kg of EtOH increased AChE mRNA in both strains of mice. EtOH failed to change the levels of NGF or BDNF at any dose. Aldh2-KO mice exhibited a distinctly lower expression of ChAT and a higher expression of NGF both at mRNA and protein levels in the hippocampus compared with WT mice. Our observations suggest that administration of EtOH and elevated AcH can alter cholinergic markers in the hippocampus of mice, and this effect did not change the levels of NGF or BDNF.
ESTHER : Jamal_2013_Brain.Res_1539_41
PubMedSearch : Jamal_2013_Brain.Res_1539_41
PubMedID: 24096209

Title : Complete genome sequence of Bradyrhizobium sp. S23321: insights into symbiosis evolution in soil oligotrophs - Okubo_2012_Microbes.Environ_27_306
Author(s) : Okubo T , Tsukui T , Maita H , Okamoto S , Oshima K , Fujisawa T , Saito A , Futamata H , Hattori R , Shimomura Y , Haruta S , Morimoto S , Wang Y , Sakai Y , Hattori M , Aizawa S , Nagashima KV , Masuda S , Hattori T , Yamashita A , Bao Z , Hayatsu M , Kajiya-Kanegae H , Yoshinaga I , Sakamoto K , Toyota K , Nakao M , Kohara M , Anda M , Niwa R , Jung-Hwan P , Sameshima-Saito R , Tokuda S , Yamamoto S , Yokoyama T , Akutsu T , Nakamura Y , Nakahira-Yanaka Y , Takada Hoshino Y , Hirakawa H , Mitsui H , Terasawa K , Itakura M , Sato S , Ikeda-Ohtsubo W , Sakakura N , Kaminuma E , Minamisawa K
Ref : Microbes Environ , 27 :306 , 2012
Abstract : Bradyrhizobium sp. S23321 is an oligotrophic bacterium isolated from paddy field soil. Although S23321 is phylogenetically close to Bradyrhizobium japonicum USDA110, a legume symbiont, it is unable to induce root nodules in siratro, a legume often used for testing Nod factor-dependent nodulation. The genome of S23321 is a single circular chromosome, 7,231,841 bp in length, with an average GC content of 64.3%. The genome contains 6,898 potential protein-encoding genes, one set of rRNA genes, and 45 tRNA genes. Comparison of the genome structure between S23321 and USDA110 showed strong colinearity; however, the symbiosis islands present in USDA110 were absent in S23321, whose genome lacked a chaperonin gene cluster (groELS3) for symbiosis regulation found in USDA110. A comparison of sequences around the tRNA-Val gene strongly suggested that S23321 contains an ancestral-type genome that precedes the acquisition of a symbiosis island by horizontal gene transfer. Although S23321 contains a nif (nitrogen fixation) gene cluster, the organization, homology, and phylogeny of the genes in this cluster were more similar to those of photosynthetic bradyrhizobia ORS278 and BTAi1 than to those on the symbiosis island of USDA110. In addition, we found genes encoding a complete photosynthetic system, many ABC transporters for amino acids and oligopeptides, two types (polar and lateral) of flagella, multiple respiratory chains, and a system for lignin monomer catabolism in the S23321 genome. These features suggest that S23321 is able to adapt to a wide range of environments, probably including low-nutrient conditions, with multiple survival strategies in soil and rhizosphere.
ESTHER : Okubo_2012_Microbes.Environ_27_306
PubMedSearch : Okubo_2012_Microbes.Environ_27_306
PubMedID: 22452844
Gene_locus related to this paper: 9brad-i0g2u8 , 9brad-i0gf89 , braja-pcaD , 9brad-i0fzh8 , 9brad-i0gfv2 , 9brad-i0g2y4

Title : No associations found between the genes situated at 6p22.1, HIST1H2BJ, PRSS16, and PGBD1 in Japanese patients diagnosed with schizophrenia - Kitazawa_2012_Am.J.Med.Genet.B.Neuropsychiatr.Genet_159B_456
Author(s) : Kitazawa M , Ohnuma T , Takebayashi Y , Shibata N , Baba H , Ohi K , Yasuda Y , Nakamura Y , Aleksic B , Yoshimi A , Okochi T , Ikeda M , Naitoh H , Hashimoto R , Iwata N , Ozaki N , Takeda M , Arai H
Ref : American Journal of Medicine Genet B Neuropsychiatr Genet , 159B :456 , 2012
Abstract : Recent GWAS demonstrated an association between candidate genes located at region 6p22.1 and schizophrenia. This region has been reported to house certain candidate SNPs, which may be associated with schizophrenia at HIST1H2BJ, PRSS16, and PGBD1. These genes may presumably be associated with pathophysiology in schizophrenia, namely epigenetics and psychoneuroimmunology. A three-step study was undertaken to focus on these genes with the following aims: (1) whether these genes may be associated in Japanese patients with schizophrenia by performing a 1st stage case-control study (514 cases and 706 controls) using Japanese tagging SNPs; (2) if the genetic regions of interest for the disease from the 1st stage of analyses were found, re-sequencing was performed to search for new mutations; (3) finally, a replication study was undertaken to confirm positive findings from the 1st stage were reconfirmed using a larger number of subjects (2,583 cases and 2,903 controls) during a 2nd stage multicenter replication study in Japan. Genotyping was performed using TaqMan PCR method for the selected nine tagging SNPs. Although three SNPs situated at the 3' side of PGBD1; rs3800324, rs3800327, and rs2142730, and two-window haplotypes between rs3800327 and rs2142730 showed positive associations with schizophrenia, these associations did not have enough power to sustain significance during the 2nd stage replication study. In addition, re-sequencing for exons 5 and 6 situated at this region did not express any new mutations for schizophrenia. Taken together these results indicate that the genes HIST1H2BJ, PRSS16, and PGBD1 were not associated with Japanese patients with schizophrenia.
ESTHER : Kitazawa_2012_Am.J.Med.Genet.B.Neuropsychiatr.Genet_159B_456
PubMedSearch : Kitazawa_2012_Am.J.Med.Genet.B.Neuropsychiatr.Genet_159B_456
PubMedID: 22488895
Gene_locus related to this paper: human-PRSS16

Title : Understanding the functional significance of ghrelin processing and degradation - Satou_2011_Peptides_32_2183
Author(s) : Satou M , Nakamura Y , Ando H , Sugimoto H
Ref : Peptides , 32 :2183 , 2011
Abstract : Post-translational modification, cleavage and processing of circulating hormones are common themes in the control of hormone activities. Full-length ghrelin is a 28 amino acid protein that exists in several modified and processed forms, including addition of an acyl moiety at the third serine of the N-terminus. When modified with octanoic acid, the first five N-terminal residues of ghrelin can modulate a signaling pathway via the ghrelin receptor GHSR1a. Although modification via a lipid moiety is essential for binding and activation of GHSR1a by ghrelin, many reports suggest that a desacyl form of ghrelin exists and has synergistic, opposing and distinct properties as compared to the acyl form. Therefore, it is important to clarify the physiological relevance of ghrelin derivatives. Based on lines of evidence from various studies, we propose that a larger proportion of secreted ghrelin is present in the deacylated form and furthermore, that circulating acyl and desacyl forms of ghrelin may be hydrolyzed to form short peptide fragments. Here, we summarize the results of studies aimed at understanding ghrelin processing and its implications for physiological function, as well as our recent findings regarding enzymes in the blood capable of generating processed forms of ghrelin.
ESTHER : Satou_2011_Peptides_32_2183
PubMedSearch : Satou_2011_Peptides_32_2183
PubMedID: 21763742

Title : The dynamic genome of Hydra - Chapman_2010_Nature_464_592
Author(s) : Chapman JA , Kirkness EF , Simakov O , Hampson SE , Mitros T , Weinmaier T , Rattei T , Balasubramanian PG , Borman J , Busam D , Disbennett K , Pfannkoch C , Sumin N , Sutton GG , Viswanathan LD , Walenz B , Goodstein DM , Hellsten U , Kawashima T , Prochnik SE , Putnam NH , Shu S , Blumberg B , Dana CE , Gee L , Kibler DF , Law L , Lindgens D , Martinez DE , Peng J , Wigge PA , Bertulat B , Guder C , Nakamura Y , Ozbek S , Watanabe H , Khalturin K , Hemmrich G , Franke A , Augustin R , Fraune S , Hayakawa E , Hayakawa S , Hirose M , Hwang JS , Ikeo K , Nishimiya-Fujisawa C , Ogura A , Takahashi T , Steinmetz PR , Zhang X , Aufschnaiter R , Eder MK , Gorny AK , Salvenmoser W , Heimberg AM , Wheeler BM , Peterson KJ , Bottger A , Tischler P , Wolf A , Gojobori T , Remington KA , Strausberg RL , Venter JC , Technau U , Hobmayer B , Bosch TC , Holstein TW , Fujisawa T , Bode HR , David CN , Rokhsar DS , Steele RE
Ref : Nature , 464 :592 , 2010
Abstract : The freshwater cnidarian Hydra was first described in 1702 and has been the object of study for 300 years. Experimental studies of Hydra between 1736 and 1744 culminated in the discovery of asexual reproduction of an animal by budding, the first description of regeneration in an animal, and successful transplantation of tissue between animals. Today, Hydra is an important model for studies of axial patterning, stem cell biology and regeneration. Here we report the genome of Hydra magnipapillata and compare it to the genomes of the anthozoan Nematostella vectensis and other animals. The Hydra genome has been shaped by bursts of transposable element expansion, horizontal gene transfer, trans-splicing, and simplification of gene structure and gene content that parallel simplification of the Hydra life cycle. We also report the sequence of the genome of a novel bacterium stably associated with H. magnipapillata. Comparisons of the Hydra genome to the genomes of other animals shed light on the evolution of epithelia, contractile tissues, developmentally regulated transcription factors, the Spemann-Mangold organizer, pluripotency genes and the neuromuscular junction.
ESTHER : Chapman_2010_Nature_464_592
PubMedSearch : Chapman_2010_Nature_464_592
PubMedID: 20228792
Gene_locus related to this paper: 9burk-c9y6c0 , 9burk-c9y8q9 , 9burk-c9y9d4 , 9burk-c9ya28 , 9burk-c9yb37 , 9burk-c9ycr9 , 9burk-c9ydq0 , 9burk-c9ydr2 , 9burk-c9yew1 , 9burk-c9yf78 , 9burk-c9ygh2 , 9burk-c9y7j2

Title : Complete genomic structure of the cultivated rice endophyte Azospirillum sp. B510 - Kaneko_2010_DNA.Res_17_37
Author(s) : Kaneko T , Minamisawa K , Isawa T , Nakatsukasa H , Mitsui H , Kawaharada Y , Nakamura Y , Watanabe A , Kawashima K , Ono A , Shimizu Y , Takahashi C , Minami C , Fujishiro T , Kohara M , Katoh M , Nakazaki N , Nakayama S , Yamada M , Tabata S , Sato S
Ref : DNA Research , 17 :37 , 2010
Abstract : We determined the nucleotide sequence of the entire genome of a diazotrophic endophyte, Azospirillum sp. B510. Strain B510 is an endophytic bacterium isolated from stems of rice plants (Oryza sativa cv. Nipponbare). The genome of B510 consisted of a single chromosome (3,311,395 bp) and six plasmids, designated as pAB510a (1,455,109 bp), pAB510b (723,779 bp), pAB510c (681,723 bp), pAB510d (628,837 bp), pAB510e (537,299 bp), and pAB510f (261,596 bp). The chromosome bears 2893 potential protein-encoding genes, two sets of rRNA gene clusters (rrns), and 45 tRNA genes representing 37 tRNA species. The genomes of the six plasmids contained a total of 3416 protein-encoding genes, seven sets of rrns, and 34 tRNAs representing 19 tRNA species. Eight genes for plasmid-specific tRNA species are located on either pAB510a or pAB510d. Two out of eight genomic islands are inserted in the plasmids, pAB510b and pAB510e, and one of the islands is inserted into trnfM-CAU in the rrn located on pAB510e. Genes other than the nif gene cluster that are involved in N(2) fixation and are homologues of Bradyrhizobium japonicum USDA110 include fixABCX, fixNOQP, fixHIS, fixG, and fixLJK. Three putative plant hormone-related genes encoding tryptophan 2-monooxytenase (iaaM) and indole-3-acetaldehyde hydrolase (iaaH), which are involved in IAA biosynthesis, and ACC deaminase (acdS), which reduces ethylene levels, were identified. Multiple gene-clusters for tripartite ATP-independent periplasmic-transport systems and a diverse set of malic enzymes were identified, suggesting that B510 utilizes C(4)-dicarboxylate during its symbiotic relationship with the host plant.
ESTHER : Kaneko_2010_DNA.Res_17_37
PubMedSearch : Kaneko_2010_DNA.Res_17_37
PubMedID: 20047946
Gene_locus related to this paper: azos1-d3nrk5 , azos1-d3ns85 , azos1-d3nsh5 , azos1-d3nt15 , azos1-d3ntk4 , azos1-d3nv04 , azos1-d3nx23 , azos1-d3ny33 , azos1-d3p0k9 , azos1-d3p0n8 , azos1-d3p1p1 , azos1-d3p2z0 , azos1-d3p4h2 , azos1-d3p4k9 , azos1-d3p5e7 , azos1-d3p281 , azos1-d3p626

Title : Polymorphisms in NRXN3, TFAP2B, MSRA, LYPLAL1, FTO and MC4R and their effect on visceral fat area in the Japanese population - Hotta_2010_J.Hum.Genet_55_738
Author(s) : Hotta K , Nakamura M , Nakamura T , Matsuo T , Nakata Y , Kamohara S , Miyatake N , Kotani K , Komatsu R , Itoh N , Mineo I , Wada J , Yoneda M , Nakajima A , Funahashi T , Miyazaki S , Tokunaga K , Kawamoto M , Masuzaki H , Ueno T , Hamaguchi K , Tanaka K , Yamada K , Hanafusa T , Oikawa S , Yoshimatsu H , Nakao K , Sakata T , Matsuzawa Y , Nakamura Y , Kamatani N
Ref : J Hum Genet , 55 :738 , 2010
Abstract : The predominant risk factor of metabolic syndrome is intra-abdominal fat accumulation, which is determined by waist circumference and waist-hip ratio measurements and visceral fat area (VFA) that is measured by computed tomography (CT). There is evidence that waist circumference and waist-hip ratio in the Caucasian population are associated with variations in several genes, including neurexin 3 (NRXN3), transcription factor AP-2beta (TFAP2B), methionine sulfoxide reductase A (MSRA), lysophospholipase-like-1 (LYPLAL1), fat mass and obesity associated (FTO) and melanocortin 4 receptor (MC4R) genes. To investigate the relationship between VFA and subcutaneous fat area (SFA) and these genes in the recruited Japanese population, we genotyped 8 single-nucleotide polymorphisms (SNPs) in these 6 genes from 1228 subjects. Multiple regression analysis revealed that gender, age, and rs1558902 and rs1421085 genotypes (additive model) in FTO were significantly associated with body mass index (BMI; P=0.0039 and 0.0039, respectively), SFA (P=0.0027 and 0.0023, respectively) and VFA (P=0.045 and 0.040, respectively). However, SNPs in other genes, namely, NRXN3, TFAP2B, MSRA, LYPLAL1 and MC4R were not significantly associated with BMI, SFA or VFA. Our data suggest that some SNPs, which were identified in genome-wide studies in the Caucasians, also confer susceptibility to fat distribution in the Japanese subjects.
ESTHER : Hotta_2010_J.Hum.Genet_55_738
PubMedSearch : Hotta_2010_J.Hum.Genet_55_738
PubMedID: 20703240

Title : [How long should drug therapy be continued for Alzheimer disease?] -
Author(s) : Nakamura Y
Ref : Seishin Shinkeigaku Zasshi , 111 :43 , 2009
PubMedID: 19378499

Title : [Diagnosis of and therapy for Alzheimer-type dementia] -
Author(s) : Nakamura Y
Ref : Seishin Shinkeigaku Zasshi , 110 :577 , 2008
PubMedID: 18928020

Title : Decreased valproate level caused by VPA-glucuronidase inhibition by carbapenem antibiotics - Nakamura_2008_Drug.Metab.Lett_2_280
Author(s) : Nakamura Y , Nakahira K , Mizutani T
Ref : Drug Metab Lett , 2 :280 , 2008
Abstract : The serum concentration of valproic acid (VPA) in epilepsy patients decreased in the administration of carbapenem antibiotics (CP), such as meropenem, panipenem, biapenem or imipenem, to a sub-therapeutic level. The liver is the key organ for the decrease of VPA concentration by CP, because it has been reported that no decrease of the VPA level by CP was found in hepatectomized rats. This effect was also shown with monkey and rat liver slices. In this report, we show the results of in vitro inhibition of VPA-glucuronidase in human liver microsomes and cytosol by CP. We found the highest metabolic activity of VPA-glucuronide in human liver cytosol. The level in liver cytosol was 149 pmol/min/mg protein. The level in human liver microsomes (HLM) was one-fifth of that in cytosol and the level in serum was negligible. We found that this hydrolysis depends on VPA-glucuronidase in cytosol, because digestion was inhibited by D-saccharic acid 1,4-lactonemonohydrate of a specific inhibitor of beta-glucuronidase, but not by phenylmethylsulfonylfluoride of an esterase inhibitor. We also found the inhibition of VPA-glucuronidase in cytosol by CP, and the maximum inhibition was found with panipenem (IC(50) = 3 microM). We also found inhibition of VPA-glucuronidase in HLM by meropenem. These results showed that the inhibition in liver slices depended on the inhibition of VPA-glucuronidase by CP. We considered that the inhibition of VPA-glucuronidase by CP in cytosol is a key factor to decrease the plasma VPA level.
ESTHER : Nakamura_2008_Drug.Metab.Lett_2_280
PubMedSearch : Nakamura_2008_Drug.Metab.Lett_2_280
PubMedID: 19356106

Title : Complete genomic structure of the bloom-forming toxic cyanobacterium Microcystis aeruginosa NIES-843 - Kaneko_2007_DNA.Res_14_247
Author(s) : Kaneko T , Nakajima N , Okamoto S , Suzuki I , Tanabe Y , Tamaoki M , Nakamura Y , Kasai F , Watanabe A , Kawashima K , Kishida Y , Ono A , Shimizu Y , Takahashi C , Minami C , Fujishiro T , Kohara M , Katoh M , Nakazaki N , Nakayama S , Yamada M , Tabata S , Watanabe MM
Ref : DNA Research , 14 :247 , 2007
Abstract : The nucleotide sequence of the complete genome of a cyanobacterium, Microcystis aeruginosa NIES-843, was determined. The genome of M. aeruginosa is a single, circular chromosome of 5,842,795 base pairs (bp) in length, with an average GC content of 42.3%. The chromosome comprises 6312 putative protein-encoding genes, two sets of rRNA genes, 42 tRNA genes representing 41 tRNA species, and genes for tmRNA, the B subunit of RNase P, SRP RNA, and 6Sa RNA. Forty-five percent of the putative protein-encoding sequences showed sequence similarity to genes of known function, 32% were similar to hypothetical genes, and the remaining 23% had no apparent similarity to reported genes. A total of 688 kb of the genome, equivalent to 11.8% of the entire genome, were composed of both insertion sequences and miniature inverted-repeat transposable elements. This is indicative of a plasticity of the M. aeruginosa genome, through a mechanism that involves homologous recombination mediated by repetitive DNA elements. In addition to known gene clusters related to the synthesis of microcystin and cyanopeptolin, novel gene clusters that may be involved in the synthesis and modification of toxic small polypeptides were identified. Compared with other cyanobacteria, a relatively small number of genes for two component systems and a large number of genes for restriction-modification systems were notable characteristics of the M. aeruginosa genome.
ESTHER : Kaneko_2007_DNA.Res_14_247
PubMedSearch : Kaneko_2007_DNA.Res_14_247
PubMedID: 18192279
Gene_locus related to this paper: micae-a8yde8 , micae-a8yen2 , micae-a8yma5 , micae-MCYC , mican-b0jqg0 , mican-b0jqq0 , mican-b0jsa2 , mican-b0jxh1 , mican-b0jux6 , mican-b0jyg0

Title : The in vitro metabolism of a pyrethroid insecticide, permethrin, and its hydrolysis products in rats - Nakamura_2007_Toxicology_235_176
Author(s) : Nakamura Y , Sugihara K , Sone T , Isobe M , Ohta S , Kitamura S
Ref : Toxicology , 235 :176 , 2007
Abstract : The in vitro metabolism of permethrin and its hydrolysis products in rats was investigated. Cis- and trans-permethrin were mainly hydrolyzed by liver microsomes, and also by small-intestinal microsomes of rats. trans-Permethrin was much more effectively hydrolyzed than the cis-isomer. When NADPH was added to the incubation mixture of the liver microsomes, three metabolites, 3-phenoxybenzyl alcohol (PBAlc), 3-phenoxybenzaldehyde (PBAld) and 3-phenoxybenzoic acid (PBAcid), were formed. However, only PBAlc was formed by rat liver microsomes in the absence of cofactors. The microsomal activities of rat liver and small intestine were inhibited by bis-p-nitrophenyl phosphate, an inhibitor of carboxylesterase (CES). ES-3 and ES-10, isoforms of the CES 1 family, exhibited significant hydrolytic activities toward trans-permethrin. When PBAlc was incubated with rat liver microsomes in the presence of NADPH, PBAld and PBAcid were formed. The NADPH-linked oxidizing activity was inhibited by SKF 525-A. Rat recombinant cytochrome P450, CYP 2C6 and 3A1, exhibited significant oxidase activities with NADPH. When PBAld was incubated with the microsomes in the presence of NADPH, PBAcid was formed. CYP 1A2, 2B1, 2C6, 2D1 and 3A1 exhibited significant oxidase activities in this reaction. Thus, permethrin was hydrolyzed by CES, and PBAlc formed was oxidized to PBAld and PBAcid by the cytochrome P450 system in rats.
ESTHER : Nakamura_2007_Toxicology_235_176
PubMedSearch : Nakamura_2007_Toxicology_235_176
PubMedID: 17451859

Title : Lipoprotein lipase PvuII polymorphism is associated with variations in serum lipid levels in non-diabetic pregnant women - Sepetiba_2007_Braz.J.Med.Biol.Res_40_919
Author(s) : Sepetiba RJ , Andrade J , Hirata RD , Hirata MH , Sepetiba CR , Nakamura Y , Matsumoto LO , Cavalli SA , Bertolami MC
Ref : Brazilian Journal of Medical & Biological Research , 40 :919 , 2007
Abstract : The aim of the present study was to determine if there is an association between the single nucleotide polymorphisms (SNPs) of the lipoprotein lipase (LPL) and apolipoprotein E (apo E) genes and the serum lipid profile in pregnancy and puerperium. Non-diabetic women of European descent in the third semester of pregnancy (N = 120) were selected. Those with diseases or other condition that could modify their lipid profile were excluded from the study (N = 32). Serum lipids were measured by routine laboratory procedures and genomic DNA was extracted by a salting out method. LPL (PvuII and HindIII) and apo E (HhaI) SNPs were detected by the polymerase chain reaction and restriction fragment length polymorphism. Categorical and continuous variables were compared by the chi-square test and Student t-test or ANOVA, respectively. Women carrying the LPL P1P1 genotype had higher serum LDL cholesterol (N = 21; 155 +/- 45 mg/dL) than women carrying the P1P2/P2P2 genotypes (N = 67; 133 +/- 45 mg/dL; P = 0.032). During the puerperium period, serum levels of triglycerides and VLDL cholesterol were significantly reduced in women carrying the P1P1 (73%, P = 0.006) and P1P2 (51%, P = 0.002) genotypes but not in women carrying the P2P2 genotype (23%, P > 0.05). On the other hand, serum concentrations of lipids did not differ between the LPL HindIII and apo E genotypes during pregnancy and after delivery. We conclude that LPL PvuII SNP is associated with variations in serum lipids during pregnancy and the puerperal period in non-diabetic women.
ESTHER : Sepetiba_2007_Braz.J.Med.Biol.Res_40_919
PubMedSearch : Sepetiba_2007_Braz.J.Med.Biol.Res_40_919
PubMedID: 17653444

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

Title : 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 : Comparative complete genome sequence analysis of the amino acid replacements responsible for the thermostability of Corynebacterium efficiens - Nishio_2003_Genome.Res_13_1572
Author(s) : Nishio Y , Nakamura Y , Kawarabayasi Y , Usuda Y , Kimura E , Sugimoto S , Matsui K , Yamagishi A , Kikuchi H , Ikeo K , Gojobori T
Ref : Genome Res , 13 :1572 , 2003
Abstract : Corynebacterium efficiens is the closest relative of Corynebacterium glutamicum, a species widely used for the industrial production of amino acids. C. efficiens but not C. glutamicum can grow above 40 degrees C. We sequenced the complete C. efficiens genome to investigate the basis of its thermostability by comparing its genome with that of C. glutamicum. The difference in GC content between the species was reflected in codon usage and nucleotide substitutions. Our comparative genomic study clearly showed that there was tremendous bias in amino acid substitutions in all orthologous ORFs. Analysis of the direction of the amino acid substitutions suggested that three substitutions are important for the stability of the C. efficiens proteins: from lysine to arginine, serine to alanine, and serine to threonine. Our results strongly suggest that the accumulation of these three types of amino acid substitutions correlates with the acquisition of thermostability and is responsible for the greater GC content of C. efficiens.
ESTHER : Nishio_2003_Genome.Res_13_1572
PubMedSearch : Nishio_2003_Genome.Res_13_1572
PubMedID: 12840036
Gene_locus related to this paper: coref-CE0007 , coref-CE0093 , coref-CE0094 , coref-CE0096 , coref-CE0103 , coref-CE0104 , coref-CE0150 , coref-CE0293 , coref-CE0354 , coref-CE0356 , coref-CE0596 , coref-CE0984 , coref-CE1275 , coref-CE1488 , coref-CE1571 , coref-CE1601 , coref-CE1609 , coref-CE1895 , coref-CE2149 , coref-CE2296 , coref-CE2371 , coref-CE2453 , coref-CE2486 , coref-CE2499 , coref-CE2705 , coref-CE2710 , coref-CE2923 , coref-CSPA , coref-METX , coref-q8flv5 , coref-q8fm83 , coref-q8fmd4 , coref-q8fm02

Title : Complete genome structure of Gloeobacter violaceus PCC 7421, a cyanobacterium that lacks thylakoids - Nakamura_2003_DNA.Res_10_137
Author(s) : Nakamura Y , Kaneko T , Sato S , Mimuro M , Miyashita H , Tsuchiya T , Sasamoto S , Watanabe A , Kawashima K , Kishida Y , Kiyokawa C , Kohara M , Matsumoto M , Matsuno A , Nakazaki N , Shimpo S , Takeuchi C , Yamada M , Tabata S
Ref : DNA Research , 10 :137 , 2003
Abstract : The nucleotide sequence of the entire genome of a cyanobacterium Gloeobacter violaceus PCC 7421 was determined. The genome of G. violaceus was a single circular chromosome 4,659,019 bp long with an average GC content of 62%. No plasmid was detected. The chromosome comprises 4430 potential protein-encoding genes, one set of rRNA genes, 45 tRNA genes representing 44 tRNA species and genes for tmRNA, B subunit of RNase P, SRP RNA and 6Sa RNA. Forty-one percent of the potential protein-encoding genes showed sequence similarity to genes of known function, 37% to hypothetical genes, and the remaining 22% had no apparent similarity to reported genes. Comparison of the assigned gene components with those of other cyanobacteria has unveiled distinctive features of the G. violaceus genome. Genes for PsaI, PsaJ, PsaK, and PsaX for Photosystem I and PsbY, PsbZ and Psb27 for Photosystem II were missing, and those for PsaF, PsbO, PsbU, and PsbV were poorly conserved. cpcG for a rod core linker peptide for phycobilisomes and nblA related to the degradation of phycobilisomes were also missing. Potential signal peptides of the presumptive products of petJ and petE for soluble electron transfer catalysts were less conserved than the remaining portions. These observations may be related to the fact that photosynthesis in G. violaceus takes place not in thylakoid membranes but in the cytoplasmic membrane. A large number of genes for sigma factors and transcription factors in the LuxR, LysR, PadR, TetR, and MarR families could be identified, while those for major elements for circadian clock, kaiABC were not found. These differences may reflect the phylogenetic distance between G. violaceus and other cyanobacteria.
ESTHER : Nakamura_2003_DNA.Res_10_137
PubMedSearch : Nakamura_2003_DNA.Res_10_137
PubMedID: 14621292
Gene_locus related to this paper: glovi-GLL0053 , glovi-GLL0778 , glovi-GLL1217 , glovi-GLL1281 , glovi-GLL1310 , glovi-GLL1435 , glovi-GLL2002 , glovi-gll2009 , glovi-GLL2335 , glovi-GLL2500 , glovi-GLL3208 , glovi-GLL3677 , glovi-GLL4259 , glovi-GLR0796 , glovi-GLR1368 , glovi-GLR1422 , glovi-GLR2241 , glovi-GLR2809 , glovi-GLR3058 , glovi-GLR3329 , glovi-GLR3546 , glovi-GLR3833 , glovi-q7ncx6 , glovi-q7nd10 , glovi-q7ndi8 , glovi-q7ndy7 , glovi-q7nek8 , glovi-q7net1 , glovi-q7new7 , glovi-q7ney7 , glovi-q7nfx3 , glovi-q7nga2 , glovi-q7ngw1 , glovi-q7nj78 , glovi-q7nj91 , glovi-q7nj98 , glovi-q7njx8 , glovi-q7njz2 , glovi-q7nkk7 , glovi-q7nly3 , glovi-q7nm82 , glovi-q7nmt4 , glovi-q7nmz0 , glovi-q7nn33 , glovi-q7nn46 , glovi-q7nn64 , glovi-q7nny4 , glovi-q7np81 , glovi-q7npc6

Title : Complete genome structure of Gloeobacter violaceus PCC 7421, a cyanobacterium that lacks thylakoids (supplement) -
Author(s) : Nakamura Y , Kaneko T , Sato S , Mimuro M , Miyashita H , Tsuchiya T , Sasamoto S , Watanabe A , Kawashima K , Kishida Y , Kiyokawa C , Kohara M , Matsumoto M , Matsuno A , Nakazaki N , Shimpo S , Takeuchi C , Yamada M , Tabata S
Ref : DNA Research , 10 :181 , 2003
PubMedID: 14621296
Gene_locus related to this paper: glovi-gll2009

Title : Catalog of 680 variations among eight cytochrome p450 ( CYP) genes, nine esterase genes, and two other genes in the Japanese population - Saito_2003_J.Hum.Genet_48_249
Author(s) : Saito S , Iida A , Sekine A , Kawauchi S , Higuchi S , Ogawa C , Nakamura Y
Ref : J Hum Genet , 48 :249 , 2003
Abstract : We screened DNAs from 48 Japanese individuals for single-nucleotide polymorphisms (SNPs) in eight cytochrome p450 ( CYP) genes, nine esterase genes, and two other genes by directly sequencing the relevant genomic regions in their entirety except for repetitive elements. This approach identified 607 SNPs and 73 insertion/deletion polymorphisms among the 19 genes examined. Of the 607 SNPs, 284 were identified in CYP genes, 302 in esterase genes, and 21 in the other two genes ( GGT1, and TGM1); overall, 37 SNPs were located in 5' flanking regions, 496 in introns, 55 in exons, and 19 in 3' flanking regions. These variants should contribute to studies designed to investigate possible correlations between genotypes and phenotypes of disease susceptibility or responsiveness to drug therapy.
ESTHER : Saito_2003_J.Hum.Genet_48_249
PubMedSearch : Saito_2003_J.Hum.Genet_48_249
PubMedID: 12721789
Gene_locus related to this paper: human-CES2 , human-ESD

Title : Structural analysis of four large plasmids harboring in a unicellular cyanobacterium, Synechocystis sp. PCC 6803 - Kaneko_2003_DNA.Res_10_221
Author(s) : Kaneko T , Nakamura Y , Sasamoto S , Watanabe A , Kohara M , Matsumoto M , Shimpo S , Yamada M , Tabata S
Ref : DNA Research , 10 :221 , 2003
Abstract : The genome of the unicellular cyanobacterium Synechocystis sp. PCC 6803 consists of a single chromosome and several plasmids of different sizes, and the nucleotide sequences of the chromosome and three small plasmids (5.2 kb, 2.4 kb, and 2.3 kb) have already been sequenced. We newly determined the nucleotide sequences of four large plasmids, which have been identified in our laboratory (pSYSM:120 kb, pSYSX:106 kb, pSYSA:103 kb, and pSYSG:44 kb). Computer-aided analysis was performed to explore the genetic information carried by these plasmids. A total of 397 potential protein-encoding genes were predicted, but little information was obtained about the functional relationship of plasmids to host cell, as a large portion of the predicted genes (77%) were of unknown function. The occurrence of the potential genes on plasmids was divergent, and parA was the only gene common to all four large plasmids. The distribution data of a Cyanobacterium-specific sequence (HIP1: 5'-GCGATCGC-3') suggested that respective plasmids could have originated from different cyanobacterial strains.
ESTHER : Kaneko_2003_DNA.Res_10_221
PubMedSearch : Kaneko_2003_DNA.Res_10_221
PubMedID: 14686584
Gene_locus related to this paper: syny3-q6zeq0 , 9sync-m1mb45

Title : Complete genome structure of the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 - Nakamura_2002_DNA.Res_9_123
Author(s) : Nakamura Y , Kaneko T , Sato S , Ikeuchi M , Katoh H , Sasamoto S , Watanabe A , Iriguchi M , Kawashima K , Kimura T , Kishida Y , Kiyokawa C , Kohara M , Matsumoto M , Matsuno A , Nakazaki N , Shimpo S , Sugimoto M , Takeuchi C , Yamada M , Tabata S
Ref : DNA Research , 9 :123 , 2002
Abstract : The entire genome of a thermophilic unicellular cyanobacterium, Thermosynechococcus elongatus BP-1, was sequenced. The genome consisted of a circular chromosome 2,593,857 bp long, and no plasmid was detected. A total of 2475 potential protein-encoding genes, one set of rRNA genes, 42 tRNA genes representing 42 tRNA species and 4 genes for small structural RNAs were assigned to the chromosome by similarity search and computer prediction. The translated products of 56% of the potential protein-encoding genes showed sequence similarity to experimentally identified and predicted proteins of known function, and the products of 34% of these genes showed sequence similarity to the translated products of hypothetical genes. The remaining 10% lacked significant similarity to genes for predicted proteins in the public DNA databases. Sixty-three percent of the T. elongatus genes showed significant sequence similarity to those of both Synechocystis sp. PCC 6803 and Anabaena sp. PCC 7120, while 22% of the genes were unique to this species, indicating a high degree of divergence of the gene information among cyanobacterial strains. The lack of genes for typical fatty acid desaturases and the presence of more genes for heat-shock proteins in comparison with other mesophilic cyanobacteria may be genomic features of thermophilic strains. A remarkable feature of the genome is the presence of 28 copies of group II introns, 8 of which contained a presumptive gene for maturase/reverse transcriptase. A trace of genome rearrangement mediated by the group II introns was also observed.
ESTHER : Nakamura_2002_DNA.Res_9_123
PubMedSearch : Nakamura_2002_DNA.Res_9_123
PubMedID: 12240834
Gene_locus related to this paper: theeb-q8dg48 , theeb-TLL0292 , theeb-TLL0340 , theeb-TLL0918 , theeb-TLL0989 , theeb-TLL1717 , theeb-TLL2163 , theeb-TLR0492 , theeb-TLR1045 , theeb-TLR1157 , theeb-TLR1274 , theeb-TLR1393 , theeb-TLR1423 , theeb-TLR1685 , theeb-TLR1725 , theeb-TLR1892 , theeb-TLR1982 , theeb-TLR2038 , theeb-TLR2066

Title : Characterization of a VNTR polymorphism in the coding region of the CEL gene - Higuchi_2002_J.Hum.Genet_47_213
Author(s) : Higuchi S , Nakamura Y , Saito S
Ref : J Hum Genet , 47 :213 , 2002
Abstract : Human carboxyl ester lipase (CEL) secreted by the pancreas into the duodenum is a glycoprotein playing an essential role in the intestinal processing of cholesterol and lipid-soluble vitamins. The gene encoding CEL was known to contain a tandemly repeated sequence of the 11-amino-acid motif in the C-terminal region. We characterized its polymorphic features and found that there are five different alleles in Japanese populations and six in Caucasians. The allele containing 16 repeats is the most common in both populations. Although the distribution of the alleles seemed to be different in the two populations, the difference was not statistically significant. This polymorphism may influence the function of this enzyme and be a useful genetic marker to study diseases associated with cholesterol absorption.
ESTHER : Higuchi_2002_J.Hum.Genet_47_213
PubMedSearch : Higuchi_2002_J.Hum.Genet_47_213
PubMedID: 12166660

Title : Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110 - Kaneko_2002_DNA.Res_9_189
Author(s) : Kaneko T , Nakamura Y , Sato S , Minamisawa K , Uchiumi T , Sasamoto S , Watanabe A , Idesawa K , Iriguchi M , Kawashima K , Kohara M , Matsumoto M , Shimpo S , Tsuruoka H , Wada T , Yamada M , Tabata S
Ref : DNA Research , 9 :189 , 2002
Abstract : The complete nucleotide sequence of the genome of a symbiotic bacterium Bradyrhizobium japonicum USDA110 was determined. The genome of B. japonicum was a single circular chromosome 9,105,828 bp in length with an average GC content of 64.1%. No plasmid was detected. The chromosome comprises 8317 potential protein-coding genes, one set of rRNA genes and 50 tRNA genes. Fifty-two percent of the potential protein genes showed sequence similarity to genes of known function and 30% to hypothetical genes. The remaining 18% had no apparent similarity to reported genes. Thirty-four percent of the B. japonicum genes showed significant sequence similarity to those of both Mesorhizobium loti and Sinorhizobium meliloti, while 23% were unique to this species. A presumptive symbiosis island 681 kb in length, which includes a 410-kb symbiotic region previously reported by Gottfert et al., was identified. Six hundred fifty-five putative protein-coding genes were assigned in this region, and the functions of 301 genes, including those related to symbiotic nitrogen fixation and DNA transmission, were deduced. A total of 167 genes for transposases/104 copies of insertion sequences were identified in the genome. It was remarkable that 100 out of 167 transposase genes are located in the presumptive symbiotic island. DNA segments of 4 to 97 kb inserted into tRNA genes were found at 14 locations in the genome, which generates partial duplication of the target tRNA genes. These observations suggest plasticity of the B. japonicum genome, which is probably due to complex genome rearrangements such as horizontal transfer and insertion of various DNA elements, and to homologous recombination.
ESTHER : Kaneko_2002_DNA.Res_9_189
PubMedSearch : Kaneko_2002_DNA.Res_9_189
PubMedID: 12597275
Gene_locus related to this paper: braja-BLL0118 , braja-BLL0272 , braja-BLL0546 , braja-BLL0558 , braja-BLL0837 , braja-BLL0839 , braja-BLL1016 , braja-BLL1128 , braja-BLL1234 , braja-BLL1350 , braja-BLL1401 , braja-BLL2323 , braja-BLL2387 , braja-BLL2443 , braja-BLL2527 , braja-BLL2884 , braja-BLL2902 , braja-BLL3246 , braja-BLL3359 , braja-BLL3416 , braja-BLL3418 , braja-BLL3470 , braja-BLL3759 , braja-BLL3777 , braja-BLL4001 , braja-BLL4189 , braja-BLL4284 , braja-BLL4335 , braja-BLL4360 , braja-BLL4548 , braja-BLL4985 , braja-BLL4989 , braja-BLL4997 , braja-BLL5160 , braja-BLL5514 , braja-BLL5588 , braja-BLL5740 , braja-bll6073 , braja-BLL6264 , braja-BLL6275 , braja-BLL6428 , braja-bll6463 , braja-BLL6574 , braja-BLL6577 , braja-BLL6614 , braja-bll6820 , braja-BLL6841 , braja-BLL6890 , braja-BLL6974 , braja-BLL7123 , braja-BLL7368 , braja-BLL7370 , braja-BLL7497 , braja-BLL7506 , braja-BLL7509 , braja-BLL7545 , braja-BLL7692 , braja-BLL7862 , braja-BLL8011 , braja-BLL8277 , braja-BLR0230 , braja-BLR0418 , braja-BLR0711 , braja-BLR0899 , braja-BLR0908 , braja-BLR1078 , braja-BLR1197 , braja-BLR1251 , braja-BLR2261 , braja-BLR2321 , braja-BLR2487 , braja-BLR2879 , braja-BLR2885 , braja-BLR2889 , braja-BLR2982 , braja-BLR3322 , braja-BLR3456 , braja-BLR3519 , braja-blr3732 , braja-BLR3878 , braja-BLR4157 , braja-BLR4181 , braja-BLR5346 , braja-BLR5359 , braja-BLR6083 , braja-BLR6127 , braja-BLR6186 , braja-BLR6271 , braja-BLR6465 , braja-BLR6576 , braja-BLR6677 , braja-BLR6703 , braja-BLR6960 , braja-BLR6965 , braja-BLR7068 , braja-BLR7144 , braja-BLR7443 , braja-BLR7556 , braja-BLR7622 , braja-BLR7741 , braja-BLR7809 , braja-BLR7810 , braja-BLR7894 , braja-BLR8188 , braja-dhaa , braja-EPHA , braja-EPHB , braja-ID587 , braja-ID930 , braja-METX , braja-pcaD , braja-PIP , braja-PLDB , braja-PTRB , braja-q89c18 , braja-q89c36 , braja-q89mj3 , braja-q89ql9 , braja-q89y23

Title : Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110 (supplement) -
Author(s) : Kaneko T , Nakamura Y , Sato S , Minamisawa K , Uchiumi T , Sasamoto S , Watanabe A , Idesawa K , Iriguchi M , Kawashima K , Kohara M , Matsumoto M , Shimpo S , Tsuruoka H , Wada T , Yamada M , Tabata S
Ref : DNA Research , 9 :225 , 2002
PubMedID: 12597279
Gene_locus related to this paper: braja-bll6463 , braja-bll6820 , braja-EPHB , braja-ID930 , braja-pcaD

Title : Seventy genetic variations in human microsomal and soluble epoxide hydrolase genes (EPHX1 and EPHX2) in the Japanese population - Saito_2001_J.Hum.Genet_46_325
Author(s) : Saito S , Iida A , Sekine A , Eguchi C , Miura Y , Nakamura Y
Ref : J Hum Genet , 46 :325 , 2001
Abstract : Human microsomal and soluble epoxide hydrolases (mEH and sEH) are enzymes that metabolize xenobiotic molecules. We screened DNA from 48 Japanese individuals for single-nucleotide polymorphisms (SNPs) in both genes by direct sequencing of the entire genomic regions containing EPHX1 and EPHX2, except for repetitive elements. This approach identified 33 SNPs in the EPHX1 gene; 6 of them were located in the 5' flanking region, 17 in introns, 8 in exons, and 2 in the 3' flanking region. In the EPHX2 gene, we identified 36 SNPs, including 4 in the 5' flanking region, 24 in introns, 5 in exons, and 3 in the 3' flanking region, as well as one insertion/deletion polymorphism in the 5' flanking region. These variants may contribute to a more precise understanding of the nature of correlations between genotypes and disease-susceptibility phenotypes that have been postulated in regard to human microsomal and soluble epoxide hydrolases.
ESTHER : Saito_2001_J.Hum.Genet_46_325
PubMedSearch : Saito_2001_J.Hum.Genet_46_325
PubMedID: 11393535
Gene_locus related to this paper: human-EPHX2

Title : Growth-suppressive effects of BPOZ and EGR2, two genes involved in the PTEN signaling pathway - Unoki_2001_Oncogene_20_4457
Author(s) : Unoki M , Nakamura Y
Ref : Oncogene , 20 :4457 , 2001
Abstract : Defects in PTEN, a tumor suppressor, have been found in cancers arising in a variety of human tissues. To elucidate the tumor-suppressive function of this gene, we have been analysing expression profiles of cancer cells after introduction of exogenous PTEN. Those experiments identified 99 candidate genes that were transcriptionally transactivated. Among them, we report here the further analyses of eight genes, EGR2/Krox-20, BPOZ, APS, HCLS1/HS1, DUSP1/MKP1, NDRG1/Drg1/RTP, NFIL3/E4BP4, and a novel gene (PINK1, PTEN-induced putative kinase). Expression of six of them (PINK1, EGR2, HCLS1, DUSP1, BPOZ, and NFIL3) was decreased in ovarian tumors compared with corresponding normal tissues. Colony-formation assays using plasmid clones designed to express each gene indicated that EGR2 and BPOZ were able to suppress growth of cancer cells significantly; in particular, cancer-cell lines stably expressing BPOZ grew more slowly than control cells containing mock vector. Flow cytometry suggested that over-expression of BPOZ inhibited progression of the cell cycle at the G(1)/S transition. Anti-sense oligonucleotides for BPOZ or EGR2 effectively inhibited their expression, and cell growth was accelerated. Therefore both genes appear to be novel candidates as mediators of the PTEN growth-suppressive signaling pathway.
ESTHER : Unoki_2001_Oncogene_20_4457
PubMedSearch : Unoki_2001_Oncogene_20_4457
PubMedID: 11494141

Title : Complete genomic sequence of the filamentous nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120 - Kaneko_2001_DNA.Res_8_205
Author(s) : Kaneko T , Nakamura Y , Wolk CP , Kuritz T , Sasamoto S , Watanabe A , Iriguchi M , Ishikawa A , Kawashima K , Kimura T , Kishida Y , Kohara M , Matsumoto M , Matsuno A , Muraki A , Nakazaki N , Shimpo S , Sugimoto M , Takazawa M , Yamada M , Yasuda M , Tabata S
Ref : DNA Research , 8 :205 , 2001
Abstract : The nucleotide sequence of the entire genome of a filamentous cyanobacterium, Anabaena sp. strain PCC 7120, was determined. The genome of Anabaena consisted of a single chromosome (6,413,771 bp) and six plasmids, designated pCC7120alpha (408,101 bp), pCC7120beta (186,614 bp), pCC7120gamma (101,965 bp), pCC7120delta (55,414 bp), pCC7120epsilon (40,340 bp), and pCC7120zeta (5,584 bp). The chromosome bears 5368 potential protein-encoding genes, four sets of rRNA genes, 48 tRNA genes representing 42 tRNA species, and 4 genes for small structural RNAs. The predicted products of 45% of the potential protein-encoding genes showed sequence similarity to known and predicted proteins of known function, and 27% to translated products of hypothetical genes. The remaining 28% lacked significant similarity to genes for known and predicted proteins in the public DNA databases. More than 60 genes involved in various processes of heterocyst formation and nitrogen fixation were assigned to the chromosome based on their similarity to the reported genes. One hundred and ninety-five genes coding for components of two-component signal transduction systems, nearly 2.5 times as many as those in Synechocystis sp. PCC 6803, were identified on the chromosome. Only 37% of the Anabaena genes showed significant sequence similarity to those of Synechocystis, indicating a high degree of divergence of the gene information between the two cyanobacterial strains.
ESTHER : Kaneko_2001_DNA.Res_8_205
PubMedSearch : Kaneko_2001_DNA.Res_8_205
PubMedID: 11759840
Gene_locus related to this paper: anasp-ALL0111 , anasp-ALL0193 , anasp-ALL0254 , anasp-ALL0316 , anasp-ALL0955 , anasp-ALL0969 , anasp-ALL1161 , anasp-ALL1205 , anasp-ALL1353 , anasp-ALL1695 , anasp-ALL2050 , anasp-ALL2056 , anasp-ALL2058 , anasp-ALL2068 , anasp-ALL2529 , anasp-ALL2533 , anasp-ALL2753 , anasp-ALL2761 , anasp-ALL3898 , anasp-ALL4221 , anasp-ALL4875 , anasp-ALL8511 , anasp-ALR0039 , anasp-ALR0079 , anasp-ALR0130 , anasp-ALR0235 , anasp-ALR0851 , anasp-ALR1077 , anasp-ALR1270 , anasp-ALR1352 , anasp-ALR1362 , anasp-ALR1709 , anasp-ALR2045 , noss1-ALR3140 , anasp-ALR3514 , anasp-ALR3685 , anasp-ALR3911 , anasp-ALR4625 , anasp-ALR5028 , anasp-AROE , anasp-q8ymv5 , anasp-q8yxx2 , anasp-y1448 , noss1-ALL3113 , noss1-ALL4967 , noss1-ALR4786 , noss1-q8yrg0 , noss1-y2406

Title : Structural analysis of Arabidopsis thaliana chromosome 3. I. Sequence features of the regions of 4,504,864 bp covered by sixty P1 and TAC clones - Sato_2000_DNA.Res_7_131
Author(s) : Sato S , Nakamura Y , Kaneko T , Katoh T , Asamizu E , Tabata S
Ref : DNA Research , 7 :131 , 2000
Abstract : Based on the physical map of Arabidopsis thaliana chromosome 3 previously constructed with CIC YAC, TAC, P1 and BAC clones (Sato, S. et al., DNA Res., 5, 163-168, 1998), a total of 60 P1 and TAC clones were sequenced, and the sequence features of the resulting 4,504,864 bp regions were analyzed by applying various computer programs for similarity search and gene modeling. As a result, a total of 1054 potential protein-coding genes were identified. The average density of the genes identified was 1 gene per 4066 bp. Introns were observed in 77% of the genes, and the average number per gene and the average length of the introns were 3.9 and 156 bp, respectively. These sequence features are essentially identical to those of chromosome 5 in our previous reports, but the gene density was slightly higher than that observed for chromosomes 2 and 4. The regions also contained 10 tRNA genes when searched by similarity to reported tRNA genes and the tRNA scan-SE program. The sequence data and information on the potential genes are available through the World Wide Web database KAOS (Kazusa Arabidopsis data Opening Site) at http:\/\/www.kazusa.or.jp/kaos/.
ESTHER : Sato_2000_DNA.Res_7_131
PubMedSearch : Sato_2000_DNA.Res_7_131
PubMedID: 10819329
Gene_locus related to this paper: arath-At3g14360 , arath-At3g27325 , arath-Y3684 , arath-Q9LI62 , arath-Q9LUG8 , arath-Q9LUH1 , arath-Q6NKN2 , arath-Q9LW14 , arath-Q9LW28 , arath-SCP21 , arath-SCP33

Title : Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana - Tabata_2000_Nature_408_823
Author(s) : Tabata S , Kaneko T , Nakamura Y , Kotani H , Kato T , Asamizu E , Miyajima N , Sasamoto S , Kimura T , Hosouchi T , Kawashima K , Kohara M , Matsumoto M , Matsuno A , Muraki A , Nakayama S , Nakazaki N , Naruo K , Okumura S , Shinpo S , Takeuchi C , Wada T , Watanabe A , Yamada M , Yasuda M , Sato S , de la Bastide M , Huang E , Spiegel L , Gnoj L , O'Shaughnessy A , Preston R , Habermann K , Murray J , Johnson D , Rohlfing T , Nelson J , Stoneking T , Pepin K , Spieth J , Sekhon M , Armstrong J , Becker M , Belter E , Cordum H , Cordes M , Courtney L , Courtney W , Dante M , Du H , Edwards J , Fryman J , Haakensen B , Lamar E , Latreille P , Leonard S , Meyer R , Mulvaney E , Ozersky P , Riley A , Strowmatt C , Wagner-McPherson C , Wollam A , Yoakum M , Bell M , Dedhia N , Parnell L , Shah R , Rodriguez M , See LH , Vil D , Baker J , Kirchoff K , Toth K , King L , Bahret A , Miller B , Marra M , Martienssen R , McCombie WR , Wilson RK , Murphy G , Bancroft I , Volckaert G , Wambutt R , Dusterhoft A , Stiekema W , Pohl T , Entian KD , Terryn N , Hartley N , Bent E , Johnson S , Langham SA , McCullagh B , Robben J , Grymonprez B , Zimmermann W , Ramsperger U , Wedler H , Balke K , Wedler E , Peters S , van Staveren M , Dirkse W , Mooijman P , Lankhorst RK , Weitzenegger T , Bothe G , Rose M , Hauf J , Berneiser S , Hempel S , Feldpausch M , Lamberth S , Villarroel R , Gielen J , Ardiles W , Bents O , Lemcke K , Kolesov G , Mayer K , Rudd S , Schoof H , Schueller C , Zaccaria P , Mewes HW , Bevan M , Fransz P
Ref : Nature , 408 :823 , 2000
Abstract : The genome of the model plant Arabidopsis thaliana has been sequenced by an international collaboration, The Arabidopsis Genome Initiative. Here we report the complete sequence of chromosome 5. This chromosome is 26 megabases long; it is the second largest Arabidopsis chromosome and represents 21% of the sequenced regions of the genome. The sequence of chromosomes 2 and 4 have been reported previously and that of chromosomes 1 and 3, together with an analysis of the complete genome sequence, are reported in this issue. Analysis of the sequence of chromosome 5 yields further insights into centromere structure and the sequence determinants of heterochromatin condensation. The 5,874 genes encoded on chromosome 5 reveal several new functions in plants, and the patterns of gene organization provide insights into the mechanisms and extent of genome evolution in plants.
ESTHER : Tabata_2000_Nature_408_823
PubMedSearch : Tabata_2000_Nature_408_823
PubMedID: 11130714
Gene_locus related to this paper: arath-At5g11650 , arath-At5g16120 , arath-at5g18630 , arath-AT5G20520 , arath-At5g21950 , arath-AT5G27320 , arath-CXE15 , arath-F1N13.220 , arath-F14F8.240 , arath-q3e9e4 , arath-q8lae9 , arath-Q8LFB7 , arath-q9ffg7 , arath-q9fij5 , arath-Q9LVU7 , arath-q66gm8 , arath-SCPL34 , arath-B9DFR3 , arath-a0a1p8bcz0

Title : Structural analysis of Arabidopsis thaliana chromosome 5. X. Sequence features of the regions of 3,076,755 bp covered by sixty P1 and TAC clones - Sato_2000_DNA.Res_7_31
Author(s) : Sato S , Nakamura Y , Kaneko T , Katoh T , Asamizu E , Kotani H , Tabata S
Ref : DNA Research , 7 :31 , 2000
Abstract : In our ongoing project to deduce the nucleotide sequence of Arabidopsis thaliana chromosome 5, non-redundant P1 and TAC clones have been sequenced on the basis of the fine physical map, and as of January, 2000, the sequences of 16.6 Mb representing approximately 60% of chromosome 5 have been accumulated and released at our web site. Along with the sequence determination, structural features of the sequenced regions have been analyzed by applying a variety of computer programs, and we already predicted a total of 2697 potential protein coding genes in the 11,166,130 bp regions, which are covered by 159 P1 and TAC clones. In this paper, we describe the structural features of the 3,076,755 bp regions covered by newly analyzed 60 P1 and TAC clones. A total of 715 potential protein coding genes were identified, giving an average density of the genes identified of 1 gene per 4001 bp. Introns were observed in 80% of the genes, and the average number per gene and the average length of the introns were 4.5 and 147 bp, respectively. These sequence features are nearly identical to those in our latest report in which the data were compiled based on a new standard of gene assignment including the computer-predicted hypothetical genes. The regions also contained 12 tRNA genes when searched by similarity to reported tRNA genes and the tRNA scan-SE program. The sequence data and information on the potential genes are available through the World Wide Web database KAOS (Kazusa Arabidopsis data Opening Site) at http:\/\/www.kazusa.or.jp/kaos/.
ESTHER : Sato_2000_DNA.Res_7_31
PubMedSearch : Sato_2000_DNA.Res_7_31
PubMedID: 10718197
Gene_locus related to this paper: arath-At5g47330 , arath-AT5G51180 , arath-AT5G62180 , arath-At5g67050 , arath-MES18 , arath-CXE18 , arath-Q9LTX5 , arath-Q9LVS4 , arath-Q9LVS5 , arath-Q9LVU7 , arath-Q9LVX9 , arath-SCP41 , arath-SCP42

Title : Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana - Salanoubat_2000_Nature_408_820
Author(s) : Salanoubat M , Lemcke K , Rieger M , Ansorge W , Unseld M , Fartmann B , Valle G , Blocker H , Perez-Alonso M , Obermaier B , Delseny M , Boutry M , Grivell LA , Mache R , Puigdomenech P , de Simone V , Choisne N , Artiguenave F , Robert C , Brottier P , Wincker P , Cattolico L , Weissenbach J , Saurin W , Quetier F , Schafer M , Muller-Auer S , Gabel C , Fuchs M , Benes V , Wurmbach E , Drzonek H , Erfle H , Jordan N , Bangert S , Wiedelmann R , Kranz H , Voss H , Holland R , Brandt P , Nyakatura G , Vezzi A , D'Angelo M , Pallavicini A , Toppo S , Simionati B , Conrad A , Hornischer K , Kauer G , Lohnert TH , Nordsiek G , Reichelt J , Scharfe M , Schon O , Bargues M , Terol J , Climent J , Navarro P , Collado C , Perez-Perez A , Ottenwalder B , Duchemin D , Cooke R , Laudie M , Berger-Llauro C , Purnelle B , Masuy D , de Haan M , Maarse AC , Alcaraz JP , Cottet A , Casacuberta E , Monfort A , Argiriou A , Flores M , Liguori R , Vitale D , Mannhaupt G , Haase D , Schoof H , Rudd S , Zaccaria P , Mewes HW , Mayer KF , Kaul S , Town CD , Koo HL , Tallon LJ , Jenkins J , Rooney T , Rizzo M , Walts A , Utterback T , Fujii CY , Shea TP , Creasy TH , Haas B , Maiti R , Wu D , Peterson J , Van Aken S , Pai G , Militscher J , Sellers P , Gill JE , Feldblyum TV , Preuss D , Lin X , Nierman WC , Salzberg SL , White O , Venter JC , Fraser CM , Kaneko T , Nakamura Y , Sato S , Kato T , Asamizu E , Sasamoto S , Kimura T , Idesawa K , Kawashima K , Kishida Y , Kiyokawa C , Kohara M , Matsumoto M , Matsuno A , Muraki A , Nakayama S , Nakazaki N , Shinpo S , Takeuchi C , Wada T , Watanabe A , Yamada M , Yasuda M , Tabata S
Ref : Nature , 408 :820 , 2000
Abstract : Arabidopsis thaliana is an important model system for plant biologists. In 1996 an international collaboration (the Arabidopsis Genome Initiative) was formed to sequence the whole genome of Arabidopsis and in 1999 the sequence of the first two chromosomes was reported. The sequence of the last three chromosomes and an analysis of the whole genome are reported in this issue. Here we present the sequence of chromosome 3, organized into four sequence segments (contigs). The two largest (13.5 and 9.2 Mb) correspond to the top (long) and the bottom (short) arms of chromosome 3, and the two small contigs are located in the genetically defined centromere. This chromosome encodes 5,220 of the roughly 25,500 predicted protein-coding genes in the genome. About 20% of the predicted proteins have significant homology to proteins in eukaryotic genomes for which the complete sequence is available, pointing to important conserved cellular functions among eukaryotes.
ESTHER : Salanoubat_2000_Nature_408_820
PubMedSearch : Salanoubat_2000_Nature_408_820
PubMedID: 11130713
Gene_locus related to this paper: arath-MES17 , arath-AT3G12150 , arath-At3g61680 , arath-AT3g62590 , arath-CXE12 , arath-eds1 , arath-SCP25 , arath-F1P2.110 , arath-F1P2.140 , arath-F11F8.28 , arath-F14D17.80 , arath-F16B3.4 , arath-SCP27 , arath-At3g50790 , arath-At3g05600 , arath-PAD4 , arath-At3g51000 , arath-SCP16 , arath-gid1 , arath-GID1B , arath-Q9LUG8 , arath-Q84JS1 , arath-Q9SFF6 , arath-q9m236 , arath-q9sr22 , arath-q9sr23 , arath-SCP7 , arath-SCP14 , arath-SCP15 , arath-SCP17 , arath-SCP36 , arath-SCP37 , arath-SCP39 , arath-SCP40 , arath-SCP49 , arath-T19F11.2

Title : [Treatment of the elderly dementia patients] -
Author(s) : Takeda M , Shinosaki K , Nishikawa T , Tanaka T , Kudo T , Nakamura Y , Kashiwagi Y
Ref : Nippon Ronen Igakkai Zasshi , 37 :879 , 2000
PubMedID: 11193359

Title : Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti - Kaneko_2000_DNA.Res_7_331
Author(s) : Kaneko T , Nakamura Y , Sato S , Asamizu E , Kato T , Sasamoto S , Watanabe A , Idesawa K , Ishikawa A , Kawashima K , Kimura T , Kishida Y , Kiyokawa C , Kohara M , Matsumoto M , Matsuno A , Mochizuki Y , Nakayama S , Nakazaki N , Shimpo S , Sugimoto M , Takeuchi C , Yamada M , Tabata S
Ref : DNA Research , 7 :331 , 2000
Abstract : The complete nucleotide sequence of the genome of a symbiotic bacterium Mesorhizobium loti strain MAFF303099 was determined. The genome of M. loti consisted of a single chromosome (7,036,071 bp) and two plasmids, designated as pMLa (351,911 bp) and pMLb (208, 315 bp). The chromosome comprises 6752 potential protein-coding genes, two sets of rRNA genes and 50 tRNA genes representing 47 tRNA species. Fifty-four percent of the potential protein genes showed sequence similarity to genes of known function, 21% to hypothetical genes, and the remaining 25% had no apparent similarity to reported genes. A 611-kb DNA segment, a highly probable candidate of a symbiotic island, was identified, and 30 genes for nitrogen fixation and 24 genes for nodulation were assigned in this region. Codon usage analysis suggested that the symbiotic island as well as the plasmids originated and were transmitted from other genetic systems. The genomes of two plasmids, pMLa and pMLb, contained 320 and 209 potential protein-coding genes, respectively, for a variety of biological functions. These include genes for the ABC-transporter system, phosphate assimilation, two-component system, DNA replication and conjugation, but only one gene for nodulation was identified.
ESTHER : Kaneko_2000_DNA.Res_7_331
PubMedSearch : Kaneko_2000_DNA.Res_7_331
PubMedID: 11214968
Gene_locus related to this paper: meslo-acoc , meslo-EphB , meslo-est , meslo-lipest , meslo-MLL0014 , meslo-MLL0351 , meslo-MLL0537 , meslo-mll0601 , meslo-MLL0618 , meslo-MLL1209 , meslo-MLL1226 , meslo-mll1328 , meslo-MLL1329 , meslo-MLL1495 , meslo-MLL1869 , meslo-mll1900 , meslo-MLL2018 , meslo-MLL2072 , meslo-mll2481 , meslo-mll2689 , meslo-MLL2788 , meslo-MLL3556 , meslo-MLL3568 , meslo-MLL3682 , meslo-mll3776 , meslo-MLL4497 , meslo-MLL4552 , meslo-MLL5128 , meslo-mll5179 , meslo-mll5392 , meslo-MLL5717 , meslo-mll5743 , meslo-MLL6746 , meslo-MLL6752 , meslo-mll6871 , meslo-MLL7643 , meslo-mll7742 , meslo-MLL9722 , meslo-MLR0094 , meslo-mlr0145 , meslo-mlr0170 , meslo-MLR0240 , meslo-mlr0493 , meslo-MLR0937 , meslo-mlr0978 , meslo-MLR0992 , meslo-MLR1612 , meslo-mlr1789 , meslo-mlr1864 , meslo-mlr2176 , meslo-MLR2262 , meslo-mlr2612 , meslo-mlr2710 , meslo-mlr3034 , meslo-MLR3538 , meslo-mlr3816 , meslo-mlr4436 , meslo-MLR4903 , meslo-MLR5045 , meslo-MLR5063 , rhilo-dhaa , meslo-MLR6087 , meslo-MLR6657 , meslo-mlr6682 , meslo-mlr6683 , meslo-MLR6684 , meslo-MLR6787 , meslo-MLR6993 , meslo-mlr6999 , meslo-mlr7206 , meslo-mlr7232 , meslo-mlr7803 , meslo-MLR9053 , meslo-mlr9622 , meslo-mlr9641 , rhilo-MLL0076 , rhilo-MLL1824 , rhilo-MLL7123 , rhilo-MLL8374 , rhilo-MLR1247 , rhilo-MLR2444 , rhilo-MLR4383 , rhilo-MLR8175 , rhilo-q98nf6 , rhilo-q98nf8 , rhilo-q988i9

Title : Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis - Takami_2000_Nucleic.Acids.Res_28_4317
Author(s) : Takami H , Nakasone K , Takaki Y , Maeno G , Sasaki R , Masui N , Fuji F , Hirama C , Nakamura Y , Ogasawara N , Kuhara S , Horikoshi K
Ref : Nucleic Acids Research , 28 :4317 , 2000
Abstract : The 4 202 353 bp genome of the alkaliphilic bacterium Bacillus halodurans C-125 contains 4066 predicted protein coding sequences (CDSs), 2141 (52.7%) of which have functional assignments, 1182 (29%) of which are conserved CDSs with unknown function and 743 (18. 3%) of which have no match to any protein database. Among the total CDSs, 8.8% match sequences of proteins found only in Bacillus subtilis and 66.7% are widely conserved in comparison with the proteins of various organisms, including B.subtilis. The B. halodurans genome contains 112 transposase genes, indicating that transposases have played an important evolutionary role in horizontal gene transfer and also in internal genetic rearrangement in the genome. Strain C-125 lacks some of the necessary genes for competence, such as comS, srfA and rapC, supporting the fact that competence has not been demonstrated experimentally in C-125. There is no paralog of tupA, encoding teichuronopeptide, which contributes to alkaliphily, in the C-125 genome and an ortholog of tupA cannot be found in the B.subtilis genome. Out of 11 sigma factors which belong to the extracytoplasmic function family, 10 are unique to B. halodurans, suggesting that they may have a role in the special mechanism of adaptation to an alkaline environment.
ESTHER : Takami_2000_Nucleic.Acids.Res_28_4317
PubMedSearch : Takami_2000_Nucleic.Acids.Res_28_4317
PubMedID: 11058132
Gene_locus related to this paper: bacha-BH0727 , bacha-BH0763 , bacha-BH0848 , bacha-BH0879 , bacha-BH1308 , bacha-BH1440 , bacha-BH1838 , bacha-BH1839 , bacha-BH2174 , bacha-BH2248 , bacha-BH2279 , bacha-BH2806 , bacha-BH2917 , bacha-BH3288 , bacha-BH3306 , bacha-BH3326 , bacha-BH3554 , bacha-BH3805 , bacha-BH3908 , bacha-YvaM , bachd-q9k8w0 , bachd-q9kbn0

Title : An improved physical and genetic map of the genome of alkaliphilic Bacillus sp. C-125 - Takami_1999_Extremophiles_3_21
Author(s) : Takami H , Nakasone K , Hirama C , Takaki Y , Masui N , Fuji F , Nakamura Y , Inoue A
Ref : Extremophiles , 3 :21 , 1999
Abstract : Among alkaliphilic bacteria reported so far, Bacillus sp. C-125 is the strain most thoroughly characterized physiologically, biochemically, and genetically. A physical map of the chromosome of this strain was constructed to facilitate further genome analysis, and the genome size was revised from 3.7 to 4.25Mb. Complete digestion of the chromosomal DNA with two rare cut restriction endonucleases, AscI and Sse8387I, each yielded 20 fragments ranging in size from 20 to 600 kb. Seventeen linking clones were isolated in each instance to join the adjacent AscI or Sse8387I fragments in the chromosomal map. All AscI linking clones isolated were sequenced and analyzed by comparison with the BSORF database to map the genes in the chromosome of strain C-125. Several ORFs showing significant similarities to those of B. subtilis in the AscI linking clones were positioned on the physical map. The oriC region of the C-125 chromosome was identified by southern blot analysis with a DNA probe containing the gyrB region.
ESTHER : Takami_1999_Extremophiles_3_21
PubMedSearch : Takami_1999_Extremophiles_3_21
PubMedID: 10086841

Title : Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum pernix K1 - Kawarabayasi_1999_DNA.Res_6_83
Author(s) : Kawarabayasi Y , Hino Y , Horikawa H , Yamazaki S , Haikawa Y , Jin-no K , Takahashi M , Sekine M , Baba S , Ankai A , Kosugi H , Hosoyama A , Fukui S , Nagai Y , Nishijima K , Nakazawa H , Takamiya M , Masuda S , Funahashi T , Tanaka T , Kudoh Y , Yamazaki J , Kushida N , Oguchi A , Aoki KI , Kubota K , Nakamura Y , Nomura N , Sako Y , Kikuchi H
Ref : DNA Research , 6 :83 , 1999
Abstract : The complete sequence of the genome of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum pernix K1, which optimally grows at 95 degrees C, has been determined by the whole genome shotgun method with some modifications. The entire length of the genome was 1,669,695 bp. The authenticity of the entire sequence was supported by restriction analysis of long PCR products, which were directly amplified from the genomic DNA. As the potential protein-coding regions, a total of 2,694 open reading frames (ORFs) were assigned. By similarity search against public databases, 633 (23.5%) of the ORFs were related to genes with putative function and 523 (19.4%) to the sequences registered but with unknown function. All the genes in the TCA cycle except for that of alpha-ketoglutarate dehydrogenase were included, and instead of the alpha-ketoglutarate dehydrogenase gene, the genes coding for the two subunits of 2-oxoacid:ferredoxin oxidoreductase were identified. The remaining 1,538 ORFs (57.1%) did not show any significant similarity to the sequences in the databases. Sequence comparison among the assigned ORFs suggested that a considerable member of ORFs were generated by sequence duplication. The RNA genes identified were a single 16S-23S rRNA operon, two 5S rRNA genes and 47 tRNA genes including 14 genes with intron structures. All the assigned ORFs and RNA coding regions occupied 89.12% of the whole genome. The data presented in this paper are available on the internet homepage (http:\/\/www.mild.nite.go.jp).
ESTHER : Kawarabayasi_1999_DNA.Res_6_83
PubMedSearch : Kawarabayasi_1999_DNA.Res_6_83
PubMedID: 10382966
Gene_locus related to this paper: aerpe-APE1244 , aerpe-APE1547 , aerpe-APE1832 , aerpe-APE2290 , aerpe-APE2361 , aerpe-APE2441

Title : The genes degQ, pps, and lpa-8 (sfp) are responsible for conversion of Bacillus subtilis 168 to plipastatin production - Tsuge_1999_Antimicrob.Agents.Chemother_43_2183
Author(s) : Tsuge K , Ano T , Hirai M , Nakamura Y , Shoda M
Ref : Antimicrobial Agents & Chemotherapy , 43 :2183 , 1999
Abstract : Bacillus subtilis YB8 produces the lipopeptide antibiotic plipastatin. B. subtilis MI113, which is a derivative of strain 168, was converted into a new plipastatin producer, strain 406, by competence transformation with the chromosomal DNA of YB8. Transposon mini-Tn10 insertional mutagenesis was applied to strain 406, which revealed that lpa-8 (sfp) (encoding 4'-phosphopantetheinyl transferase) and the pps operon (located between 167 and 171 degrees ) are essential for plipastatin production. The pps operon was previously suggested to encode putative peptide synthetases (A. Tognoni, E. Franchi, C. Magistrelli, E. Colombo, P. Cosmina, and G. Grandi, Microbiology 141:645-648, 1995) and was thought to be the fengycin operon (V. Tosato, A. M. Albertini, M. Zotti, S. Sonda, and C. V. Bruschi, Microbiology 143:3443-3450, 1997). We claim that the pps operon is the pli operon, encoding plipastatin synthetase. By using a new high-performance liquid chromatography system, we revealed that strain 168 expressing only lpa-8 can also produce plipastatin, although the yield is very low. However, the introduction of the pleiotropic regulator degQ of strain YB8 into strain 168 expressing lpa-8 resulted in a 10-fold increase in the production of plipastatin.
ESTHER : Tsuge_1999_Antimicrob.Agents.Chemother_43_2183
PubMedSearch : Tsuge_1999_Antimicrob.Agents.Chemother_43_2183
PubMedID: 10471562
Gene_locus related to this paper: bacsu-PPSE

Title : Structural analysis of Arabidopsis thaliana chromosome 5. IX. Sequence features of the regions of 1,011,550 bp covered by seventeen P1 and TAC clones - Kaneko_1999_DNA.Res_6_183
Author(s) : Kaneko T , Katoh T , Sato S , Nakamura Y , Asamizu E , Kotani H , Miyajima N , Tabata S
Ref : DNA Research , 6 :183 , 1999
Abstract : In this series of projects sequencing the entire genome of Arabidopsis thaliana chromosome 5, non-redundant P1 and TAC clones have been sequenced according to the fine physical map, and as of May 7, 1999, the sequences of 16.2 Mb representing approximately 60% of chromosome 5 have been accumulated and released at our web site. In parallel, structural features of the sequenced regions have been analyzed by applying a variety of computer programs, and to date we have predicted a total of 2380 potential protein-coding genes in the 10,154,580 bp regions, which are covered by 142 P1 and TAC clones. In this paper, we newly analyzed the structural features of the 1,011,550 bp regions covered by additional 17 P1 and TAC clones, and predicted 298 protein-coding genes. The average density of the genes identified was 1 gene per 3394 bp. Introns were observed in 67% of the genes, and the average number per gene and the average length of the introns were 3.2 and 159 bp, respectively. The gene density became higher than the value estimated in the previously analyzed regions (1 gene per 4,267 bp), as the data in this paper were compiled based on a new standard of gene assignment including the computer-predicted hypothetical genes. The regions also contained 8 tRNA genes when searched by similarity to reported tRNA genes and the tRNA scan-SE program. The sequence data and information on the potential genes are available on the database KAOS (Kazusa Arabidopsis data Opening Site) at http:\/\/www.kazusa.or.jp/arabi/.
ESTHER : Kaneko_1999_DNA.Res_6_183
PubMedSearch : Kaneko_1999_DNA.Res_6_183
PubMedID: 10470850
Gene_locus related to this paper: arath-At5g37710 , arath-SCP19 , arath-Q9FI59

Title : Structural analysis of Arabidopsis thaliana chromosome 5. VIII. Sequence features of the regions of 1,081,958 bp covered by seventeen physically assigned P1 and TAC clones. -
Author(s) : Asamizu E , Sato S , Kaneko T , Nakamura Y , Kotani H , Miyajima N , Tabata S
Ref : DNA Research , 5 :379 , 1998
PubMedID: 10048488
Gene_locus related to this paper: arath-At5g14930 , arath-at5g18630 , arath-AT5G19050 , arath-At5g24180 , arath-AT5G24190 , arath-At5g24200 , arath-F2G14.100 , arath-F6H11.120 , arath-F9G14.280 , arath-F14F8.240 , arath-HNL , arath-At5g14310

Title : Structural analysis of Arabidopsis thaliana chromosome 5. VII. Sequence features of the regions of 1,013,767 bp covered by sixteen physically assigned P1 and TAC clones - Nakamura_1998_DNA.Res_5_297
Author(s) : Nakamura Y , Sato S , Asamizu E , Kaneko T , Kotani H , Miyajima N , Tabata S
Ref : DNA Research , 5 :297 , 1998
Abstract : Sixteen P1 and TAC clones assigned to Arabidopsis thaliana chromosome 5 were sequenced, and their sequence features were analyzed using various computer programs. The total length of the sequences determined was 1,013,767 bp. Together with the nucleotide sequences of 109 clones previously reported, the regions of chromosome 5 sequenced so far now total 9,072,622 bp, which presumably covers approximately one-third of the chromosome. A similarity search against the reported gene sequences predicted the presence of a total of 225 protein-coding genes and/or gene segments in the newly sequenced regions, indicating an average gene density of one gene per 4.5 kb. Introns were identified in 72.4% of the potential protein genes for which the entire gene structure was predicted, and the average number per gene and the average length of the introns were 3.3 and 163 bp, respectively. These sequence features are essentially identical to those in the previously reported sequences. The sequence data and gene information are available on the World Wide Web database KAOS (Kazusa Arabidopsis data Opening Site) at http://www.kazusa.or.jp/arabi/.
ESTHER : Nakamura_1998_DNA.Res_5_297
PubMedSearch : Nakamura_1998_DNA.Res_5_297
PubMedID: 9872454
Gene_locus related to this paper: arath-At5g41900 , arath-Q9FJ29

Title : Structural analysis of Arabidopsis thaliana chromosome 5. V. Sequence features of the regions of 1,381,565 bp covered by twenty one physically assigned P1 and TAC clones - Kaneko_1998_DNA.Res_5_131
Author(s) : Kaneko T , Kotani H , Nakamura Y , Sato S , Asamizu E , Miyajima N , Tabata S
Ref : DNA Research , 5 :131 , 1998
Abstract : The nucleotide sequences of 21 P1 and TAC clones which have been precisely localized to the fine physical map of the Arabidopsis thaliana chromosome 5, were determined, and their sequence features were analyzed. The total length of the regions sequenced in this study were 1,381,565 bp, bringing the total length of the chromosome 5 sequences determined so far to 6,691,670 bp together with the regions of the 69 clones previously reported. By computer-aided analyses including similarity search against protein and EST databases and gene modeling with computer programs, a total of 337 potential protein-coding genes and/or gene segments were identified on the basis of similarity to the reported gene sequences. An average density of the genes and/or gene segments thus assigned was 1 gene/4,100 bp. Introns were identified in 76.7% of the potential protein genes for which the entire gene structure were predicted, and the average number per gene and the average length of the introns were 3.9 and 176 bp, respectively. These sequence features are essentially identical to those in the previously reported sequences. The numbers of the Arabidopsis ESTs matched to each of the predicted genes have been counted to monitor the transcription level. The sequence data and gene information are available on the World Wide Web database KAOS (Kazusa Arabidopsis data Opening Site) at http:@www.kazusa.or.jp@arabi
ESTHER : Kaneko_1998_DNA.Res_5_131
PubMedSearch : Kaneko_1998_DNA.Res_5_131
PubMedID: 9679202
Gene_locus related to this paper: arath-AT5G39220 , arath-Q9FKP9

Title : Structural analysis of Arabidopsis thaliana chromosome 5. IV. Sequence features of the regions of 1,456,315 bp covered by nineteen physically assigned P1 and TAC clones - Sato_1998_DNA.Res_5_41
Author(s) : Sato S , Kaneko T , Kotani H , Nakamura Y , Asamizu E , Miyajima N , Tabata S
Ref : DNA Research , 5 :41 , 1998
Abstract : Nineteen P1 and TAC clones, which have been precisely localized to the fine physical map of Arabidopsis thaliana chromosome 5, were newly sequenced, and their sequence features were analysed. The total length of the clones sequenced was 1,456,315 bp. Together with the previously reported sequences, the regions of chromosome 5 that have been sequenced to date is now 5,310,105 bp. When the sequences determined in this study were subjected to similarity search against protein and expressed sequence tag (EST) databases and analysis with computer programs for gene modeling, a total of 354 potential protein-coding genes and/or gene segments were identified. The average density of the assigned genes and/or gene segments was one gene per 4,114 bp. Introns were identified in 75% of the potential protein genes, and the average number per gene and the average length of the introns were 3.7 and 194 bp, respectively. These sequence features are essentially identical to those in the previously reported sequences. The numbers of the Arabidopsis ESTs matched to each of the predicted genes have been counted to monitor the transcription level. The sequence data and gene information are available on the World Wide Web database KAOS (the Kazusa Arabidopsis data Opening Site) at http://www.kazusa.or.jp/arabi/.
ESTHER : Sato_1998_DNA.Res_5_41
PubMedSearch : Sato_1998_DNA.Res_5_41
PubMedID: 9628582
Gene_locus related to this paper: arath-AT5G41120 , arath-At5g41130 , arath-F6H11.120

Title : Structural analysis of Arabidopsis thaliana chromosome 5. VI. Sequence features of the regions of 1,367,185 bp covered by 19 physically assigned P1 and TAC clones. -
Author(s) : Kotani H , Nakamura Y , Sato S , Asamizu E , Kaneko T , Miyajima N , Tabata S
Ref : DNA Research , 5 :203 , 1998
PubMedID: 9734815
Gene_locus related to this paper: arath-At5g56750

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 : Structural analysis of Arabidopsis thaliana chromosome 5. II. Sequence features of the regions of 1,044,062 bp covered by thirteen physically assigned P1 clones - Kotani_1997_DNA.Res_4_291
Author(s) : Kotani H , Nakamura Y , Sato S , Kaneko T , Asamizu E , Miyajima N , Tabata S
Ref : DNA Research , 4 :291 , 1997
Abstract : A total of 13 P1 clones, each containing a marker(s) specifically mapped on chromosome 5, were isolated from a P1 library of the Arabidopsis thaliana Columbia genome, and their nucleotide sequences were determined according to the shot gun based strategy and precisely located on the physical map of chromosome 5. The total length of the sequenced regions was 1,044,062 bp. Since we have previously reported the sequence of 1,621,245 bp by analysis of 20 non-redundant P1 clones, the total length of the sequences of chromosome 5 determined so far reached 2,665,307 bp. The regions sequenced in this study were analysed by comparison with the sequences in protein and EST databases and analysis with computer programs for gene modeling; a total of 225 potential protein-coding genes and/or gene segments with known or predicted functions were identified. The positions of exons which do not exhibit similarity to known genes were also predicted by computer-aided analysis. An average density of the genes and/or gene was 1 gene/4,640 bp. Introns were identified in approximately 84% of the potential genes, and the average number and length of the introns per gene were 5.3 and 184 bp, respectively. These sequence features are essentially identical to those for the previously sequenced regions. The transcription level of the predicted genes has been roughly monitored by counting the numbers of matched Arabidopsis ESTs. The sequence data and gene information are available through the World Wide Web at https://www.kazusa.or.jp/kaos/.
ESTHER : Kotani_1997_DNA.Res_4_291
PubMedSearch : Kotani_1997_DNA.Res_4_291
PubMedID: 9405937
Gene_locus related to this paper: arath-At5g13640 , arath-AT5G24210 , arath-At5g24220 , arath-AT5G24230 , arath-At5g17670 , arath-Q9FN74 , arath-Q9FN79 , arath-Q9FNF6

Title : Structural analysis of Arabidopsis thaliana chromosome 5. III. Sequence features of the regions of 1,191,918 bp covered by seventeen physically assigned P1 clones - Nakamura_1997_DNA.Res_4_401
Author(s) : Nakamura Y , Sato S , Kaneko T , Kotani H , Asamizu E , Miyajima N , Tabata S
Ref : DNA Research , 4 :401 , 1997
Abstract : A total of 17 P1 and TAC clones each containing a marker(s) specifically mapped on chromosome 5 were isolated from P1 and TAC libraries of the Arabidopsis thaliana Columbia genome, and their nucleotide sequences were determined according to the shot gun-based strategy and precisely located on the physical map of chromosome 5. The total length of the clones sequenced in this study was 1,191,918 bp. As we have previously reported the sequence of 2,662,078 bp by analysis of 33 P1 clones, the total length of the sequences of chromosome 5 determined so far is now 3,853,996 bp. The sequences determined in this study were subjected to similarity search against protein and EST databases and analysis with computer programs for gene modeling, and a total of 310 potential protein-coding genes and/or gene segments with known or predicted functions were identified. The positions of exons which do not show apparent similarity to known genes were also predicted by computer-aided analysis. An average density of the assigned genes and/or gene segments was 1 gene/3,845 bp. Introns were identified in 78% of the potential protein genes, and the average number per gene and the average length of the introns were 3.7 and 185 bp, respectively. The numbers of the Arabidopsis ESTs matched to each of the predicted genes have been counted to monitor the transcription level. The sequence data and gene information are available on the World Wide Web database KAOS (Kazusa Arabidopsis data Opening Site) at http://www.kazusa.or.jp/arabi/.
ESTHER : Nakamura_1997_DNA.Res_4_401
PubMedSearch : Nakamura_1997_DNA.Res_4_401
PubMedID: 9501997
Gene_locus related to this paper: arath-AT5G22460 , arath-At5g42930 , arath-LIP2 , arath-SCPL34

Title : Structural analysis of Arabidopsis thaliana chromosome 5. I. Sequence features of the 1.6 Mb regions covered by twenty physically assigned P1 clones - Sato_1997_DNA.Res_4_215
Author(s) : Sato S , Kotani H , Nakamura Y , Kaneko T , Asamizu E , Fukami M , Miyajima N , Tabata S
Ref : DNA Research , 4 :215 , 1997
Abstract : A total of 20 P1 clones with an average insert size of 80 kb and each containing a marker(s) specifically mapped on chromosome 5 were isolated from a P1 library of the Arabidopsis thaliana genome, and their nucleotide sequences were determined according to a shotgun-based strategy and precisely located on the physical map of chromosome 5 separately constructed. The total length of the sequenced regions were summed up to 1,621,245 bp. By comparison with the sequences in protein and EST databases and analysis with computer programs for gene modeling, a total of 347 potential protein-coding genes and/or gene segments with known or predicted functions were identified. The positions of exons which do not exhibit any similarity to known genes were also predicted. An average density of the genes and/or gene segments assigned so far as 1 gene/4,672 bp. Introns were identified in approximately 78% of the potential genes, and the average number and length of the introns per gene were 3.7 and 161 bp. The transcription level of the predicted genes was roughly monitored by counting the numbers of identified Arabidopsis ESTs. The sequence data and gene information are available through the World Wide Web at http:/(/)www.kazusa.or.jp/arabi/.
ESTHER : Sato_1997_DNA.Res_4_215
PubMedSearch : Sato_1997_DNA.Res_4_215
PubMedID: 9330910
Gene_locus related to this paper: arath-AT5G38220 , arath-At5g38520 , arath-Q8LFB7 , arath-Q9FF27 , arath-q9ffg7 , arath-Q9FFZ1 , arath-SCP47 , arath-B9DFR3

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 : Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions - Kaneko_1996_DNA.Res_3_109
Author(s) : Kaneko T , Sato S , Kotani H , Tanaka A , Asamizu E , Nakamura Y , Miyajima N , Hirosawa M , Sugiura M , Sasamoto S , Kimura T , Hosouchi T , Matsuno A , Muraki A , Nakazaki N , Naruo K , Okumura S , Shimpo S , Takeuchi C , Wada T , Watanabe A , Yamada M , Yasuda M , Tabata S
Ref : DNA Research , 3 :109 , 1996
Abstract : The sequence determination of the entire genome of the Synechocystis sp. strain PCC6803 was completed. The total length of the genome finally confirmed was 3,573,470 bp, including the previously reported sequence of 1,003,450 bp from map position 64% to 92% of the genome. The entire sequence was assembled from the sequences of the physical map-based contigs of cosmid clones and of lambda clones and long PCR products which were used for gap-filling. The accuracy of the sequence was guaranteed by analysis of both strands of DNA through the entire genome. The authenticity of the assembled sequence was supported by restriction analysis of long PCR products, which were directly amplified from the genomic DNA using the assembled sequence data. To predict the potential protein-coding regions, analysis of open reading frames (ORFs), analysis by the GeneMark program and similarity search to databases were performed. As a result, a total of 3,168 potential protein genes were assigned on the genome, in which 145 (4.6%) were identical to reported genes and 1,257 (39.6%) and 340 (10.8%) showed similarity to reported and hypothetical genes, respectively. The remaining 1,426 (45.0%) had no apparent similarity to any genes in databases. Among the potential protein genes assigned, 128 were related to the genes participating in photosynthetic reactions. The sum of the sequences coding for potential protein genes occupies 87% of the genome length. By adding rRNA and tRNA genes, therefore, the genome has a very compact arrangement of protein- and RNA-coding regions. A notable feature on the gene organization of the genome was that 99 ORFs, which showed similarity to transposase genes and could be classified into 6 groups, were found spread all over the genome, and at least 26 of them appeared to remain intact. The result implies that rearrangement of the genome occurred frequently during and after establishment of this species.
ESTHER : Kaneko_1996_DNA.Res_3_109
PubMedSearch : Kaneko_1996_DNA.Res_3_109
PubMedID: 8905231
Gene_locus related to this paper: synsp-ester , synsp-PHBC , synsp-prxc , synsp-Q55130 , synsp-SLL0482 , synsp-sll0553 , synsp-SLL0992 , synsp-sll1305 , synsp-SLL1969 , synsp-SLR0825 , synsp-slr1235 , synsp-SLR1506 , synsp-SLR1771 , synsp-SLR1807 , synsp-slr1827 , synsp-slr1916 , synsp-slr1917 , synsp-slr1932 , synsp-SLR1944 , synsp-SLR2053 , synsp-todF , syny3-dlhh , syny3-P73192 , syny3-p73194 , syny3-y249 , syny3-y264

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 : Mutations of human butyrylcholinesterase gene in a family with hypocholinesterasemia -
Author(s) : Iida S , Kinoshita M , Fujii H , Moriyama Y , Nakamura Y , Yura N , Moriwaki K
Ref : Hum Mutat , 6 :349 , 1995
PubMedID: 8680411

Title : Determination of basal acetylcholine release in vivo by rat brain dialysis with a U-shaped cannula: effect of SM-10888, a putative therapeutic drug for Alzheimer's disease - Xu_1991_Neurosci.Lett_123_179
Author(s) : Xu M , Nakamura Y , Yamamoto T , Natori K , Irie T , Utsumi H , Kato T
Ref : Neuroscience Letters , 123 :179 , 1991
Abstract : A U-shaped dialysis cannula was implanted into rat frontal cortex, hippocampus and striatum, and after 1 day for surgical recovery the cannula was perfused with Ringer's solution without any acetylcholinesterase (AChE) inhibitor under freely moving conditions. With a highly sensitive assay method for acetylcholine (ACh), the basal ACh content in the dialysates were detectable in those brain regions for several hours. The basal levels in the frontal cortex, hippocampus and striatum were 82 +/- 9, 72 +/- 4, 70 +/- 8 fmol/20 microliters (mean +/- S.E.M.), respectively. When SM-10888, a novel AChE inhibitor and putative therapeutic drug for Alzheimer's disease, was injected intraperitoneally, ACh in the dialysate of the cortex increased in a dose-dependent manner. Changes in the levels of hippocampal and striatal ACh release evoked by SM-10888 were similar to, but smaller than, that in the cortex. These data suggest that since the present assay method is able to determine in vivo basal ACh release in the dialysate without any AChE inhibitor, it is possible to study the effect of a novel drug such as SM-10888 in the brain regions.
ESTHER : Xu_1991_Neurosci.Lett_123_179
PubMedSearch : Xu_1991_Neurosci.Lett_123_179
PubMedID: 2027531