Matsumoto M

References (20)

Title : Hepatic FASN deficiency differentially affects nonalcoholic fatty liver disease and diabetes in mouse obesity models - Matsukawa_2023_JCI.Insight_8__e161282
Author(s) : Matsukawa T , Yagi T , Uchida T , Sakai M , Mitsushima M , Naganuma T , Yano H , Inaba Y , Inoue H , Yanagida K , Uematsu M , Nakao K , Nakao H , Aiba A , Nagashima Y , Kubota T , Kubota N , Izumida Y , Yahagi N , Unoki-Kubota H , Kaburagi Y , Asahara SI , Kido Y , Shindou H , Itoh M , Ogawa Y , Minami S , Terauchi Y , Tobe K , Ueki K , Kasuga M , Matsumoto M
Ref : JCI Insight , 8 : , 2023
Abstract : Nonalcoholic fatty liver disease (NAFLD) and type 2 diabetes are interacting comorbidities of obesity, and increased hepatic de novo lipogenesis (DNL), driven by hyperinsulinemia and carbohydrate overload, contributes to their pathogenesis. Fatty acid synthase (FASN), a key enzyme of hepatic DNL, is upregulated in association with insulin resistance. However, the therapeutic potential of targeting FASN in hepatocytes for obesity-associated metabolic diseases is unknown. Here, we show that hepatic FASN deficiency differentially affects NAFLD and diabetes depending on the etiology of obesity. Hepatocyte-specific ablation of FASN ameliorated NAFLD and diabetes in melanocortin 4 receptor-deficient mice but not in mice with diet-induced obesity. In leptin-deficient mice, FASN ablation alleviated hepatic steatosis and improved glucose tolerance but exacerbated fed hyperglycemia and liver dysfunction. The beneficial effects of hepatic FASN deficiency on NAFLD and glucose metabolism were associated with suppression of DNL and attenuation of gluconeogenesis and fatty acid oxidation, respectively. The exacerbation of fed hyperglycemia by FASN ablation in leptin-deficient mice appeared attributable to impairment of hepatic glucose uptake triggered by glycogen accumulation and citrate-mediated inhibition of glycolysis. Further investigation of the therapeutic potential of hepatic FASN inhibition for NAFLD and diabetes in humans should thus consider the etiology of obesity.
ESTHER : Matsukawa_2023_JCI.Insight_8__e161282
PubMedSearch : Matsukawa_2023_JCI.Insight_8__e161282
PubMedID: 37681411
Gene_locus related to this paper: human-FASN , mouse-FASN

Title : Lipase-a single-nucleotide polymorphism rs143793106 is associated with increased risk of aggressive periodontitis by negative influence on the cytodifferentiation of human periodontal ligament cells - Matsumoto_2022_J.Periodontal.Res__
Author(s) : Matsumoto M , Fujihara C , Nantakeeratipat T , Kitagaki J , Yamamoto Y , Yamada S , Kitamura M , Murakami S
Ref : J Periodontal Res , : , 2022
Abstract : BACKGROUND AND OBJECTIVE: Aggressive periodontitis (AgP) is characterized by general health and rapid destruction of periodontal tissue. The familial aggregation of this disease highlights the involvement of genetic factors in its pathogeny. We conducted a genome-wide association study (GWAS) to identify AgP-related genes in a Japanese population, and the lipid metabolism-related gene, lipase-a, lysosomal acid type (LIPA), was suggested as an AgP candidate gene. However, there is no report about the expression and function(s) of LIPA in periodontal tissue. Hence, we studied the involvement of how LIPA and its single-nucleotide polymorphism (SNP) rs143793106 in AgP by functional analyses of LIPA and its SNP in human periodontal ligament (HPDL) cells. MATERIALS AND METHODS: GWAS was performed using the genome database of Japanese AgP patients, and the GWAS result was confirmed using Sanger sequencing. We examined the mRNA expression level of LIPA and the protein expression level of the encoded protein lysosomal acid lipase (LAL) in periodontium-composing cells using conventional and real-time polymerase chain reaction (PCR) and western blotting, respectively. Lentiviral vectors expressing LIPA wild-type (LIPA WT) and LIPA SNP rs143793106 (LIPA mut) were transfected into HPDL cells. Western blotting was performed to confirm the transfection. LAL activity of transfected HPDL cells was determined using the lysosomal acid lipase activity assay. Transfected HPDL cells were cultured in mineralization medium. During the cytodifferentiation of transfected HPDL cells, mRNA expression of calcification-related genes, alkaline phosphatase (ALPase) activity and calcified nodule formation were assessed using real-time PCR, ALPase assay, and alizarin red staining, respectively. RESULTS: The GWAS study identified 11 AgP-related candidate genes, including LIPA SNP rs143793106. The minor allele frequency of LIPA SNP rs143793106 in AgP patients was higher than that in healthy subjects. LIPA mRNA and LAL protein were expressed in HPDL cells; furthermore, they upregulated the cytodifferentiation of HPDL cells. LAL activity was lower in LIPA SNP-transfected HPDL cells during cytodifferentiation than that in LIPA WT-transfected HPDL cells. In addition, ALPase activity, calcified nodule formation, and calcification-related gene expression levels were lower during cytodifferentiation in LIPA SNP-transfected HPDL cells than those in LIPA WT-transfected HPDL cells. CONCLUSION: LIPA, identified as an AgP-related gene in a Japanese population, is expressed in HPDL cells and is involved in regulating cytodifferentiation of HPDL cells. LIPA SNP rs143793106 suppressed cytodifferentiation of HPDL cells by decreasing LAL activity, thereby contributing to the development of AgP.
ESTHER : Matsumoto_2022_J.Periodontal.Res__
PubMedSearch : Matsumoto_2022_J.Periodontal.Res__
PubMedID: 36494917

Title : Bassiamide A, a new alkaloid from xero-halophyte Bassia indica Wight - Othman_2021_Nat.Prod.Res__1
Author(s) : Othman A , Amen Y , Matsumoto M , Nagata M , Shimizu K
Ref : Nat Prod Res , :1 , 2021
Abstract : N-[(3-(3-methyl-1-oxo-butyl)amino)propyl]-3-(3,4-dihydroxyphenyl)prop-2-enamide (7), named 'Bassiamide A', a new alkaloid, together with six known compounds including one lignan (1) and five lignanamides (2-6), were isolated from the aerial parts of Bassia indica Wight. The study also reported an optimal separation of a rare occurring R-isomer lignanamide derivative (6) from a natural origin, in addition to its known corresponding S-isomer (5). Structures of isolated compounds were elucidated based on NMR spectroscopic data, HR-MS, and comparison with known related ones, and they were identified as syringaresinol (1), N-trans-feruloyl-3-methoxytyramine (2), N-trans-feruloyltyramine (3), S-(-)-N-trans-feruloyl normetanephrine (4), S-(-)-N-trans-feruloyl octopamine (5), R-(+)-N-trans-feruloyl octopamine (6). The isolated compounds were evaluated for their anti-acetylcholinesterase activity, and they showed weak inhibitory activity.
ESTHER : Othman_2021_Nat.Prod.Res__1
PubMedSearch : Othman_2021_Nat.Prod.Res__1
PubMedID: 33459047

Title : Treatment with anagliptin, a DPP-4 inhibitor, decreases FABP4 concentration in patients with type 2 diabetes mellitus at a high risk for cardiovascular disease who are receiving statin therapy - Furuhashi_2020_Cardiovasc.Diabetol_19_89
Author(s) : Furuhashi M , Sakuma I , Morimoto T , Higashiura Y , Sakai A , Matsumoto M , Sakuma M , Shimabukuro M , Nomiyama T , Arasaki O , Node K , Ueda S
Ref : Cardiovasc Diabetol , 19 :89 , 2020
Abstract : BACKGROUND: Fatty acid-binding protein 4 (FABP4) acts as a novel adipokine, and elevated FABP4 concentration is associated with obesity, insulin resistance and atherosclerosis. Dipeptidyl peptidase-4 (DPP-4) inhibitors, a class of antidiabetic drugs, have distinct structures among the drugs, possibly leading to a drug class effect and each drug effect. Sitagliptin, a DPP-4 inhibitor, has been reported to decrease FABP4 concentration in drug-naive and sulfonylurea-treated patients with type 2 diabetes mellitus. Anagliptin, another DPP-4 inhibitor, was shown to decrease low-density lipoprotein cholesterol (LDL-C) level to a greater extent than that by sitagliptin in the Randomized Evaluation of Anagliptin vs. Sitagliptin On low-density lipoproteiN cholesterol in diabetes (REASON) trial. AIM AND METHODS: As a sub-analysis study using data obtained from the REASON trial, we investigated the effects of treatment with anagliptin (n = 148, male/female: 89/59) and treatment with sitagliptin (n = 159, male/female: 93/66) for 52 weeks on FABP4 concentration in patients with type 2 diabetes mellitus at a high risk for cardiovascular events who were receiving statin therapy. RESULTS: The DPP-4 inhibitor had been administered in 82% of the patients in the anagliptin group and 81% of the patients in sitagliptin group prior to randomization. Serum FABP4 level was significantly decreased by 7.9% by treatment with anagliptin (P = 0.049) and was not significantly decreased by treatment with sitagliptin (P = 0.660). Change in FABP4 level was independently associated with basal FABP4 level and changes in waist circumference and creatinine after adjustment of age, sex and the treatment group. CONCLUSION: Anagliptin decreases serum FABP4 concentration independent of change in hemoglobin A1c or LDL-C in patients with type 2 diabetes mellitus and dyslipidemia who are on statin therapy. Trial registration ClinicalTrials.gov number NCT02330406.
ESTHER : Furuhashi_2020_Cardiovasc.Diabetol_19_89
PubMedSearch : Furuhashi_2020_Cardiovasc.Diabetol_19_89
PubMedID: 32539832

Title : Donepezil prevents RANK-induced bone loss via inhibition of osteoclast differentiation by downregulating acetylcholinesterase - Sato_2015_Heliyon_1_e00013
Author(s) : Sato T , Enoki Y , Sakamoto Y , Yokota K , Okubo M , Matsumoto M , Hayashi N , Usui M , Kokabu S , Mimura T , Nakazato Y , Araki N , Fukuda T , Okazaki Y , Suda T , Takeda S , Yoda T
Ref : Heliyon , 1 :e00013 , 2015
Abstract : OBJECTIVE: Donepezil, an inhibitor of acetylcholinesterase (AChE) targeting the brain, is a common medication for Alzheimer's disease. Interestingly, a recent clinical study found that administration of this agent is associated with lower risk of hip fracture independently of falling, suggesting its direct effect on bone tissues as well. AChE has been reported to be involved in osteoblast function, but the role of AChE on osteoclastogenesis still remains unclear. We analyzed the effect of AChE and donepezil on osteoclastogenesis in vivo and in vitro.
METHODS: Cell-based assays were conducted using osteoclasts generated in cultures of murine bone marrow macrophages (BMMs) with receptor activator of nuclear factor-kappa B ligand (RANKL). The effect of donepezil was also determined in vivo using a mouse model of RANKL-induced bone loss.
RESULTS: Recombinant AChE in BMMs cultured with RANKL further promoted RANKL-induced tartrate-resistant acid phosphatase (TRAP)-positive osteoclast differentiation. RANKL also upregulated AChE expression in BMMs. RNA interference-mediated knockdown of AChE significantly inhibited RANKL-induced osteoclast differentiation and suppressed gene expression specific for osteoclasts. AChE upregulated expression of RANK, the receptor of RANKL, in BMMs. Donepezil decreased cathepsin K expression in BMMs and the resorptive function of osteoclasts on dentine slices. Donepezil decreased RANK expression in BMMs, resulting in the inhibition of osteoclast differentiation with downregulation of c-Fos and upregulation of Id2. Moreover, administration of donepezil prevented RANKL-induced bone loss in vivo, which was associated with the inhibition of bone resorption by osteoclasts.
CONCLUSIONS: AChE promotes osteoclast differentiation in vitro. Donepezil inhibits osteoclast function in vitro and prevents bone loss by suppressing bone resorption in vivo, suggesting the possibility that donepezil reduces fracture risk in patients with Alzheimer's disease.
ESTHER : Sato_2015_Heliyon_1_e00013
PubMedSearch : Sato_2015_Heliyon_1_e00013
PubMedID: 27441211

Title : Oil accumulation by the oleaginous diatom Fistulifera solaris as revealed by the genome and transcriptome - Tanaka_2015_Plant.Cell_27_162
Author(s) : Tanaka T , Maeda Y , Veluchamy A , Tanaka M , Abida H , Marechal E , Bowler C , Muto M , Sunaga Y , Yoshino T , Taniguchi T , Fukuda Y , Nemoto M , Matsumoto M , Wong PS , Aburatani S , Fujibuchi W
Ref : Plant Cell , 27 :162 , 2015
Abstract : Oleaginous photosynthetic organisms such as microalgae are promising sources for biofuel production through the generation of carbon-neutral sustainable energy. However, the metabolic mechanisms driving high-rate lipid production in these oleaginous organisms remain unclear, thus impeding efforts to improve productivity through genetic modifications. We analyzed the genome and transcriptome of the oleaginous diatom Fistulifera solaris JPCC DA0580. Next-generation sequencing technology provided evidence of an allodiploid genome structure, suggesting unorthodox molecular evolutionary and genetic regulatory systems for reinforcing metabolic efficiencies. Although major metabolic pathways were shared with nonoleaginous diatoms, transcriptome analysis revealed unique expression patterns, such as concomitant upregulation of fatty acid/triacylglycerol biosynthesis and fatty acid degradation (beta-oxidation) in concert with ATP production. This peculiar pattern of gene expression may account for the simultaneous growth and oil accumulation phenotype and may inspire novel biofuel production technology based on this oleaginous microalga.
ESTHER : Tanaka_2015_Plant.Cell_27_162
PubMedSearch : Tanaka_2015_Plant.Cell_27_162
PubMedID: 25634988

Title : Effect of fasting on PPARgamma and AMPK activity in adipocytes - Kajita_2008_Diabetes.Res.Clin.Pract_81_144
Author(s) : Kajita K , Mune T , Ikeda T , Matsumoto M , Uno Y , Sugiyama C , Matsubara K , Morita H , Takemura M , Seishima M , Takeda J , Ishizuka T
Ref : Diabetes Res Clin Pract , 81 :144 , 2008
Abstract : We investigated the effects of fasting on gene expression and intracellular signals regulating energy metabolism in adipose tissue. Following fasting for 15h or 39h, epididymal fat pads were isolated from Wistar rats. PPARgamma mRNA levels decreased in the adipose tissues isolated from rats fasted for 39h, whereas adipocyte lipid-binding protein (aP2) and lipoprotein lipase (LPL) mRNA levels increased. Overnight fasting increased the AMP/ATP ratio and AMP-activated protein kinase (AMPK) in adipose tissue, but not in muscle or liver tissue. In addition, the effect of 5-aminoimidazole-4-carboxyamide-ribonucleoside (AICAR) on PPARgamma expression in primary cultured adipocytes was investigated. AICAR reduced PPARgamma mRNA levels but increased aP2 and LPL mRNA levels. Thus, fasting-induced AMPK activation may affect on the regulation of gene expression in adipocytes.
ESTHER : Kajita_2008_Diabetes.Res.Clin.Pract_81_144
PubMedSearch : Kajita_2008_Diabetes.Res.Clin.Pract_81_144
PubMedID: 18562038

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 : 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 : 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 : Dizocilpine but not ketamine reduces the volume of ischaemic damage after acute subdural haematoma in the rat - Uchida_2001_Eur.J.Anaesthesiol_18_295
Author(s) : Uchida K , Nakakimura K , Kuroda Y , Haranishi Y , Matsumoto M , Sakabe T
Ref : European Journal of Anaesthesiologyiol , 18 :295 , 2001
Abstract : BACKGROUND AND OBJECTIVE: Increased glutamate concentration in the cerebrospinal fluid has been reported in severely head-injured patients, suggesting that an excessive release of glutamate may be involved in the process of neuronal damage. Ischaemic damage after subdural haematoma has been reported to be reduced by glutamate (N-methyl-D-aspartate: NMDA) receptor antagonists such as dizocilpine and CGS 19755; even though these drugs were given 20-30 min after insult. Excessive release of excitatory amino acids may produce the neural damage after subdural haematoma and NMDA receptor antagonists may become valuable therapeutic drugs. This study compared the effects of ketamine and dizocilpine, on intracranial pressure and histopathological changes after acute subdural haematoma produced by an injection of autologous blood (150 microL) in rats.
METHODS: The control (n = 9), ketamine (n = 9) and dizocilpine (n = 9) groups, respectively, received saline, ketamine (total dose: 210 mg kg-1) or dizocilpine (total dose: 1.0 mg kg-1) from 0.5 to 8 h after acute subdural haematoma. A silicone group (n = 9) had the same volume of silicone injected subdurally.
RESULTS: The volume of ischaemic damage in the silicone group (1.3 +/- 1.2 mm3) was significantly smaller than in the control group (11.9 +/- 3.8 mm3). Ketamine and dizocilpine did not increase intracranial pressure. Dizocilpine significantly decreased the volume of ischaemic damage (6.1 +/- 3.8 mm3). Ketamine failed to significantly decrease damage (7.8 +/- 5.0 mm3).
CONCLUSIONS: These results suggest that the factors elicited by the clotted blood contribute to the ischaemic damage after subdural haematoma, and that the glutamate receptor antagonist dizocilpine reduces the damage, while ketamine shows only a trend reduction of the damage.
ESTHER : Uchida_2001_Eur.J.Anaesthesiol_18_295
PubMedSearch : Uchida_2001_Eur.J.Anaesthesiol_18_295
PubMedID: 11350471

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 : 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 : 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 : 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 : Characterization of serum platelet-activating factor (PAF) acetylhydrolase. Correlation between deficiency of serum PAF acetylhydrolase and respiratory symptoms in asthmatic children - Miwa_1988_J.Clin.Invest_82_1983
Author(s) : Miwa M , Miyake T , Yamanaka T , Sugatani J , Suzuki Y , Sakata S , Araki Y , Matsumoto M
Ref : J Clinical Investigation , 82 :1983 , 1988
Abstract : Platelet-activating factor (PAF) acetylhydrolase has been recognized as an enzyme that inactivates PAF. We developed a convenient and reproducible method for determining human serum PAF acetylhydrolase activity. The assay was based on measurement of [14C]acetate produced from 1-O-alkyl-2-[14C]-acetyl-sn-glycero-3-phosphocholine upon precipitation of the complex of radioactive substrate and albumin with TCA. The apparent Km value of PAF acetylhydrolase (near the physiological concentration of serum protein) was 1.5 X 10(-4) M PAF. 32 subjects with serum PAF acetylhydrolase deficiency were found among 816 healthy Japanese adults. The low PAF acetylhydrolase activity in the deficient serum might not be due to the presence of enzyme inhibitor. Both the sensitivity to PAF and the metabolism of PAF in platelets from PAF acetylhydrolase-deficient subjects were almost the same as those of normal subjects. Deficiency in serum PAF acetylhydrolase appeared to be transmitted by autosomal recessive heredity among five Japanese families. Among healthy adults, healthy children, and asthmatic children, who were grouped into five classes on the basis of respiratory symptoms (remission, wheezy, mild, moderate, and severe groups), the probability of PAF acetylhydrolase deficiency was significantly higher in groups with severe symptoms (moderate and severe) (P less than 0.01). These results suggest that deficiency of serum PAF acetylhydrolase might be one of the factors leading to severe respiratory symptoms in asthmatic children.
ESTHER : Miwa_1988_J.Clin.Invest_82_1983
PubMedSearch : Miwa_1988_J.Clin.Invest_82_1983
PubMedID: 3198761
Gene_locus related to this paper: human-PLA2G7

Title : Enzyme histochemical studies on the hypothalamus of spontaneously hypertensive rats with special reference to that of rats subjected to various endocrine interferences -
Author(s) : Okamoto K , Tabei R , Nosaka S , Fukushima A , Yamori Y , Matsumoto M , Yamabe H , Morisawa T , Suzuki Y , Tamegai M
Ref : Japanese Circulation Journal , 30 :1483 , 1966
PubMedID: 4290391