Suzuki Y

References (76)

Title : Physiological roles and regulation of hepatic angiopoietin-like protein 3 in Japanese Black cattle (Bos taurus) during the fattening period - Shikida_2023_J.Anim.Sci__
Author(s) : Shikida R , Kim M , Futohashi M , Nishihara K , Lee H , Suzuki Y , Baek Y , Masaki T , Ikuta K , Iwamoto E , Uemoto Y , Haga S , Terada F , Roh S
Ref : J Anim Sci , : , 2023
Abstract : Angiopoietin-like protein 3 (ANGPTL3) is expressed predominantly in the liver and plays a major role in regulating the circulating triglyceride and lipoprotein fraction concentrations by inhibiting lipoprotein lipase (LPL) activity. Given these physiological roles, ANGPTL3 may play an important role in metabolic changes related to fat accumulation during the fattening period in Japanese Black. This study aimed to reveal the physiological roles of hepatic ANGPTL3 in Japanese Black steers (Bos taurus) during the fattening period and investigate the regulatory effects of hepatic ANGPTL3. To investigate the gene expression and protein localization of ANGPTL3, 18 tissue samples were collected from tree male Holstein bull calves aged 7 weeks. Biopsied liver tissues and blood samples were collected from 21 Japanese Black steers during the early (T1; 13 months of age), middle (T2; 20 months), and late fattening phases (T3; 28 months). Relative mRNA expression, blood metabolite concentrations, hormone concentrations, growth, and carcass traits were analyzed. To identify the regulatory factors of hepatic ANGPTL3, primary bovine hepatocytes collected by 2 Holstein calves aged 7 weeks were incubated with insulin, palmitate, oleate, propionate, acetate, or beta-hydroxybutyric acid (BHBA). The ANGPTL3 gene was most highly expressed in the liver, with minor expression in the renal cortex, lungs, reticulum, and jejunum in Holstein bull calves. In Japanese Black steers, relative ANGPTL3 mRNA expressions were less as fattening progressed, and blood triglyceride, total cholesterol, and non-esterified fatty acid (NEFA) concentrations increased. Relative ANGPTL8 and Liver X receptor alpha (LXRalpha) mRNA expressions decreased in late and middle fattening phases, respectively. Furthermore, relative ANGTPL3 mRNA expression was positively correlated with ANGPTL8 (r = 0.650; P < 0.01) and ANGPTL4 (r = 0.540; P < 0.05) in T3 and T1, respectively, and LXRalpha showed no correlation with ANGPTL3. Relative ANGTPL3 mRNA expression was negatively correlated with total cholesterol (r = -0.434; P < 0.05) and triglyceride (r = -0.645; P < 0.01) concentrations in T3 and T1, respectively; There was no significant correlation between ANGTPL3 and carcass traits. Relative ANGTPL3 mRNA expression in cultured bovine hepatocytes was downregulated in oleate treatment. Together, these findings suggest that ANGPTL3 downregulation in late fattening phases is associated with the changes in lipid metabolism.
ESTHER : Shikida_2023_J.Anim.Sci__
PubMedSearch : Shikida_2023_J.Anim.Sci__
PubMedID: 37317898

Title : Glycaemic control efficacy of switching from dipeptidyl peptidase-4 inhibitors to oral semaglutide in subjects with type 2 diabetes: A multicentre, prospective, randomized, open-label, parallel-group comparison study (SWITCH-SEMA 2 study) - Furusawa_2023_Diabetes.Obes.Metab__
Author(s) : Furusawa S , Nomoto H , Yokoyama H , Suzuki Y , Tsuzuki A , Takahashi K , Miya A , Kameda H , Cho KY , Takeuchi J , Nagai S , Taneda S , Kurihara Y , Nakamura A , Atsumi T
Ref : Diabetes Obes Metab , : , 2023
Abstract : AIM: To assess whether oral semaglutide provides better glycaemic control, compared with dipeptidyl peptidase-4 inhibitor (DPP-4i) continuation, in people with type 2 diabetes. MATERIALS AND METHODS: In this multicentre, open-label, prospective, randomized, parallel-group comparison study, participants receiving DPP-4is were either switched to oral semaglutide (3-14 mg/day) or continued on DPP-4is. The primary endpoint was the change in glycated haemoglobin (HbA1c) over 24 weeks. Secondary endpoints included changes in metabolic parameters and biomarkers, along with the occurrence of adverse events. Factors associated with HbA1c improvement were also explored. RESULTS: In total, 174 eligible participants were enrolled; 17 dropped out of the study. Consequently, 82 participants in the DPP-4i group and 75 participants in the semaglutide group completed the study and were included in the analysis. Improvement in HbA1c at week 24 was significantly greater when switching to semaglutide compared with DPP-4i continuation [-0.65 (95% confidence interval: -0.79, -0.51) vs. +0.05 (95% confidence interval: -0.07, 0.16) (p < .001)]. Body weight, lipid profiles and liver enzymes were significantly improved in the semaglutide group than in the DPP-4i continuation group. Multiple linear regression analysis revealed that baseline HbA1c and homeostasis model assessment 2-R were independently associated with HbA1c improvement after switching to semaglutide. Seven participants in the semaglutide group discontinued medication because of gastrointestinal symptoms. CONCLUSIONS: Although the potential for gastrointestinal symptoms should be carefully considered, switching from DPP-4is to oral semaglutide may be beneficial for glycaemic control and metabolic abnormalities in people with higher HbA1c and insulin resistance.
ESTHER : Furusawa_2023_Diabetes.Obes.Metab__
PubMedSearch : Furusawa_2023_Diabetes.Obes.Metab__
PubMedID: 38073422

Title : A New Anesthetic, Remimazolam, Is Useful in the Management of Anesthesia in Patients with Liver Cirrhosis - Onoda_2022_Case.Rep.Anesthesiol_2022_9268454
Author(s) : Onoda A , Suzuki Y
Ref : Case Rep Anesthesiol , 2022 :9268454 , 2022
Abstract : BACKGROUND: Management of general anesthesia in patients with liver cirrhosis is challenging because it is difficult to maintain the circulation and concentration of anesthetics within a safe range. Unlike many other anesthetics, which are metabolized by cytochrome P450 enzymes, remimazolam is metabolized by carboxylesterase. In a liver cirrhosis model, cytochrome P450 activity is suppressed by approximately 30%; however, carboxylesterase activity is maintained at approximately 60%. Also, remimazolam is less likely to inhibit circulation. A 77-year-old woman was scheduled to undergo laparoscopic cholecystectomy. The patient was diagnosed with Child-Pugh B liver cirrhosis due to type C viral hepatitis. General anesthesia with remimazolam stabilized the intraoperative circulation and resulted in rapid postoperative awakening. CONCLUSION: We report a case in which a patient with Child-Pugh B cirrhosis was safely managed under general anesthesia using remimazolam during laparoscopic cholecystectomy.
ESTHER : Onoda_2022_Case.Rep.Anesthesiol_2022_9268454
PubMedSearch : Onoda_2022_Case.Rep.Anesthesiol_2022_9268454
PubMedID: 35578641

Title : Imaging mass spectrometry to visualise increased acetylcholine in lungs of asthma model mice - Matsuda_2020_Anal.Bioanal.Chem__
Author(s) : Matsuda T , Suzuki Y , Fujisawa T , Suga Y , Saito N , Suda T , Yao I
Ref : Anal Bioanal Chem , : , 2020
Abstract : Acetylcholine (ACh) is a crucial neurotransmitter that is involved in airway constriction. In fact, excessive ACh binding to M3 muscarinic receptor leads to airflow obstruction via smooth muscle contraction. Previous studies have suggested cholinergic malfunction in the pathogenesis of asthma; however, the distribution and abundance of ACh in asthmatic lungs remain unclear because of the challenges of imaging ACh in lung tissue. In this study, we successfully detected and visualised ACh in mouse lung tissue by using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). Here, we applied the ACh imaging method to the two groups of house dust mite-sensitised asthma model mice harbouring different inflammatory levels. The imaging results showed that the lungs of mice had a relatively uniform ACh distribution with some areas of heterogeneity. The lungs of asthma model mice had significantly more ACh than control mice, and the ACh increase was potentiated with intense eosinophil infiltration without acetylcholinesterase deficits. These results indicate that ACh hypersecretion is mediated by an increased infiltration of eosinophils in asthma aggravation. This study provides the first evidence that secreted ACh is elevated with asthma severity in the lungs of asthma model animals by a direct ACh imaging technique with FT-ICR-MS.
ESTHER : Matsuda_2020_Anal.Bioanal.Chem__
PubMedSearch : Matsuda_2020_Anal.Bioanal.Chem__
PubMedID: 32367293

Title : Protective effects of DPP-4 inhibitor on podocyte injury in glomerular diseases - Kubo_2020_BMC.Nephrol_21_402
Author(s) : Kubo A , Hidaka T , Nakayama M , Sasaki Y , Takagi M , Suzuki H , Suzuki Y
Ref : BMC Nephrol , 21 :402 , 2020
Abstract : BACKGROUND: Dipeptidyl peptidase-4 (DPP-4) is a serine protease that inhibits the degradation of glucagon-like peptide 1. DPP-4 inhibitors are used worldwide to treat type 2 diabetes mellitus and were recently shown to have pleiotropic effects such as anti-oxidant, anti-inflammatory, and anti-fibrotic actions. DPP-4 inhibitors improve albuminuria and renal injury including glomerular damage independent of its hypoglycemic effect. Although DPP-4 is mainly expressed in the kidney, the physiological function of DPP-4 remains unclear. METHODS: The localization of renal DPP-4 activity was determined in human renal biopsy specimens with glycyl-1-prolyl-4-methoxy-2-naphthylamide and the effects of a DPP-4 inhibitor were examined in human cultured podocyte. RESULTS: DPP-4 activity under normal conditions was observed in some Bowman's capsular epithelial cells and proximal tubules, but not in the glomerulus. DPP-4 activity was observed in crescent formation in anti-neutrophil myeloperoxidase cytoplasmic antigen antibody nephritis, nodular lesions in diabetic nephropathy, and some podocytes in focal segmental glomerulosclerosis. Notably, the DPP-4 inhibitor saxagliptin suppressed DPP-4 activity in podocytes and the proximal tubules. To assess the effect of DPP-4 inhibitor on podocytes, human cultured podocytes were injured by Adriamycin, which increased DPP-4 activity; this activity was dose-dependently suppressed by saxagliptin. Treatment with saxagliptin maintained the structure of synaptopodin and RhoA. Saxagliptin also improved the detachment of podocytes. CONCLUSIONS: DPP-4 activity induces degradation of synaptopodin and reduction of RhoA, resulting in destruction of the podocyte cytoskeleton. Saxagliptin may have pleiotropic effects to prevent podocyte injury.
ESTHER : Kubo_2020_BMC.Nephrol_21_402
PubMedSearch : Kubo_2020_BMC.Nephrol_21_402
PubMedID: 32948146

Title : Crystal structures of a bacterial dipeptidyl peptidase IV reveal a novel substrate recognition mechanism distinct from that of mammalian orthologues - Roppongi_2018_Sci.Rep_8_2714
Author(s) : Roppongi S , Suzuki Y , Tateoka C , Fujimoto M , Morisawa S , Iizuka I , Nakamura A , Honma N , Shida Y , Ogasawara W , Tanaka N , Sakamoto Y , Nonaka T
Ref : Sci Rep , 8 :2714 , 2018
Abstract : Dipeptidyl peptidase IV (DPP IV, DPP4, or DAP IV) preferentially cleaves substrate peptides with Pro or Ala at the P1 position. The substrate recognition mechanism has been fully elucidated for mammalian DPP IV by crystal structure analyses but not for bacterial orthologues. Here, we report the crystal structures of a bacterial DPP IV (PmDAP IV) in its free form and in complexes with two kinds of dipeptides as well as with a non-peptidyl inhibitor at 1.90 to 2.47 A resolution. Acyl-enzyme intermediates were observed for the dipeptide complexes of PmDAP IV, whereas tetrahedral intermediates were reported for the oligopeptide complexes of mammalian DPP IVs. This variation reflects the different structural environments of the active site Arg residues, which are involved in the recognition of a substrate carbonyl group, of mammalian and bacterial enzymes. A phylogenetic analysis revealed that PmDAP IV is a closer relative of dipeptidyl peptidases 8 and 9 (DPP8 and DPP9, DPP IV-family enzymes) than DPP IV. These results provide new insights into the substrate recognition mechanism of bacterial DAP IVs and may assist in the development of selective inhibitors for DAP IVs from pathogenic asaccharolytic bacteria, which utilise proteins or peptides as an energy source.
ESTHER : Roppongi_2018_Sci.Rep_8_2714
PubMedSearch : Roppongi_2018_Sci.Rep_8_2714
PubMedID: 29426867
Gene_locus related to this paper: 9psed-q6f3i7

Title : The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization - Nishiyama_2018_Cell_174_448
Author(s) : Nishiyama T , Sakayama H , de Vries J , Buschmann H , Saint-Marcoux D , Ullrich KK , Haas FB , Vanderstraeten L , Becker D , Lang D , Vosolsobe S , Rombauts S , Wilhelmsson PKI , Janitza P , Kern R , Heyl A , Rumpler F , Villalobos L , Clay JM , Skokan R , Toyoda A , Suzuki Y , Kagoshima H , Schijlen E , Tajeshwar N , Catarino B , Hetherington AJ , Saltykova A , Bonnot C , Breuninger H , Symeonidi A , Radhakrishnan GV , Van Nieuwerburgh F , Deforce D , Chang C , Karol KG , Hedrich R , Ulvskov P , Glockner G , Delwiche CF , Petrasek J , Van de Peer Y , Friml J , Beilby M , Dolan L , Kohara Y , Sugano S , Fujiyama A , Delaux PM , Quint M , Theissen G , Hagemann M , Harholt J , Dunand C , Zachgo S , Langdale J , Maumus F , Van Der Straeten D , Gould SB , Rensing SA
Ref : Cell , 174 :448 , 2018
Abstract : Land plants evolved from charophytic algae, among which Charophyceae possess the most complex body plans. We present the genome of Chara braunii; comparison of the genome to those of land plants identified evolutionary novelties for plant terrestrialization and land plant heritage genes. C. braunii employs unique xylan synthases for cell wall biosynthesis, a phragmoplast (cell separation) mechanism similar to that of land plants, and many phytohormones. C. braunii plastids are controlled via land-plant-like retrograde signaling, and transcriptional regulation is more elaborate than in other algae. The morphological complexity of this organism may result from expanded gene families, with three cases of particular note: genes effecting tolerance to reactive oxygen species (ROS), LysM receptor-like kinases, and transcription factors (TFs). Transcriptomic analysis of sexual reproductive structures reveals intricate control by TFs, activity of the ROS gene network, and the ancestral use of plant-like storage and stress protection proteins in the zygote.
ESTHER : Nishiyama_2018_Cell_174_448
PubMedSearch : Nishiyama_2018_Cell_174_448
PubMedID: 30007417
Gene_locus related to this paper: chabu-a0a388kgf1 , chabu-a0a388jwy2

Title : Cholinesterase levels predict exercise capacity in cardiac recipients early after transplantation - Kitagaki_2018_Clin.Transplant_32_
Author(s) : Kitagaki K , Nakanishi M , Ono R , Yamamoto K , Suzuki Y , Fukui N , Yanagi H , Konishi H , Yanase M , Fukushima N
Ref : Clin Transplant , 32 : , 2018
Abstract : PURPOSE: Although cardiac rehabilitation is recommended for patients early after heart transplantation (HTx), adequate exercise effect cannot always be obtained, partly because in patients with chronic heart failure, exercise capacity is reduced due to malnutrition while waiting for HTx. This study aimed to investigate the relationships between exercise capacity and clinical variables, including nutritional indicators, early after HTx. PATIENTS AND METHODS: Forty-three HTx recipients were studied. The mean age at HTx was 38 +/- 14 years, and 86% were male. We assessed the relationships between peak oxygen uptake (VO2 ) and clinical variables, including plasma B-type natriuretic peptide (BNP), isometric knee extensor muscle strength (KEMS), and nutritional indicators within 1 week of their respective discharges. RESULTS: Peak VO2 correlated positively with isometric KEMS (r = .63, P < .0001) and negatively with BNP level (r = -.37, P = .015). Of the nutritional indicators, only cholinesterase levels had a significant relationship with peak VO2 (r = .34, P = .028), whereas the Geriatric Nutritional Risk Index and the Controlling Nutritional Status scores did not. In multiple linear regression analysis, cholinesterase levels and isometric KEMS were independent predictors of peak VO2 . CONCLUSION: Cholinesterase levels predicted exercise capacity early after HTx.
ESTHER : Kitagaki_2018_Clin.Transplant_32_
PubMedSearch : Kitagaki_2018_Clin.Transplant_32_
PubMedID: 29194762

Title : Periplasmic form of dipeptidyl aminopeptidase IV from Pseudoxanthomonas mexicana WO24: purification, kinetic characterization, crystallization and X-ray crystallographic analysis - Roppongi_2017_Acta.Crystallogr.F.Struct.Biol.Commun_73_601
Author(s) : Roppongi S , Tateoka C , Fujimoto M , Iizuka I , Morisawa S , Nakamura A , Honma N , Suzuki Y , Shida Y , Ogasawara W , Tanaka N , Sakamoto Y , Nonaka T
Ref : Acta Crystallographica F Struct Biol Commun , 73 :601 , 2017
Abstract : Dipeptidyl aminopeptidase IV (DAP IV or DPP IV) from Pseudoxanthomonas mexicana WO24 (PmDAP IV) preferentially cleaves substrate peptides with Pro or Ala at the P1 position [NH2-P2-P1(Pro/Ala)-P1'-P2'...]. For crystallographic studies, the periplasmic form of PmDAP IV was overproduced in Escherichia coli, purified and crystallized in complex with the tripeptide Lys-Pro-Tyr using the hanging-drop vapour-diffusion method. Kinetic parameters of the purified enzyme against a synthetic substrate were also determined. X-ray diffraction data to 1.90 A resolution were collected from a triclinic crystal form belonging to space group P1, with unit-cell parameters a = 88.66, b = 104.49, c = 112.84 A, alpha = 67.42, beta = 68.83, gamma = 65.46 degrees . Initial phases were determined by the molecular-replacement method using Stenotrophomonas maltophilia DPP IV (PDB entry 2ecf) as a template and refinement of the structure is in progress.
ESTHER : Roppongi_2017_Acta.Crystallogr.F.Struct.Biol.Commun_73_601
PubMedSearch : Roppongi_2017_Acta.Crystallogr.F.Struct.Biol.Commun_73_601
PubMedID: 29095153
Gene_locus related to this paper: 9psed-q6f3i7

Title : Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments - Hernsdorf_2017_ISME.J_11_1915
Author(s) : Hernsdorf AW , Amano Y , Miyakawa K , Ise K , Suzuki Y , Anantharaman K , Probst A , Burstein D , Thomas BC , Banfield JF
Ref : Isme J , 11 :1915 , 2017
Abstract : Geological sequestration in deep underground repositories is the prevailing proposed route for radioactive waste disposal. After the disposal of radioactive waste in the subsurface, H2 may be produced by corrosion of steel and, ultimately, radionuclides will be exposed to the surrounding environment. To evaluate the potential for microbial activities to impact disposal systems, we explored the microbial community structure and metabolic functions of a sediment-hosted ecosystem at the Horonobe Underground Research Laboratory, Hokkaido, Japan. Overall, we found that the ecosystem hosted organisms from diverse lineages, including many from the phyla that lack isolated representatives. The majority of organisms can metabolize H2, often via oxidative [NiFe] hydrogenases or electron-bifurcating [FeFe] hydrogenases that enable ferredoxin-based pathways, including the ion motive Rnf complex. Many organisms implicated in H2 metabolism are also predicted to catalyze carbon, nitrogen, iron and sulfur transformations. Notably, iron-based metabolism is predicted in a novel lineage of Actinobacteria and in a putative methane-oxidizing ANME-2d archaeon. We infer an ecological model that links microorganisms to sediment-derived resources and predict potential impacts of microbial activity on H2 consumption and retardation of radionuclide migration.
ESTHER : Hernsdorf_2017_ISME.J_11_1915
PubMedSearch : Hernsdorf_2017_ISME.J_11_1915
PubMedID: 28350393
Gene_locus related to this paper: 9eury-a0a2i0pxa9 , 9spir-a0a2n1tka6 , 9firm-a0a2n2bq22 , 9firm-a0a2n2cxr7 , 9prot-a0a2n3dmk3 , 9delt-a0a2n2m1c4 , 9bact-a0a2i0q977 , 9bact-a0a2n1vaz9 , 9bact-a0a2n2vup6 , 9bact-a0a2n2w5u3 , 9bact-a0a2n2wjd9 , 9bact-a0a2n2wss4 , 9bact-a0a2n2xcb2 , 9bact-a0a2n2ylq2 , 9bact-a0a2n2yyx7 , 9bact-a0a2n2z6r2 , 9bact-a0a2n2ziv6 , 9bact-a0a2n3aau1

Title : Relationship between cardiac autonomic function and cognitive function in Alzheimer's disease - Nonogaki_2017_Geriatr.Gerontol.Int_17_92
Author(s) : Nonogaki Z , Umegaki H , Makino T , Suzuki Y , Kuzuya M
Ref : Geriatr Gerontol Int , 17 :92 , 2017
Abstract : AIM: Alzheimer's disease (AD) affects many central nervous structures and neurotransmitter systems. These changes affect not only cognitive function, but also cardiac autonomic function. However, the functional relationship between cardiac autonomic function and cognition in AD has not yet been investigated. The objective of the present study was to evaluate the association between cardiac autonomic function measured by heart rate variability and cognitive function in AD.
METHODS: A total of 78 AD patients were recruited for this study. Cardiac autonomic function was evaluated using heart rate variability analysis. Multiple linear regression analysis was used to model the association between heart rate variability and cognitive function (global cognitive function, memory, executive function and processing speed), after adjustment for covariates.
RESULTS: Global cognitive function was negatively associated with sympathetic modulation (low-to-high frequency power ratio). Memory performance was positively associated with parasympathetic modulation (high frequency power) and negatively associated with sympathetic modulation (low-to-high frequency power ratio). These associations were independent of age, sex, educational years, diabetes, hypertension and cholinesterase inhibitor use.
CONCLUSIONS: Cognitive function, especially in the areas of memory, is associated with cardiac autonomic function in AD. Specifically, lower cognitive performance was found to be associated with significantly higher cardiac sympathetic and lower parasympathetic function in AD. Geriatr Gerontol Int 2017; 17: 92-98.
ESTHER : Nonogaki_2017_Geriatr.Gerontol.Int_17_92
PubMedSearch : Nonogaki_2017_Geriatr.Gerontol.Int_17_92
PubMedID: 26643357

Title : Acute cholinergic syndrome in a patient with mild Alzheimer's type dementia who had applied a large number of rivastigmine transdermal patches on her body - Suzuki_2017_Clin.Toxicol.(Phila)__1
Author(s) : Suzuki Y , Kamijo Y , Yoshizawa T , Fujita Y , Usui K , Kishino T
Ref : Clinical Toxicology (Phila) , :1 , 2017
Abstract : CASE PRESENTATION: A 91-year-old woman was transferred to our Emergency Medical Center and Poison Center with somnolence, hypertension (186/61 mm Hg), and repeated vomiting. Three hours later, 10 transdermal patches, each containing 18 mg of rivastigmine (9.5 mg/24 h), were found on her lower back and both thighs, when miosis, facial and trunk sweating, enhanced bowel sound, hypertension, and sinus tachycardia were noted. She was diagnosed with acute cholinergic syndrome due to rivastigmine poisoning. Her hypertension and sinus tachycardia peaked 8 and 5 h after all the patches were removed, respectively. Her symptoms subsided spontaneously after 17 h. DISCUSSION: In the present case, our patient was presented with acute cholinergic syndrome due to carbamate intoxication after massive transdermal exposure to rivastigmine. Toxicological analysis revealed a remarkably high estimated serum rivastigmine concentration (150.6 ng/ml) and notably low serum butyrylcholinesterase activity (35 IU/l) on admission, with a markedly prolonged calculated elimination half-life of 6.5 h.
CONCLUSIONS: Emergency physicians should consider acetylcholinesterase inhibitor exposure (e.g., rivastigmine) when patients are present with acute cholinergic syndrome.
ESTHER : Suzuki_2017_Clin.Toxicol.(Phila)__1
PubMedSearch : Suzuki_2017_Clin.Toxicol.(Phila)__1
PubMedID: 28594244

Title : Extremotolerant tardigrade genome and improved radiotolerance of human cultured cells by tardigrade-unique protein - Hashimoto_2016_Nat.Commun_7_12808
Author(s) : Hashimoto T , Horikawa DD , Saito Y , Kuwahara H , Kozuka-Hata H , Shin IT , Minakuchi Y , Ohishi K , Motoyama A , Aizu T , Enomoto A , Kondo K , Tanaka S , Hara Y , Koshikawa S , Sagara H , Miura T , Yokobori S , Miyagawa K , Suzuki Y , Kubo T , Oyama M , Kohara Y , Fujiyama A , Arakawa K , Katayama T , Toyoda A , Kunieda T
Ref : Nat Commun , 7 :12808 , 2016
Abstract : Tardigrades, also known as water bears, are small aquatic animals. Some tardigrade species tolerate almost complete dehydration and exhibit extraordinary tolerance to various physical extremes in the dehydrated state. Here we determine a high-quality genome sequence of Ramazzottius varieornatus, one of the most stress-tolerant tardigrade species. Precise gene repertoire analyses reveal the presence of a small proportion (1.2% or less) of putative foreign genes, loss of gene pathways that promote stress damage, expansion of gene families related to ameliorating damage, and evolution and high expression of novel tardigrade-unique proteins. Minor changes in the gene expression profiles during dehydration and rehydration suggest constitutive expression of tolerance-related genes. Using human cultured cells, we demonstrate that a tardigrade-unique DNA-associating protein suppresses X-ray-induced DNA damage by approximately 40% and improves radiotolerance. These findings indicate the relevance of tardigrade-unique proteins to tolerability and tardigrades could be a bountiful source of new protection genes and mechanisms.
ESTHER : Hashimoto_2016_Nat.Commun_7_12808
PubMedSearch : Hashimoto_2016_Nat.Commun_7_12808
PubMedID: 27649274
Gene_locus related to this paper: ramva-a0a1d1uki4 , ramva-a0a1d1uvm7 , ramva-a0a1d1ula4 , ramva-a0a1d1v5e3 , ramva-a0a1d1unv1 , ramva-a0a1d1vjq5 , ramva-a0a1d1vlp2 , ramva-a0a1d1vh75 , ramva-a0a1d1vzz5

Title : Genome evolution in the allotetraploid frog Xenopus laevis - Session_2016_Nature_538_336
Author(s) : Session AM , Uno Y , Kwon T , Chapman JA , Toyoda A , Takahashi S , Fukui A , Hikosaka A , Suzuki A , Kondo M , van Heeringen SJ , Quigley I , Heinz S , Ogino H , Ochi H , Hellsten U , Lyons JB , Simakov O , Putnam N , Stites J , Kuroki Y , Tanaka T , Michiue T , Watanabe M , Bogdanovic O , Lister R , Georgiou G , Paranjpe SS , van Kruijsbergen I , Shu S , Carlson J , Kinoshita T , Ohta Y , Mawaribuchi S , Jenkins J , Grimwood J , Schmutz J , Mitros T , Mozaffari SV , Suzuki Y , Haramoto Y , Yamamoto TS , Takagi C , Heald R , Miller K , Haudenschild C , Kitzman J , Nakayama T , Izutsu Y , Robert J , Fortriede J , Burns K , Lotay V , Karimi K , Yasuoka Y , Dichmann DS , Flajnik MF , Houston DW , Shendure J , DuPasquier L , Vize PD , Zorn AM , Ito M , Marcotte EM , Wallingford JB , Ito Y , Asashima M , Ueno N , Matsuda Y , Veenstra GJ , Fujiyama A , Harland RM , Taira M , Rokhsar DS
Ref : Nature , 538 :336 , 2016
Abstract : To explore the origins and consequences of tetraploidy in the African clawed frog, we sequenced the Xenopus laevis genome and compared it to the related diploid X. tropicalis genome. We characterize the allotetraploid origin of X. laevis by partitioning its genome into two homoeologous subgenomes, marked by distinct families of 'fossil' transposable elements. On the basis of the activity of these elements and the age of hundreds of unitary pseudogenes, we estimate that the two diploid progenitor species diverged around 34 million years ago (Ma) and combined to form an allotetraploid around 17-18 Ma. More than 56% of all genes were retained in two homoeologous copies. Protein function, gene expression, and the amount of conserved flanking sequence all correlate with retention rates. The subgenomes have evolved asymmetrically, with one chromosome set more often preserving the ancestral state and the other experiencing more gene loss, deletion, rearrangement, and reduced gene expression.
ESTHER : Session_2016_Nature_538_336
PubMedSearch : Session_2016_Nature_538_336
PubMedID: 27762356
Gene_locus related to this paper: xenla-a0a1l8f4t7 , xenla-a0a1l8fbc6 , xenla-a0a1l8fct2 , xenla-q2tap9 , xenla-q4klb6 , xenla-q5xh09 , xenla-q6ax59 , xenla-q6dcw6 , xenla-q6irp4 , xenla-q6pad5 , xenla-q7sz70 , xenla-Q7ZXQ6 , xenla-q66kx1 , xenla-q640y7 , xenla-q642r3 , xenla-Q860X9 , xenla-BCHE2 , xenla-a0a1l8g7v4 , xenla-a0a1l8g1u7 , xenla-a0a1l8fmc5 , xenla-a0a1l8g467 , xenla-a0a1l8g4e4 , xenla-a0a1l8ga66 , xenla-a0a1l8gaw4 , xenla-a0a1l8gt68 , xenla-a0a1l8h0b2 , xenla-a0a1l8fdr1 , xenla-a0a1l8fdt7 , xenla-a0a1l8fi72 , xenla-a0a1l8fi73 , xenla-a0a1l8fi77 , xenla-a0a1l8fi96 , xenla-a0a1l8hc38 , xenla-a0a1l8hn27 , xenla-a0a1l8hry6 , xenla-a0a1l8hw96 , xenla-a0a1l8i2x6 , xenla-a0a1l8hei7 , xenla-a0a1l8gnd1 , xenla-a0a1l8i2g3 , xenla-a0a1l8hdn0 , xenla-a0a1l8h622

Title : Genetic basis of the highly efficient yeast Kluyveromyces marxianus: complete genome sequence and transcriptome analyses - Lertwattanasakul_2015_Biotechnol.Biofuels_8_47
Author(s) : Lertwattanasakul N , Kosaka T , Hosoyama A , Suzuki Y , Rodrussamee N , Matsutani M , Murata M , Fujimoto N , Suprayogi , Tsuchikane K , Limtong S , Fujita N , Yamada M
Ref : Biotechnol Biofuels , 8 :47 , 2015
Abstract : BACKGROUND: High-temperature fermentation technology with thermotolerant microbes has been expected to reduce the cost of bioconversion of cellulosic biomass to fuels or chemicals. Thermotolerant Kluyveromyces marxianus possesses intrinsic abilities to ferment and assimilate a wide variety of substrates including xylose and to efficiently produce proteins. These capabilities have been found to exceed those of the traditional ethanol producer Saccharomyces cerevisiae or lignocellulose-bioconvertible ethanologenic Scheffersomyces stipitis. RESULTS: The complete genome sequence of K. marxianus DMKU 3-1042 as one of the most thermotolerant strains in the same species has been determined. A comparison of its genomic information with those of other yeasts and transcriptome analysis revealed that the yeast bears beneficial properties of temperature resistance, wide-range bioconversion ability, and production of recombinant proteins. The transcriptome analysis clarified distinctive metabolic pathways under three different growth conditions, static culture, high temperature, and xylose medium, in comparison to the control condition of glucose medium under a shaking condition at 30 degrees C. Interestingly, the yeast appears to overcome the issue of reactive oxygen species, which tend to accumulate under all three conditions. CONCLUSIONS: This study reveals many gene resources for the ability to assimilate various sugars in addition to species-specific genes in K. marxianus, and the molecular basis of its attractive traits for industrial applications including high-temperature fermentation. Especially, the thermotolerance trait may be achieved by an integrated mechanism consisting of various strategies. Gene resources and transcriptome data of the yeast are particularly useful for fundamental and applied researches for innovative applications.
ESTHER : Lertwattanasakul_2015_Biotechnol.Biofuels_8_47
PubMedSearch : Lertwattanasakul_2015_Biotechnol.Biofuels_8_47
PubMedID: 25834639
Gene_locus related to this paper: klumd-w0tha9

Title : Real Time Ligand-Induced Motion Mappings of AChBP and nAChR Using X-ray Single Molecule Tracking - Sekiguchi_2014_Sci.Rep_4_6384
Author(s) : Sekiguchi H , Suzuki Y , Nishino Y , Kobayashi S , Shimoyama Y , Cai W , Nagata K , Okada M , Ichiyanagi K , Ohta N , Yagi N , Miyazawa A , Kubo T , Sasaki YC
Ref : Sci Rep , 4 :6384 , 2014
Abstract : We observed the dynamic three-dimensional (3D) single molecule behaviour of acetylcholine-binding protein (AChBP) and nicotinic acetylcholine receptor (nAChR) using a single molecule tracking technique, diffracted X-ray tracking (DXT) with atomic scale and 100 mus time resolution. We found that the combined tilting and twisting motions of the proteins were enhanced upon acetylcholine (ACh) binding. We present the internal motion maps of AChBP and nAChR in the presence of either ACh or alpha-bungarotoxin (alphaBtx), with views from two rotational axes. Our findings indicate that specific motion patterns represented as biaxial angular motion maps are associated with channel function in real time and on an atomic scale.
ESTHER : Sekiguchi_2014_Sci.Rep_4_6384
PubMedSearch : Sekiguchi_2014_Sci.Rep_4_6384
PubMedID: 25223459

Title : Identification of the carotenoid modifying gene PALE YELLOW PETAL 1 as an essential factor in xanthophyll esterification and yellow flower pigmentation in tomato (Solanum lycopersicum) - Ariizumi_2014_Plant.J_79_453
Author(s) : Ariizumi T , Kishimoto S , Kakami R , Maoka T , Hirakawa H , Suzuki Y , Ozeki Y , Shirasawa K , Bernillon S , Okabe Y , Moing A , Asamizu E , Rothan C , Ohmiya A , Ezura H
Ref : Plant J , 79 :453 , 2014
Abstract : Xanthophylls, the pigments responsible for yellow to red coloration, are naturally occurring carotenoid compounds in many colored tissues of plants. These pigments are esterified within the chromoplast; however, little is known about the mechanisms underlying their accumulation in flower organs. In this study, we characterized two allelic tomato (Solanum lycopersicum L.) mutants, pale yellow petal (pyp) 1-1 and pyp1-2, that have reduced yellow color intensity in the petals and anthers due to loss-of-function mutations. Carotenoid analyses showed that the yellow flower organs of wild-type tomato contained high levels of xanthophylls that largely consisted of neoxanthin and violaxanthin esterified with myristic and/or palmitic acids. Functional disruption of PYP1 resulted in loss of xanthophyll esters, which was associated with a reduction in the total carotenoid content and disruption of normal chromoplast development. These findings suggest that xanthophyll esterification promotes the sequestration of carotenoids in the chromoplast and that accumulation of these esters is important for normal chromoplast development. Next-generation sequencing coupled with map-based positional cloning identified the mutant alleles responsible for the pyp1 phenotype. PYP1 most likely encodes a carotenoid modifying protein that plays a vital role in the production of xanthophyll esters in tomato anthers and petals. Our results provide insight into the molecular mechanism underlying the production of xanthophyll esters in higher plants, thereby shedding light on a longstanding mystery.
ESTHER : Ariizumi_2014_Plant.J_79_453
PubMedSearch : Ariizumi_2014_Plant.J_79_453
PubMedID: 24888879
Gene_locus related to this paper: pethy-XES

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 : Activation of focal adhesion kinase via M1 muscarinic acetylcholine receptor is required in restitution of intestinal barrier function after epithelial injury - Khan_2014_Biochim.Biophys.Acta_1842_635
Author(s) : Khan MR , Yazawa T , Anisuzzaman AS , Semba S , Ma Y , Uwada J , Hayashi H , Suzuki Y , Ikeuchi H , Uchino M , Maemoto A , Muramatsu I , Taniguchi T
Ref : Biochimica & Biophysica Acta , 1842 :635 , 2014
Abstract : Impairment of epithelial barrier is observed in various intestinal disorders including inflammatory bowel diseases (IBD). Numerous factors may cause temporary damage of the intestinal epithelium. A complex network of highly divergent factors regulates healing of the epithelium to prevent inflammatory response. However, the exact repair mechanisms involved in maintaining homeostatic intestinal barrier integrity remain to be clarified. In this study, we demonstrate that activation of M1 muscarinic acetylcholine receptor (mAChR) augments the restitution of epithelial barrier function in T84 cell monolayers after ethanol-induced epithelial injury, via ERK-dependent phosphorylation of focal adhesion kinase (FAK). We have shown that ethanol injury decreased the transepithelial electrical resistance (TER) along with the reduction of ERK and FAK phosphorylation. Carbachol (CCh) increased ERK and FAK phosphorylation with enhanced TER recovery, which was completely blocked by either MT-7 (M1 antagonist) or atropine. The CCh-induced enhancement of TER recovery was also blocked by either U0126 (ERK pathway inhibitor) or PF-228 (FAK inhibitor). Treatment of T84 cell monolayers with interferon-gamma (IFN-gamma) impaired the barrier function with the reduction of FAK phosphorylation. The CCh-induced ERK and FAK phosphorylation were also attenuated by the IFN-gamma treatment. Immunological and binding experiments exhibited a significant reduction of M1 mAChR after IFN-gamma treatment. The reduction of M1 mAChR in inflammatory area was also observed in surgical specimens from IBD patients, using immunohistochemical analysis. These findings provide important clues regarding mechanisms by which M1 mAChR participates in the maintenance of intestinal barrier function under not only physiological but also pathological conditions.
ESTHER : Khan_2014_Biochim.Biophys.Acta_1842_635
PubMedSearch : Khan_2014_Biochim.Biophys.Acta_1842_635
PubMedID: 24365239

Title : Allying with armored snails: the complete genome of gammaproteobacterial endosymbiont - Nakagawa_2014_ISME.J_8_40
Author(s) : Nakagawa S , Shimamura S , Takaki Y , Suzuki Y , Murakami S , Watanabe T , Fujiyoshi S , Mino S , Sawabe T , Maeda T , Makita H , Nemoto S , Nishimura S , Watanabe H , Watsuji TO , Takai K
Ref : Isme J , 8 :40 , 2014
Abstract : Deep-sea vents harbor dense populations of various animals that have their specific symbiotic bacteria. Scaly-foot gastropods, which are snails with mineralized scales covering the sides of its foot, have a gammaproteobacterial endosymbiont in their enlarged esophageal glands and diverse epibionts on the surface of their scales. In this study, we report the complete genome sequencing of gammaproteobacterial endosymbiont. The endosymbiont genome displays features consistent with ongoing genome reduction such as large proportions of pseudogenes and insertion elements. The genome encodes functions commonly found in deep-sea vent chemoautotrophs such as sulfur oxidation and carbon fixation. Stable carbon isotope ((13)C)-labeling experiments confirmed the endosymbiont chemoautotrophy. The genome also includes an intact hydrogenase gene cluster that potentially has been horizontally transferred from phylogenetically distant bacteria. Notable findings include the presence and transcription of genes for flagellar assembly, through which proteins are potentially exported from bacterium to the host. Symbionts of snail individuals exhibited extreme genetic homogeneity, showing only two synonymous changes in 19 different genes (13 810 positions in total) determined for 32 individual gastropods collected from a single colony at one time. The extremely low genetic individuality in endosymbionts probably reflects that the stringent symbiont selection by host prevents the random genetic drift in the small population of horizontally transmitted symbiont. This study is the first complete genome analysis of gastropod endosymbiont and offers an opportunity to study genome evolution in a recently evolved endosymbiont.
ESTHER : Nakagawa_2014_ISME.J_8_40
PubMedSearch : Nakagawa_2014_ISME.J_8_40
PubMedID: 23924784
Gene_locus related to this paper: 9gamm-s6bga5

Title : Protein-anchoring strategy for delivering acetylcholinesterase to the neuromuscular junction - Ito_2012_Mol.Ther_20_1384
Author(s) : Ito M , Suzuki Y , Okada T , Fukudome T , Yoshimura T , Masuda A , Takeda S , Krejci E , Ohno K
Ref : Mol Ther , 20 :1384 , 2012
Abstract : Acetylcholinesterase (AChE) at the neuromuscular junction (NMJ) is anchored to the synaptic basal lamina via a triple helical collagen Q (ColQ). Congenital defects of ColQ cause endplate AChE deficiency and myasthenic syndrome. A single intravenous administration of adeno-associated virus serotype 8 (AAV8)-COLQ to Colq(-/-) mice recovered motor functions, synaptic transmission, as well as the morphology of the NMJ. ColQ-tailed AChE was specifically anchored to NMJ and its amount was restored to 89% of the wild type. We next characterized the molecular basis of this efficient recovery. We first confirmed that ColQ-tailed AChE can be specifically targeted to NMJ by an in vitro overlay assay in Colq(-/-) mice muscle sections. We then injected AAV1-COLQ-IRES-EGFP into the left tibialis anterior and detected AChE in noninjected limbs. Furthermore, the in vivo injection of recombinant ColQ-tailed AChE protein complex into the gluteus maximus muscle of Colq(-/-) mice led to accumulation of AChE in noninjected forelimbs. We demonstrated for the first time in vivo that the ColQ protein contains a tissue-targeting signal that is sufficient for anchoring itself to the NMJ. We propose that the protein-anchoring strategy is potentially applicable to a broad spectrum of diseases affecting extracellular matrix molecules.
ESTHER : Ito_2012_Mol.Ther_20_1384
PubMedSearch : Ito_2012_Mol.Ther_20_1384
PubMedID: 22371845

Title : Integration of the genetic map and genome assembly of fugu facilitates insights into distinct features of genome evolution in teleosts and mammals - Kai_2011_Genome.Biol.Evol_3_424
Author(s) : Kai W , Kikuchi K , Tohari S , Chew AK , Tay A , Fujiwara A , Hosoya S , Suetake H , Naruse K , Brenner S , Suzuki Y , Venkatesh B
Ref : Genome Biol Evol , 3 :424 , 2011
Abstract : The compact genome of fugu (Takifugu rubripes) has been used widely as a reference genome for understanding the evolution of vertebrate genomes. However, the fragmented nature of the fugu genome assembly has restricted its use for comparisons of genome architecture in vertebrates. To extend the contiguity of the assembly to the chromosomal level, we have generated a comprehensive genetic map of fugu and anchored the scaffolds of the assembly to the 22 chromosomes of fugu. The map consists of 1,220 microsatellite markers that provide anchor points to 697 scaffolds covering 86% of the genome assembly (http://www.fugu-sg.org/). The integrated genome map revealed a higher recombination rate in fugu compared with other vertebrates and a wide variation in the recombination rate between sexes and across chromosomes of fugu. We used the extended assembly to explore recent rearrangement events in the lineages of fugu, Tetraodon, and medaka and compared them with rearrangements in three mammalian (human, mouse, and opossum) lineages. Between the two pufferfishes, fugu has experienced fewer chromosomal rearrangements than Tetraodon. The gene order is more highly conserved in the three teleosts than in mammals largely due to a lower rate of interchromosomal rearrangements in the teleosts. These results provide new insights into the distinct patterns of genome evolution between teleosts and mammals. The consolidated genome map and the genetic map of fugu are valuable resources for comparative genomics of vertebrates and for elucidating the genetic basis of the phenotypic diversity of ~25 species of Takifugu that evolved within the last 5 My.
ESTHER : Kai_2011_Genome.Biol.Evol_3_424
PubMedSearch : Kai_2011_Genome.Biol.Evol_3_424
PubMedID: 21551351
Gene_locus related to this paper: takru-h2th79 , takru-h2st11 , takru-h2s0m3 , takru-h2uad8 , takru-h2uad9 , takru-h2v884 , takru-h2v8t3 , takru-h2uuz8 , takru-h2rw43 , takru-h2s0k7 , takru-h2v0c9 , takru-h2rzs7 , takru-h2t7u7 , takru-h2s5e3 , takru-a0a3b5k333 , takru-a0a3b5k3s5 , takru-h2tlp5 , takru-a0a3b5k5v8 , takru-h2rkk3 , takru-h2sml0

Title : Major chimpanzee-specific structural changes in sperm development-associated genes - Kim_2011_Funct.Integr.Genomics_11_507
Author(s) : Kim RN , Kim DW , Choi SH , Chae SH , Nam SH , Kim A , Kang A , Park KH , Lee YS , Hirai M , Suzuki Y , Sugano S , Hashimoto K , Kim DS , Park HS
Ref : Funct Integr Genomics , 11 :507 , 2011
Abstract : A comprehensive analysis of transcriptional structures of chimpanzee sperm development-associated genes is of significant interest for deeply understanding sperm development and male reproductive process. In this study, we sequenced 7,680 clones from a chimpanzee testis full-length cDNA library and obtained 1,933 nonredundant high-quality full-length cDNA sequences. Comparative analysis between human and chimpanzee showed that 78 sperm development-associated genes, most of which were yet uncharacterized, had undergone severe structural changes (mutations at the start/stop codons, INDELs, alternative splicing variations and fusion forms) on genomic and transcript levels throughout chimpanzee evolution. Specifically, among the 78 sperm development-associated genes, 39 including ODF2, UBC, and CD59 showed markedly chimpanzee-specific structural changes. Through dN/dS analysis, we found that 56 transcripts (including seven sperm development-associated genes) had values of greater than one when comparing human and chimpanzee DNA sequences, whereas the values were less than one when comparing humans and orangutans. Gene ontology annotation and expression profiling showed that the chimpanzee testis transcriptome was enriched with genes that are associated with chimpanzee male germ cell development. Taken together, our study provides the first comprehensive molecular evidence that many chimpanzee sperm development-associated genes had experienced severe structural changes over the course of evolution on genomic and transcript levels.
ESTHER : Kim_2011_Funct.Integr.Genomics_11_507
PubMedSearch : Kim_2011_Funct.Integr.Genomics_11_507
PubMedID: 21484476
Gene_locus related to this paper: pantr-BCHE , pantr-k7c7k7 , pantr-g2hih9 , pantr-g2hj61

Title : Genomes of two chronological isolates (Helicobacter pylori 2017 and 2018) of the West African Helicobacter pylori strain 908 obtained from a single patient - Avasthi_2011_J.Bacteriol_193_3385
Author(s) : Avasthi TS , Devi SH , Taylor TD , Kumar N , Baddam R , Kondo S , Suzuki Y , Lamouliatte H , Megraud F , Ahmed N
Ref : Journal of Bacteriology , 193 :3385 , 2011
Abstract : The diverse clinical outcomes of colonization by Helicobacter pylori reflect the need to understand the genomic rearrangements enabling the bacterium to adapt to host niches and exhibit varied colonization/virulence potential. We describe the genome sequences of the two serial isolates, H. pylori 2017 and 2018 (the chronological subclones of H. pylori 908), cultured in 2003 from the antrum and corpus, respectively, of an African patient who suffered from recrudescent duodenal ulcer disease. When compared with the genome of the parent strain, 908 (isolated from the antrum of the same patient in 1994), the genome sequences revealed genomic alterations relevant to virulence optimization or host-specific adaptation.
ESTHER : Avasthi_2011_J.Bacteriol_193_3385
PubMedSearch : Avasthi_2011_J.Bacteriol_193_3385
PubMedID: 21515762

Title : Genome of Helicobacter pylori strain 908 - Devi_2010_J.Bacteriol_192_6488
Author(s) : Devi SH , Taylor TD , Avasthi TS , Kondo S , Suzuki Y , Megraud F , Ahmed N
Ref : Journal of Bacteriology , 192 :6488 , 2010
Abstract : Helicobacter pylori is a genetically diverse and coevolved pathogen inhabiting human gastric niches and leading to a spectrum of gastric diseases in susceptible populations. We describe the genome sequence of H. pylori 908, which was originally isolated from an African patient living in France who suffered with recrudescent duodenal ulcer disease. The strain was found to be phylogenetically related to H. pylori J99, and its comparative analysis revealed several specific genome features and novel insertion-deletion and substitution events. The genome sequence revealed several strain-specific deletions and/or gain of genes exclusively present in HP908 compared with different sequenced genomes already available in the public domain. Comparative and functional genomics of HP908 and its subclones will be important in understanding genomic plasticity and the capacity to colonize and persist in a changing host environment.
ESTHER : Devi_2010_J.Bacteriol_192_6488
PubMedSearch : Devi_2010_J.Bacteriol_192_6488
PubMedID: 20952566

Title : Expression balances of structural genes in shikimate and flavonoid biosynthesis cause a difference in proanthocyanidin accumulation in persimmon (Diospyros kaki Thunb.) fruit - Akagi_2009_Planta_230_899
Author(s) : Akagi T , Ikegami A , Suzuki Y , Yoshida J , Yamada M , Sato A , Yonemori K
Ref : Planta , 230 :899 , 2009
Abstract : Persimmon fruits accumulate a large amount of proanthocyanidin (PA) during development. Fruits of pollination-constant and non-astringent (PCNA) type mutants lose their ability to produce PA at an early stage of fruit development, while fruits of the normal (non-PCNA) type remain rich in PA until fully ripened. To understand the molecular mechanism for this difference, we isolated the genes involved in PA accumulation that are differentially expressed between PCNA and non-PCNA, and confirmed their correlation with PA content and composition. The expression of structural genes of the shikimate and flavonoid biosynthetic pathways and genes encoding transferases homologous to those involved in the accumulation of phenolic compounds were downregulated coincidentally only in the PCNA type. Analysis of PA composition using the phloroglucinol method suggested that the amounts of epigallocatechin and its 3-O-gallate form were remarkably low in the PCNA type. In the PCNA type, the genes encoding flavonoid 3'5' hydroxylase (F3'5'H) and anthocyanidin reductase (ANR) for epigallocatechin biosynthesis showed remarkable downregulation, despite the continuous expression level of their competitive genes, flavonoid 3' hydroxylation (F3'H) and leucoanthocyanidin reductase (LAR). We also confirmed that the relative expression levels of F3'5'H to F3'H, and ANR to LAR, were considerably higher, and the PA composition corresponded to the seasonal expression balances in both types. These results suggest that expressions of F3'5'H and ANR are important for PA accumulation in persimmon fruit. Lastly, we tested enzymatic activity of recombinant DkANR in vitro, which is thought to be an important enzyme for PA accumulation in persimmon fruits.
ESTHER : Akagi_2009_Planta_230_899
PubMedSearch : Akagi_2009_Planta_230_899
PubMedID: 19669159

Title : Responses of hypothalamo-pituitary-adrenal axis to a cholinesterase inhibitor - Umegaki_2009_Neuroreport_20_1366
Author(s) : Umegaki H , Yamamoto A , Suzuki Y , Iguchi A
Ref : Neuroreport , 20 :1366 , 2009
Abstract : Acute gastrointestinal events (mostly manifested by nausea, vomiting, or loss of appetite) are class effects of all cholinesterase inhibitors, which are prescribed for the treatment of Alzheimer's disease. The underlying mechanism, however, has been unclear. Because corticotropin-releasing hormone is related to appetite control, we focused on the activation of the hypothalamo-pituitary-adrenal system and food intake following the administration of the cholinesterase inhibitor, donepezil, in rats. We monitored the plasma concentrations of adrenocorticotropic hormone, c-Fos, in the paraventricular nucleus, and intakes of rat chow for 3 h after the first administration of donepezil, and 2 weeks later, after daily administration of donepezil. The intragastric administration of 3 mg/kg of donepezil significantly increased the plasma adrenocorticotropic hormone levels and c-Fos expression in the paraventricular nucleus, and decreased the food intake on the first day. The increase in adrenocorticotropic hormone and loss of appetite after oral administration of the drug were attenuated after daily administration for 2 weeks.
ESTHER : Umegaki_2009_Neuroreport_20_1366
PubMedSearch : Umegaki_2009_Neuroreport_20_1366
PubMedID: 19738498

Title : Discontinuation of donepezil for the treatment of Alzheimer's disease in geriatric practice - Umegaki_2008_Int.Psychogeriatr_20_800
Author(s) : Umegaki H , Itoh A , Suzuki Y , Nabeshima T
Ref : Int Psychogeriatr , 20 :800 , 2008
Abstract : BACKGROUND: Maintaining continuous pharmacological treatment of patients with dementia is often difficult. In the current study we surveyed the discontinuation of donepezil, a cholinesterase inhibitor, for the treatment of Alzheimer's disease in a Japanese geriatric outpatient clinic in a university hospital. METHODS: Using a retrospective chart review from 1 July 2003 to 30 June 2005, prescriptions of donepezil and the reasons for discontinuing the prescription in a university hospital were determined. The severity of dementia was evaluated by the clinical dementia rating (CDR). RESULTS: Out of 264 patients, 140 (53.1%) discontinued taking donepezil during the two-year observation period. The mean age of the continued group and the discontinued group did not differ significantly (79.5 +/- 6.7, 79.8 +/- 6.4, respectively). Kaplan-Meier analysis showed that the patients with more severe cognitive impairment (CDR score = 3) discontinued donepezil earlier and more frequently. The reasons for discontinuation were a change in the doctors treating the patients (n = 71), ineffectiveness (n = 16), gastrointestinal side-effects (n = 11), and others (n = 41). In patients with CDR = 1 or 2, changes of doctors were the most frequent reason for discontinuation. However, in patients with CDR = 3, ineffectiveness of the medication was the major reason for discontinuation. CONCLUSION: Donepezil was frequently discontinued, and the rate of discontinuation was higher in patients with advanced dementia.
ESTHER : Umegaki_2008_Int.Psychogeriatr_20_800
PubMedSearch : Umegaki_2008_Int.Psychogeriatr_20_800
PubMedID: 18341753

Title : The genome of a lepidopteran model insect, the silkworm Bombyx mori - Xia_2008_Insect.Biochem.Mol.Biol_38_1036
Author(s) : Xia Q , Wang J , Zhou Z , Li R , Fan W , Cheng D , Cheng T , Qin J , Duana J , Xu H , Li Q , Li N , Wang M , Dai F , Liu C , Lin Y , Zhao P , Zhang H , Liu S , Zha X , Li C , Zhao A , Pan M , Pan G , Shen Y , Gao Z , Wang Z , Wang G , Wu Z , Hou Y , Chai C , Yu Q , He N , Zhang Z , Li S , Yang H , Lu C , Xiang Z , Mita K , Kasahara M , Nakatani Y , Yamamoto K , Abe H , Ahsan B , Daimoni T , Doi K , Fujii T , Fujiwara H , Fujiyama A , Futahashi R , Hashimotol S , Ishibashi J , Iwami M , Kadono-Okuda K , Kanamori H , Kataoka H , Katsuma S , Kawaoka S , Kawasaki H , Kohara Y , Kozaki T , Kuroshu RM , Kuwazaki S , Matsushima K , Minami H , Nagayasu Y , Nakagawa T , Narukawa J , Nohata J , Ohishi K , Ono Y , Osanai-Futahashi M , Ozaki K , Qu W , Roller L , Sasaki S , Sasaki T , Seino A , Shimomura M , Shin-I T , Shinoda T , Shiotsuki T , Suetsugu Y , Sugano S , Suwa M , Suzuki Y , Takiya S , Tamura T , Tanaka H , Tanaka Y , Touhara K , Yamada T , Yamakawa M , Yamanaka N , Yoshikawa H , Zhong YS , Shimada T , Morishita S
Ref : Insect Biochemistry & Molecular Biology , 38 :1036 , 2008
Abstract : Bombyx mori, the domesticated silkworm, is a major insect model for research, and the first lepidopteran for which draft genome sequences became available in 2004. Two independent data sets from whole-genome shotgun sequencing were merged and assembled together with newly obtained fosmid- and BAC-end sequences. The remarkably improved new assembly is presented here. The 8.5-fold sequence coverage of an estimated 432 Mb genome was assembled into scaffolds with an N50 size of approximately 3.7 Mb; the largest scaffold was 14.5 million base pairs. With help of a high-density SNP linkage map, we anchored 87% of the scaffold sequences to all 28 chromosomes. A particular feature was the high repetitive sequence content estimated to be 43.6% and that consisted mainly of transposable elements. We predicted 14,623 gene models based on a GLEAN-based algorithm, a more accurate prediction than the previous gene models for this species. Over three thousand silkworm genes have no homologs in other insect or vertebrate genomes. Some insights into gene evolution and into characteristic biological processes are presented here and in other papers in this issue. The massive silk production correlates with the existence of specific tRNA clusters, and of several sericin genes assembled in a cluster. The silkworm's adaptation to feeding on mulberry leaves, which contain toxic alkaloids, is likely linked to the presence of new-type sucrase genes, apparently acquired from bacteria. The silkworm genome also revealed the cascade of genes involved in the juvenile hormone biosynthesis pathway, and a large number of cuticular protein genes.
ESTHER : Xia_2008_Insect.Biochem.Mol.Biol_38_1036
PubMedSearch : Xia_2008_Insect.Biochem.Mol.Biol_38_1036
PubMedID: 19121390
Gene_locus related to this paper: bommo-a0mnw6 , bommo-a1yw85 , bommo-a9ls22 , bommo-ACHE1 , bommo-ACHE2 , bommo-b0fgv8 , bommo-b1q137 , bommo-b1q139 , bommo-b1q140 , bommo-b1q141 , bommo-b2zdz0 , bommo-b3gef6 , bommo-b3gef7 , bommo-b3gs55 , bommo-b3gs56 , bommo-d2ktu3 , bommo-d2ktu5 , bommo-d9ile0 , bommo-e1cga5 , bommo-e1cga6 , bommo-g8fpz6 , bommo-h9iu43 , bommo-h9iu46 , bommo-h9iu47.1 , bommo-h9iu47.2 , bommo-h9iue5 , bommo-h9ivg2 , bommo-h9iwj7 , bommo-h9iwj8 , bommo-h9ix58 , bommo-h9ixi1.1 , bommo-h9ixi1.2 , bommo-h9iy47 , bommo-h9izw1 , bommo-h9j0s4 , bommo-h9j1y0 , bommo-h9j3r0 , bommo-h9j3w6 , bommo-h9j3w7 , bommo-h9j5t0 , bommo-h9j8g3 , bommo-h9j9k9 , bommo-h9j066 , bommo-h9j067 , bommo-h9j593 , bommo-h9j594 , bommo-h9j990 , bommo-h9jde8 , bommo-h9jde9 , bommo-h9jdf0 , bommo-h9jds4 , bommo-h9jle7 , bommo-h9jn83 , bommo-h9jn85 , bommo-h9jrg2 , bommo-h9jyh9 , bommo-JHE , bommo-m1rmh6 , bommo-q1hq05 , bommo-q4tte1 , bommo-h9j592 , bommo-h9j604 , bommo-h9jpm8 , bommo-h9iss4 , bommo-h9j2c7

Title : Preparation and comparative characterization of immobilized Aspergillus oryzae expressing Fusarium heterosporum lipase for enzymatic biodiesel production - Hama_2008_Appl.Microbiol.Biotechnol_81_637
Author(s) : Hama S , Tamalampudi S , Suzuki Y , Yoshida A , Fukuda H , Kondo A
Ref : Applied Microbiology & Biotechnology , 81 :637 , 2008
Abstract : In this paper, we provide the first report of utilizing recombinant fungal whole cells in enzymatic biodiesel production. Aspergillus oryzae, transformed with a heterologous lipase-encoding gene from Fusarium heterosporum, produced fully processed and active forms of recombinant F. heterosporum lipase (FHL). Cell immobilization within porous biomass support particles enabled the convenient usage of FHL-producing A. oryzae as a whole-cell biocatalyst for lipase-catalyzed methanolysis. The addition of 5% water to the reaction mixture was effective in both preventing the lipase inactivation by methanol and facilitating the acyl migration in partial glycerides, resulting in the final methyl ester content of 94% even in the tenth batch cycle. A comparative study showed that FHL-producing A. oryzae attained a higher final methyl ester content and higher lipase stability than Rhizopus oryzae, the previously developed whole-cell biocatalyst. Although both FHL and R. oryzae lipase exhibit 1,3-regiospecificity towards triglyceride, R. oryzae accumulated a much higher amount of sn-2 isomers of partial glycerides, whereas FHL-producing A. oryzae maintained a low level of the sn-2 isomers. This is probably because FHL efficiently facilitates the acyl migration from the sn-2 to the sn-1(3) position in partial glycerides. These findings indicate that the newly developed FHL-producing A. oryzae is an effective whole-cell biocatalyst for enzymatic biodiesel production.
ESTHER : Hama_2008_Appl.Microbiol.Biotechnol_81_637
PubMedSearch : Hama_2008_Appl.Microbiol.Biotechnol_81_637
PubMedID: 18795281

Title : Expression and purification of pheophorbidase, an enzyme catalyzing the formation of pyropheophorbide during chlorophyll degradation: comparison with the native enzyme - Suzuki_2008_Photochem.Photobiol.Sci_7_1260
Author(s) : Suzuki Y , Soga K , Yoshimatsu K , Shioi Y
Ref : Photochem Photobiol Sci , 7 :1260 , 2008
Abstract : Formation of pyropheophorbide (PyroPheid) during chlorophyll metabolism in some higher plants has been shown to involve the enzyme pheophorbidase (PPD). This enzyme catalyzes the conversion of pheophorbide (Pheid) a to a precursor of PyroPheid, C-13(2)-carboxylPyroPheid a, by demethylation, and then the precursor is decarboxylated non-enzymatically to yield PyroPheid a. In this study, expression, purification, and biochemical characterization of recombinant PPD from radish (Raphanus sativus L.) were performed, and its properties were compared with those of highly purified native PPD. Recombinant PPD was produced using a glutathione S-transferase (GST) fusion system. The PPD and GST genes were fused to a pGEX-2T vector and expressed in Escherichia coli under the control of a T7 promoter as a fusion protein. The recombinant PPD-GST was expressed as a 55 kDa protein as measured by SDS-PAGE and purified by single-step affinity chromatography through a GSTrap FF column. PPD-GST was purified to homogeneity with a yield of 0.42 mg L(-1) of culture. The protein purified by this method was confirmed to be PPD by measuring its activity. The purified PPD-GST fusion protein revealed potent catalytic activity for demethylation of the methoxycarbonyl group of Pheid a and showed a pH optimum, substrate specificity, and thermal stability quite similar to the native enzyme purified from radish, except for the Km values toward Pheid a: 95.5 microM for PPD-GST and about 15 microM for native PPDs.
ESTHER : Suzuki_2008_Photochem.Photobiol.Sci_7_1260
PubMedSearch : Suzuki_2008_Photochem.Photobiol.Sci_7_1260
PubMedID: 18846292
Gene_locus related to this paper: rapsa-q2v0w1

Title : The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants - Rensing_2008_Science_319_64
Author(s) : Rensing SA , Lang D , Zimmer AD , Terry A , Salamov A , Shapiro H , Nishiyama T , Perroud PF , Lindquist EA , Kamisugi Y , Tanahashi T , Sakakibara K , Fujita T , Oishi K , Shin IT , Kuroki Y , Toyoda A , Suzuki Y , Hashimoto S , Yamaguchi K , Sugano S , Kohara Y , Fujiyama A , Anterola A , Aoki S , Ashton N , Barbazuk WB , Barker E , Bennetzen JL , Blankenship R , Cho SH , Dutcher SK , Estelle M , Fawcett JA , Gundlach H , Hanada K , Heyl A , Hicks KA , Hughes J , Lohr M , Mayer K , Melkozernov A , Murata T , Nelson DR , Pils B , Prigge M , Reiss B , Renner T , Rombauts S , Rushton PJ , Sanderfoot A , Schween G , Shiu SH , Stueber K , Theodoulou FL , Tu H , Van de Peer Y , Verrier PJ , Waters E , Wood A , Yang L , Cove D , Cuming AC , Hasebe M , Lucas S , Mishler BD , Reski R , Grigoriev IV , Quatrano RS , Boore JL
Ref : Science , 319 :64 , 2008
Abstract : We report the draft genome sequence of the model moss Physcomitrella patens and compare its features with those of flowering plants, from which it is separated by more than 400 million years, and unicellular aquatic algae. This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments (e.g., flagellar arms); acquisition of genes for tolerating terrestrial stresses (e.g., variation in temperature and water availability); and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response. The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics.
ESTHER : Rensing_2008_Science_319_64
PubMedSearch : Rensing_2008_Science_319_64
PubMedID: 18079367
Gene_locus related to this paper: phypa-a9rbi6 , phypa-a9rfh1 , phypa-a9rg19 , phypa-a9rgt9 , phypa-a9rhz9 , phypa-a9rkj1 , phypa-a9rns2 , phypa-a9rp52 , phypa-a9rq03 , phypa-a9ry17 , phypa-a9ry72 , phypa-a9s5n8 , phypa-a9s6w1 , phypa-a9s8c7 , phypa-a9s299 , phypa-a9san7 , phypa-a9sc75 , phypa-a9se75 , phypa-a9sg07 , phypa-a9skf7 , phypa-a9skr1 , phypa-a9skw1 , phypa-a9sl58 , phypa-a9slp7 , phypa-a9smq5 , phypa-a9sp13 , phypa-a9ssb0 , phypa-a9sse1 , phypa-a9ssf6 , phypa-a9st85 , phypa-a9sx74 , phypa-a9sy58 , phypa-a9syy4 , phypa-a9t0n4 , phypa-a9t0p4 , phypa-a9t1j2 , phypa-a9t5h1 , phypa-a9t7g6 , phypa-a9t8u8 , phypa-a9t9c9 , phypa-a9t9d9 , phypa-a0a7i4d2t7 , phypa-a9t498 , phypa-a9tbu4 , phypa-a9tc36 , phypa-a9tds0 , phypa-a9te64 , phypa-a9tfw2 , phypa-a9tin6 , phypa-a9tja4 , phypa-a9tmp3 , phypa-a9tmr4 , phypa-a9tql4 , phypa-a9tr83 , phypa-a9tsl1 , phypa-a9tsv6 , phypa-a9tu05 , phypa-a9tw81 , phypa-a9tyr8 , phypa-a9u0c9 , phypa-a9u0k3 , phypa-a9u0p4 , phypa-a9u2u7 , phypa-a9u3s0 , phypa-a9tfm7 , phypa-a9tfp6 , phypa-a9syg9 , phypa-a9tzk2 , phypa-a9tvg4 , phypa-a9t1y4 , phypa-a9tqt6 , phypa-a9st18 , phypa-a9tix9 , phypa-a0a2k1kfe3 , phypa-a9sqk3 , phypa-a0a2k1ie71 , phypa-a0a2k1kg29 , phypa-a0a2k1iji3

Title : Prognostic factors and toxicokinetics in acute fenitrothion self-poisoning requiring intensive care - Inoue_2008_Clin.Toxicol.(Phila)_46_528
Author(s) : Inoue S , Saito T , Suzuki Y , Iizuka S , Takazawa K , Akieda K , Yamamoto I , Inokuchi S
Ref : Clinical Toxicology (Phila) , 46 :528 , 2008
Abstract : OBJECTIVE: We aimed to evaluate prognostic factors and toxicokinetics in acute fenitrothion self-poisoning.
METHODS: We reviewed 12 patients with fenitrothion self-poisoning admitted to the intensive care unit between 2003 and 2006. We compared the characteristics, initial vital signs, physiological scores, corrected QT interval on electrocardiogram and laboratory data (serum fenitrothion concentration and cholinesterase activity) of non-survivors and survivors. Furthermore, we evaluated the correlation between the prognostic factors and severity of poisoning (lengths of intensive care unit and hospital stays), and the toxicokinetics of the patients.
RESULTS: In the 2 non-survivors, the estimated fenitrothion ingestion dose and the serum fenitrothion concentration at the emergency department and at 24 h after ingestion were significantly higher than those in the 10 survivors. (P = 0.008, 0.003, and 0.04, respectively). In the 10 survivors, the serum fenitrothion concentration at 24 h after ingestion was significantly correlated with the lengths of intensive care unit and hospital stays (P = 0.004 and 0.04, respectively); however, the initial vital signs, physiological scores, corrected QT interval on electrocardiogram at the emergency department, and serum cholinesterase activity did not show any correlation. In five patients successfully fitted to a two-compartment model, the distribution and elimination half-lives were 2.5 and 49.8 h, respectively, which is compatible with the slow and prolonged clinical course of fenitrothion poisoning. CONCLUSION. Estimated fenitrothion ingestion dose and serum fenitrothion concentration at the emergency department and at 24 h after ingestion may be useful prognostic factors in acute fenitrothion self-poisoning. Furthermore, we should take care for the patients whose serum fenitrothion concentration is high.
ESTHER : Inoue_2008_Clin.Toxicol.(Phila)_46_528
PubMedSearch : Inoue_2008_Clin.Toxicol.(Phila)_46_528
PubMedID: 18584365

Title : Structural characterization of N-glycans of cauxin by MALDI-TOF mass spectrometry and nano LC-ESI-mass spectrometry - Suzuki_2007_Biosci.Biotechnol.Biochem_71_811
Author(s) : Suzuki Y , Miyazaki M , Ito E , Suzuki M , Yamashita T , Taira H , Suzuki A
Ref : Biosci Biotechnol Biochem , 71 :811 , 2007
Abstract : Cauxin is a carboxylesterase-like glycoprotein excreted as a major component of cat urine. Cauxin contains four putative N-glycosylation sites. We characterized the structure of an N-linked oligosaccharide of cauxin using nano liquid chromatography (LC)-electrospray ionization (ESI) and matrix-assisted laser desorption/ionization quadrupole ion trap time-of-flight mass spectrometry (MALDI-QIT-TOF MS) and MS/MS, and high-performance liquid chromatography (HPLC) with an octadecylsilica (ODS) column. The structure of the N-linked oligosaccharide of cauxin attached to (83)Asn was a bisecting complex type, Galbeta1-4GlcNAcbeta1-2Manalpha1-3(Galbeta1-4GlcNAcbeta1-2Manalpha1-6)(GlcNAcbeta 1-4)Manbeta1-4GlcNAcbeta1-4(Fucalpha1-6)GlcNAc.
ESTHER : Suzuki_2007_Biosci.Biotechnol.Biochem_71_811
PubMedSearch : Suzuki_2007_Biosci.Biotechnol.Biochem_71_811
PubMedID: 17341822
Gene_locus related to this paper: felca-CAUXIN

Title : Rapid simultaneous determination for organophosphorus pesticides in human serum by LC-MS - Inoue_2007_J.Pharm.Biomed.Anal_44_258
Author(s) : Inoue S , Saito T , Mase H , Suzuki Y , Takazawa K , Yamamoto I , Inokuchi S
Ref : J Pharm Biomed Anal , 44 :258 , 2007
Abstract : A simple and rapid method was developed for measuring 10 organophosphorus pesticides (acephate, methidathion, dichlorvos, fenthion, EPN, diazinon, phenthoate, malathion, fenitrothion, and cyanophos) in the serum of acute poisoning patients by LC/MS. Following deproteinization by acetonitrile, an aliquot of the biological sample was injected into a C(18) column using 10mM ammonium formate-methanol as the mobile phase. Extraction recoveries were satisfactory and ranged between 60.0 and 108.1% in serum. The limits of detection (LODs) in serum ranged from 0.125 to 1 microg/ml, and the limits of quantitation (LOQs) ranged from 0.25 to 1.25 microg/ml. An excellent linearity was observed for these LOQs up to 8 microg/ml. Intra- and interassay precision and accuracy were satisfactory for most of the pesticides analyzed. In terms of temperature stability, of all the organophosphorus compounds analyzed, dichlorvos and malathion exhibited the most rapid degradations over 24h at room temperature. Methidathion and diazinon remained relatively stable at all temperatures during the entire 4-week testing period. The present method was successfully applied to one actual case of acute poisoning. In conclusion, this method is simple, accurate, and useful for the determination of organophosphorus pesticides and should benefit both clinical and forensic toxicology.
ESTHER : Inoue_2007_J.Pharm.Biomed.Anal_44_258
PubMedSearch : Inoue_2007_J.Pharm.Biomed.Anal_44_258
PubMedID: 17337150

Title : Regulation of self-incompatibility by acetylcholine and cAMP in Lilium longiflorum - Tezuka_2007_J.Plant.Physiol_164_878
Author(s) : Tezuka T , Akita I , Yoshino N , Suzuki Y
Ref : J Plant Physiol , 164 :878 , 2007
Abstract : Elongation of pollen tubes in pistils of Lilium longiflorum cv. Hinomoto after self-incompatible pollination was here found to be promoted by acetylcholine (ACh) and other choline derivatives, such as acetylthiocholine, l-alpha-phosphatidylcholine and chlorocholinechloride [CCC; (2-chloroethyl) trimethyl ammonium chloride]. Moreover, the elongation was promoted by neostigmine, a potent inhibitor of acetylcholinesterase (AChE; acetylcholine-decomposing enzyme) (EC 3.1.1.7.) and activities of this and choline acetyltransferase (ChAT; acetylcholine-forming enzyme) (EC 2.3.1.6.) in pistils were associated with self-incompatibility. The activity of ChAT was lower after self-incompatible as compared with cross-compatible pollination. Application of cAMP promoted ChAT activities in both cases, whereas activity of AChE in pistils after self-pollination was higher than that after cross-compatible pollination and was suppressed by cAMP in both cases. Furthermore, AChE activity was inhibited by treatment with neostigmine or heating. Our results indicate that the self-incompatibility with self-pollination is due to decrease of ACh and cAMP, causing reduction of ChAT and AC (adenylate cyclase) and concise elevation of AChE and PDE (cAMP phosphodiesterase), and therefore suppressed growth of pollen tubes.
ESTHER : Tezuka_2007_J.Plant.Physiol_164_878
PubMedSearch : Tezuka_2007_J.Plant.Physiol_164_878
PubMedID: 16882455

Title : Molecular analysis of an inactive aflatoxin biosynthesis gene cluster in Aspergillus oryzae RIB strains - Tominaga_2006_Appl.Environ.Microbiol_72_484
Author(s) : Tominaga M , Lee YH , Hayashi R , Suzuki Y , Yamada O , Sakamoto K , Gotoh K , Akita O
Ref : Applied Environmental Microbiology , 72 :484 , 2006
Abstract : To help assess the potential for aflatoxin production by Aspergillus oryzae, the structure of an aflatoxin biosynthesis gene homolog cluster in A. oryzae RIB 40 was analyzed. Although most genes in the corresponding cluster exhibited from 97 to 99% similarity to those of Aspergillus flavus, three genes shared 93% similarity or less. A 257-bp deletion in the aflT region, a frameshift mutation in norA, and a base pair substitution in verA were found in A. oryzae RIB 40. In the aflR promoter, two substitutions were found in one of the three putative AreA binding sites and in the FacB binding site. PCR primers were designed to amplify homologs of aflT, nor-1, aflR, norA, avnA, verB, and vbs and were used to detect these genes in 210 A. oryzae strains. Based on the PCR results, the A. oryzae RIB strains were classified into three groups, although most of them fell into two of the groups. Group 1, in which amplification of all seven genes was confirmed, contained 122 RIB strains (58.1% of examined strains), including RIB 40. Seventy-seven strains (36.7%) belonged to group 2, characterized by having only vbs, verB, and avnA in half of the cluster. Although slight expression of aflR was detected by reverse transcription-PCR in some group 1 strains, including RIB 40, other genes (avnA, vbs, verB, and omtA) related to aflatoxin production were not detected. aflR was not detected in group 2 strains by Southern analysis.
ESTHER : Tominaga_2006_Appl.Environ.Microbiol_72_484
PubMedSearch : Tominaga_2006_Appl.Environ.Microbiol_72_484
PubMedID: 16391082
Gene_locus related to this paper: aspor-PKSL1 , asppa-q6ueg5

Title : Characterization and cloning of the chlorophyll-degrading enzyme pheophorbidase from cotyledons of radish - Suzuki_2006_Plant.Physiol_140_716
Author(s) : Suzuki Y , Amano T , Shioi Y
Ref : Plant Physiol , 140 :716 , 2006
Abstract : Enzymatic removal of the methoxycarbonyl group of pheophorbide (Pheid) a in chlorophyll degradation was investigated in cotyledons of radish (Raphanus sativus). The enzyme pheophorbidase (PPD) catalyzes the conversion of Pheid a to a precursor of pyropheophorbide (PyroPheid), C-13(2)-carboxylPyroPheid a, by demethylation, and then the precursor is decarboxylated nonenzymatically to yield PyroPheid a. PPD activity sharply increased with the progression of senescence in radish, suggesting de novo synthesis of PPD. The enzyme activity was separated into two peaks in anion-exchange and hydrophobic chromatography; the terms type 1 and type 2 were applied according to the order of elution of these enzymes in anion-exchange chromatography. PPD types 1 and 2 were purified 9,999- and 6,476-fold, with a yield of 0.703% and 2.73%, respectively. Among 12 substrates tested, both enzymes were extremely specific for Pheids of the dihydroporphyrin and tetrahydroporphyrin types, indicating that they are responsible for the formation of these PyroPheids. Both PPDs had molecular masses of 113,000 kD on gel filtration and showed three bands of 16.8, 15.9, and 11.8 kD by SDS-PAGE. The partial N-terminal amino acid sequences for these bands of PPD (type 2) were determined. Based on their N-terminal amino acid sequences, a full-length cDNA of PPD was cloned. The molecular structure of PPD, particularly the molecular mass and subunit structure, is discussed in relation to the results of SDS-PAGE.
ESTHER : Suzuki_2006_Plant.Physiol_140_716
PubMedSearch : Suzuki_2006_Plant.Physiol_140_716
PubMedID: 16384908
Gene_locus related to this paper: arath-AT4G16690 , rapsa-q2v0w1

Title : A major urinary protein of the domestic cat regulates the production of felinine, a putative pheromone precursor - Miyazaki_2006_Chem.Biol_13_1071
Author(s) : Miyazaki M , Yamashita T , Suzuki Y , Saito Y , Soeta S , Taira H , Suzuki A
Ref : Chemical Biology , 13 :1071 , 2006
Abstract : Domestic cats spray urine with species-specific odor for territorial marking. Felinine (2-amino-7-hydroxy-5,5-dimethyl-4-thiaheptanoic acid), a putative pheromone precursor, is excreted in cat urine. Here, we report that cauxin, a carboxylesterase excreted as a major urinary component, regulates felinine production. In vitro enzyme assays indicated that cauxin hydrolyzed the felinine precursor 3-methylbutanol-cysteinylglycine to felinine and glycine. Cauxin and felinine were excreted age dependently after 3 months of age. The age-dependent increases in cauxin and felinine excretion were significantly correlated. In mature cats, cauxin and felinine levels were sex-dependently correlated and were higher in males than in females. In headspace gas of cat urine, 3-mercapto-3-methyl-1-butanol, 3-mercapto-3-methylbutyl formate, 3-methyl-3-methylthio-1-butanol, and 3-methyl-3-(2-methyldisulfanyl)-1-butanol were identified as candidates for felinine derivatives. These findings demonstrate that cauxin-dependent felinine production is a cat-specific metabolic pathway, and they provide information for the biosynthetic mechanisms of species-specific molecules in mammals.
ESTHER : Miyazaki_2006_Chem.Biol_13_1071
PubMedSearch : Miyazaki_2006_Chem.Biol_13_1071
PubMedID: 17052611
Gene_locus related to this paper: felca-CAUXIN

Title : D-threo-1-phenyl-2-decanoylamino-3-morpholino-1-propanol alters cellular cholesterol homeostasis by modulating the endosome lipid domains - Makino_2006_Biochemistry_45_4530
Author(s) : Makino A , Ishii K , Murate M , Hayakawa T , Suzuki Y , Suzuki M , Ito K , Fujisawa T , Matsuo H , Ishitsuka R , Kobayashi T
Ref : Biochemistry , 45 :4530 , 2006
Abstract : D-threo-1-phenyl-2-decanoylamino-3-morpholino-1-propanol (D-PDMP) is a frequently used inhibitor of glycosphingolipid biosynthesis. However, some interesting characteristics of D-PDMP cannot be explained by the inhibition of glycolipid synthesis alone. In the present study, we showed that d-PDMP inhibits the activation of lysosomal acid lipase by late endosome/lysosome specific lipid, bis(monoacylglycero)phosphate (also called as lysobisphosphatidic acid), through alteration of membrane structure of the lipid. When added to cultured fibroblasts, D-PDMP inhibits the degradation of low-density lipoprotein (LDL) and thus accumulates both cholesterol ester and free cholesterol in late endosomes/lysosomes. This accumulation results in the inhibition of LDL-derived cholesterol esterification and the decrease of cell surface cholesterol. We showed that D-PDMP alters cellular cholesterol homeostasis in a glycosphingolipid-independent manner using L-PDMP, a stereoisomer of D-PDMP, which does not inhibit glycosphingolipid synthesis, and mutant melanoma cell which is defective in glycolipid synthesis. Altering cholesterol homeostasis by D-PDMP explains the unique characteristics of sensitizing multidrug resistant cells by this drug.
ESTHER : Makino_2006_Biochemistry_45_4530
PubMedSearch : Makino_2006_Biochemistry_45_4530
PubMedID: 16584188

Title : Common inheritance of chromosome Ia associated with clonal expansion of Toxoplasma gondii - Khan_2006_Genome.Res_16_1119
Author(s) : Khan A , Bohme U , Kelly KA , Adlem E , Brooks K , Simmonds M , Mungall K , Quail MA , Arrowsmith C , Chillingworth T , Churcher C , Harris D , Collins M , Fosker N , Fraser A , Hance Z , Jagels K , Moule S , Murphy L , O'Neil S , Rajandream MA , Saunders D , Seeger K , Whitehead S , Mayr T , Xuan X , Watanabe J , Suzuki Y , Wakaguri H , Sugano S , Sugimoto C , Paulsen I , Mackey AJ , Roos DS , Hall N , Berriman M , Barrell B , Sibley LD , Ajioka JW
Ref : Genome Res , 16 :1119 , 2006
Abstract : Toxoplasma gondii is a globally distributed protozoan parasite that can infect virtually all warm-blooded animals and humans. Despite the existence of a sexual phase in the life cycle, T. gondii has an unusual population structure dominated by three clonal lineages that predominate in North America and Europe, (Types I, II, and III). These lineages were founded by common ancestors approximately10,000 yr ago. The recent origin and widespread distribution of the clonal lineages is attributed to the circumvention of the sexual cycle by a new mode of transmission-asexual transmission between intermediate hosts. Asexual transmission appears to be multigenic and although the specific genes mediating this trait are unknown, it is predicted that all members of the clonal lineages should share the same alleles. Genetic mapping studies suggested that chromosome Ia was unusually monomorphic compared with the rest of the genome. To investigate this further, we sequenced chromosome Ia and chromosome Ib in the Type I strain, RH, and the Type II strain, ME49. Comparative genome analyses of the two chromosomal sequences revealed that the same copy of chromosome Ia was inherited in each lineage, whereas chromosome Ib maintained the same high frequency of between-strain polymorphism as the rest of the genome. Sampling of chromosome Ia sequence in seven additional representative strains from the three clonal lineages supports a monomorphic inheritance, which is unique within the genome. Taken together, our observations implicate a specific combination of alleles on chromosome Ia in the recent origin and widespread success of the clonal lineages of T. gondii.
ESTHER : Khan_2006_Genome.Res_16_1119
PubMedSearch : Khan_2006_Genome.Res_16_1119
PubMedID: 16902086
Gene_locus related to this paper: toxgo-q1jt22

Title : Tea catechins with a galloyl moiety suppress postprandial hypertriacylglycerolemia by delaying lymphatic transport of dietary fat in rats - Ikeda_2005_J.Nutr_135_155
Author(s) : Ikeda I , Tsuda K , Suzuki Y , Kobayashi M , Unno T , Tomoyori H , Goto H , Kawata Y , Imaizumi K , Nozawa A , Kakuda T
Ref : J Nutr , 135 :155 , 2005
Abstract : Tea catechins, (-)-epicatechin (EC), (-)-epigallocatechin (EGC), (-)-epicatechin gallate (ECG), and (-)-epigallocatechin gallate (EGCG), have been shown to be epimerized to (-)-catechin (C), (-)-gallocatechin (GC), (-)-catechin gallate (CG), and (-)-gallocatechin gallate (GCG), respectively, during heat treatment. In this study, we examined the effect of tea catechins rich in ECG and EGCG and heat-treated tea catechins rich in CG and GCG on postprandial hypertriacylglycerolemia in rats. Both tea catechins and heat-treated tea catechins suppressed postprandial hypertriacylglycerolemia. Lymphatic recovery of (14)C-trioleoylglycerol in rats cannulated in the thoracic duct was delayed by the administration of tea catechins and heat-treated tea catechins. Tea catechins and heat-treated tea catechins had the same effect on all variables tested. These catechin preparations dose-dependently inhibited the activity of pancreatic lipase in vitro. When purified catechins were used, only those with a galloyl moiety inhibited the activity of pancreatic lipase. These results suggest that catechins with a galloyl moiety suppress postprandial hypertriacylglycerolemia by slowing down triacylglycerol absorption through the inhibition of pancreatic lipase. Because postprandial hypertriacylglycerolemia is a risk factor for coronary heart disease, our results suggest that catechins with a galloyl moiety may prevent this disease.
ESTHER : Ikeda_2005_J.Nutr_135_155
PubMedSearch : Ikeda_2005_J.Nutr_135_155
PubMedID: 15671206

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

Title : Substitution rate and structural divergence of 5'UTR evolution: comparative analysis between human and cynomolgus monkey cDNAs - Osada_2005_Mol.Biol.Evol_22_1976
Author(s) : Osada N , Hirata M , Tanuma R , Kusuda J , Hida M , Suzuki Y , Sugano S , Gojobori T , Shen CK , Wu CI , Hashimoto K
Ref : Molecular Biology Evolution , 22 :1976 , 2005
Abstract : The substitution rate and structural divergence in the 5'-untranslated region (UTR) were investigated by using human and cynomolgus monkey cDNA sequences. Due to the weaker functional constraint in the UTR than in the coding sequence, the divergence between humans and macaques would provide a good estimate of the nucleotide substitution rate and structural divergence in the 5'UTR. We found that the substitution rate in the 5'UTR (K5UTR) averaged approximately 10%-20% lower than the synonymous substitution rate (Ks). However, both the K5UTR and nonsynonymous substitution rate (Ka) were significantly higher in the testicular cDNAs than in the brain cDNAs, whereas the Ks did not differ. Further, an in silico analysis revealed that 27% (169/622) of macaque testicular cDNAs had an altered exon-intron structure in the 5'UTR compared with the human cDNAs. The fraction of cDNAs with an exon alteration was significantly higher in the testicular cDNAs than in the brain cDNAs. We confirmed by using reverse transcriptase-polymerase chain reaction that about one-third (6/16) of in silico "macaque-specific" exons in the 5'UTR were actually macaque specific in the testis. The results imply that positive selection increased K5UTR and structural alteration rate of a certain fraction of genes as well as Ka. We found that both positive and negative selection can act on the 5'UTR sequences.
ESTHER : Osada_2005_Mol.Biol.Evol_22_1976
PubMedSearch : Osada_2005_Mol.Biol.Evol_22_1976
PubMedID: 15944441
Gene_locus related to this paper: macfa-abhd2 , macfa-ndrg2 , macfa-PPT1 , macfa-q4r3b2 , macfa-q4r3p4 , macfa-q4r3z0 , macfa-q4r4j8 , macfa-q4r4q3 , macfa-q4r4s5 , macmu-f6rbn1 , macfa-q4r5r1 , macfa-q4r8p0 , macfa-q4r8v0 , macfa-q4r584 , macfa-q4r766 , macfa-SPG21

Title : Secretion of bacterial xenobiotic-degrading enzymes from transgenic plants by an apoplastic expressional system: an applicability for phytoremediation - Uchida_2005_Environ.Sci.Technol_39_7671
Author(s) : Uchida E , Ouchi T , Suzuki Y , Yoshida T , Habe H , Yamaguchi I , Omori T , Nojiri H
Ref : Environ Sci Technol , 39 :7671 , 2005
Abstract : In search of an effective method for phytoremediation of wastewater contaminated with organic compounds, we investigated the application of an apoplastic expressional system that secretes useful bacterial enzymes from transgenic plants into hydroponic media through the addition of a targeting signal. We constructed transgenic Arabidopsis expressing the aromatic-cleaving extradiol dioxygenase (DbfB), which degrades 2,3-dihydroxybiphenyl (2,3-DHB), and transgenic tobacco expressing haloalkane dehalogenase (DhaA), which catalyzes hydrolytic dechlorination of 1-chlorobutane (1-CB). Although crude leaf extracts of transgenic plants expressing cytoplasm-targeted degradative enzymes showed higher activity than did those from transgenic plants expressing apoplast-targeted enzymes, the hydroponic media of the latter showed 23.2 times (DbfB) and 76.4 times (DhaA) higher activity than plants containing the cytoplasm-targeted enzymes. Addition of crystalline 2,3-DHB to 100 mL of the hydroponic medium of transgenic or wild-type seedlings revealed that only medium from the transgenic Arabidopsis expressing apoplast-targeted DbfB showed rapid ring cleavage of 2,3-DHB. Transgenic tobacco expressing apoplast-targeted DhaA also resulted in the accumulation of the dehalogenation product 1-butanol in the hydroponic medium and showed a higher tolerance to 1-CB than wild-type or transgenic plants expressing cytoplasm-targeted DhaA. These results demonstrate the usefulness of the apoplastic expression of bacterial recombinant proteins in phytoremediation.
ESTHER : Uchida_2005_Environ.Sci.Technol_39_7671
PubMedSearch : Uchida_2005_Environ.Sci.Technol_39_7671
PubMedID: 16245843

Title : Genetic and functional properties of uncultivated thermophilic crenarchaeotes from a subsurface gold mine as revealed by analysis of genome fragments - Nunoura_2005_Environ.Microbiol_7_1967
Author(s) : Nunoura T , Hirayama H , Takami H , Oida H , Nishi S , Shimamura S , Suzuki Y , Inagaki F , Takai K , Nealson KH , Horikoshi K
Ref : Environ Microbiol , 7 :1967 , 2005
Abstract : Within a phylum Crenarchaeota, only some members of the hyperthermophilic class Thermoprotei, have been cultivated and characterized. In this study, we have constructed a metagenomic library from a microbial mat formation in a subsurface hot water stream of the Hishikari gold mine, Japan, and sequenced genome fragments of two different phylogroups of uncultivated thermophilic Crenarchaeota: (i) hot water crenarchaeotic group (HWCG) I (41.2 kb), and (ii) HWCG III (49.3 kb). The genome fragment of HWCG I contained a 16S rRNA gene, two tRNA genes and 35 genes encoding proteins but no 23S rRNA gene. Among the genes encoding proteins, several genes for putative aerobic-type carbon monoxide dehydrogenase represented a potential clue with regard to the yet unknown metabolism of HWCG I Archaea. The genome fragment of HWCG III contained a 16S/23S rRNA operon and 44 genes encoding proteins. In the 23S rRNA gene, we detected a homing-endonuclease encoding a group I intron similar to those detected in hyperthermophilic Crenarchaeota and Bacteria, as well as eukaryotic organelles. The reconstructed phylogenetic tree based on the 23S rRNA gene sequence reinforced the intermediate phylogenetic affiliation of HWCG III bridging the hyperthermophilic and non-thermophilic uncultivated Crenarchaeota.
ESTHER : Nunoura_2005_Environ.Microbiol_7_1967
PubMedSearch : Nunoura_2005_Environ.Microbiol_7_1967
PubMedID: 16309394
Gene_locus related to this paper: 9bact-h5srl9 , 9chlr-h5sfm8 , 9arch-e6n6u9

Title : The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC) - Gerhard_2004_Genome.Res_14_2121
Author(s) : Gerhard DS , Wagner L , Feingold EA , Shenmen CM , Grouse LH , Schuler G , Klein SL , Old S , Rasooly R , Good P , Guyer M , Peck AM , Derge JG , Lipman D , Collins FS , Jang W , Sherry S , Feolo M , Misquitta L , Lee E , Rotmistrovsky K , Greenhut SF , Schaefer CF , Buetow K , Bonner TI , Haussler D , Kent J , Kiekhaus M , Furey T , Brent M , Prange C , Schreiber K , Shapiro N , Bhat NK , Hopkins RF , Hsie F , Driscoll T , Soares MB , Casavant TL , Scheetz TE , Brown-stein MJ , Usdin TB , Toshiyuki S , Carninci P , Piao Y , Dudekula DB , Ko MS , Kawakami K , Suzuki Y , Sugano S , Gruber CE , Smith MR , Simmons B , Moore T , Waterman R , Johnson SL , Ruan Y , Wei CL , Mathavan S , Gunaratne PH , Wu J , Garcia AM , Hulyk SW , Fuh E , Yuan Y , Sneed A , Kowis C , Hodgson A , Muzny DM , McPherson J , Gibbs RA , Fahey J , Helton E , Ketteman M , Madan A , Rodrigues S , Sanchez A , Whiting M , Madari A , Young AC , Wetherby KD , Granite SJ , Kwong PN , Brinkley CP , Pearson RL , Bouffard GG , Blakesly RW , Green ED , Dickson MC , Rodriguez AC , Grimwood J , Schmutz J , Myers RM , Butterfield YS , Griffith M , Griffith OL , Krzywinski MI , Liao N , Morin R , Palmquist D , Petrescu AS , Skalska U , Smailus DE , Stott JM , Schnerch A , Schein JE , Jones SJ , Holt RA , Baross A , Marra MA , Clifton S , Makowski KA , Bosak S , Malek J
Ref : Genome Res , 14 :2121 , 2004
Abstract : The National Institutes of Health's Mammalian Gene Collection (MGC) project was designed to generate and sequence a publicly accessible cDNA resource containing a complete open reading frame (ORF) for every human and mouse gene. The project initially used a random strategy to select clones from a large number of cDNA libraries from diverse tissues. Candidate clones were chosen based on 5'-EST sequences, and then fully sequenced to high accuracy and analyzed by algorithms developed for this project. Currently, more than 11,000 human and 10,000 mouse genes are represented in MGC by at least one clone with a full ORF. The random selection approach is now reaching a saturation point, and a transition to protocols targeted at the missing transcripts is now required to complete the mouse and human collections. Comparison of the sequence of the MGC clones to reference genome sequences reveals that most cDNA clones are of very high sequence quality, although it is likely that some cDNAs may carry missense variants as a consequence of experimental artifact, such as PCR, cloning, or reverse transcriptase errors. Recently, a rat cDNA component was added to the project, and ongoing frog (Xenopus) and zebrafish (Danio) cDNA projects were expanded to take advantage of the high-throughput MGC pipeline.
ESTHER : Gerhard_2004_Genome.Res_14_2121
PubMedSearch : Gerhard_2004_Genome.Res_14_2121
PubMedID: 15489334
Gene_locus related to this paper: human-AFMID , human-CES4A , human-CES5A , human-NOTUM , human-SERAC1 , human-SERHL2 , human-TMEM53 , mouse-acot1 , mouse-adcl4 , mouse-Ces2f , mouse-Ces4a , mouse-notum , mouse-q6wqj1 , mouse-Q9DAI6 , mouse-rbbp9 , mouse-SERHL , mouse-srac1 , mouse-tmm53 , rat-abhd6 , rat-abhda , rat-abhea , rat-abheb , rat-Ldah , rat-cd029 , rat-estd , rat-Kansl3 , rat-nceh1 , ratno-acph , ratno-CMBL , mouse-b2rwd2 , rat-b5den3 , rat-ab17c

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 : Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D - Matsuzaki_2004_Nature_428_653
Author(s) : Matsuzaki M , Misumi O , Shin IT , Maruyama S , Takahara M , Miyagishima SY , Mori T , Nishida K , Yagisawa F , Yoshida Y , Nishimura Y , Nakao S , Kobayashi T , Momoyama Y , Higashiyama T , Minoda A , Sano M , Nomoto H , Oishi K , Hayashi H , Ohta F , Nishizaka S , Haga S , Miura S , Morishita T , Kabeya Y , Terasawa K , Suzuki Y , Ishii Y , Asakawa S , Takano H , Ohta N , Kuroiwa H , Tanaka K , Shimizu N , Sugano S , Sato N , Nozaki H , Ogasawara N , Kohara Y , Kuroiwa T
Ref : Nature , 428 :653 , 2004
Abstract : Small, compact genomes of ultrasmall unicellular algae provide information on the basic and essential genes that support the lives of photosynthetic eukaryotes, including higher plants. Here we report the 16,520,305-base-pair sequence of the 20 chromosomes of the unicellular red alga Cyanidioschyzon merolae 10D as the first complete algal genome. We identified 5,331 genes in total, of which at least 86.3% were expressed. Unique characteristics of this genomic structure include: a lack of introns in all but 26 genes; only three copies of ribosomal DNA units that maintain the nucleolus; and two dynamin genes that are involved only in the division of mitochondria and plastids. The conserved mosaic origin of Calvin cycle enzymes in this red alga and in green plants supports the hypothesis of the existence of single primary plastid endosymbiosis. The lack of a myosin gene, in addition to the unexpressed actin gene, suggests a simpler system of cytokinesis. These results indicate that the C. merolae genome provides a model system with a simple gene composition for studying the origin, evolution and fundamental mechanisms of eukaryotic cells.
ESTHER : Matsuzaki_2004_Nature_428_653
PubMedSearch : Matsuzaki_2004_Nature_428_653
PubMedID: 15071595
Gene_locus related to this paper: cyam1-m1vi61 , cyam1-m1vhh9

Title : A novel thermostable esterase from the thermoacidophilic archaeon Sulfolobus tokodaii strain 7 - Suzuki_2004_FEMS.Microbiol.Lett_236_97
Author(s) : Suzuki Y , Miyamoto K , Ohta H
Ref : FEMS Microbiology Letters , 236 :97 , 2004
Abstract : We have characterized an esterase expressed from the putative esterase gene (ST0071) selected from the total genome analysis from the thermoacidophilic archaeon Sulfolobus tokodaii strain 7. The ORF was cloned and expressed as a fusion protein in Escherichia coli. The protein was purified with heat treatment, affinity column chromatography, and size exclusion filtration. The optimum activity for ester cleavage against p-nitrophenyl esters was observed at around 70 degrees C and pH 7.5-8.0. The enzyme exhibited high thermostability and also showed activity in a mixture of a buffer and water-miscible organic solvents, such as acetonitrile and dimethyl sulfoxide. From the kinetic analysis, p-nitrophenyl butyrate was found to be a better substrate than caproate and caprylate.
ESTHER : Suzuki_2004_FEMS.Microbiol.Lett_236_97
PubMedSearch : Suzuki_2004_FEMS.Microbiol.Lett_236_97
PubMedID: 15212797
Gene_locus related to this paper: sulto-ST0071

Title : Type II platelet-activating factor-acetylhydrolase is essential for epithelial morphogenesis in Caenorhabditis elegans - Inoue_2004_Proc.Natl.Acad.Sci.U.S.A_101_13233
Author(s) : Inoue T , Sugimoto A , Suzuki Y , Yamamoto M , Tsujimoto M , Inoue K , Aoki J , Arai H
Ref : Proc Natl Acad Sci U S A , 101 :13233 , 2004
Abstract : Type II platelet-activating factor-acetylhydrolase [PAF-AH (II)] is an N-myristoylated enzyme that contains a lipase/esterase catalytic motif and selectively hydrolyzes the sn-2 acetyl ester of PAF and other short-chain acyl groups attached to phosphoglycerides. However, the physiological role of this enzyme remains to be elucidated. PAF-AH (II) is conserved in a variety of species ranging from a simple multicellular organism, Caenorhabditis elegans, to mammals. C. elegans possesses two homologous PAF-AH (II) genes, named paf-1 and paf-2. In this study, we generated these two loss-of-function mutants to elucidate the in vivo PAF-AH (II) function. Surprisingly, mutants of paf-2, a major isoform of C. elegans PAF-AH (II)s, exhibits gross defects in epithelial sheet formation, resulting in unsuccessful subsequent morphogenesis with complete penetrance. Moreover, paf-2 RNA interference worms show a variable abnormal morphology, including ectopic protrusions and a lumpy shape at the late embryonic and early larval stages due to epithelial organization defects. Consistent with these phenotypes, PAF-AH (II) is predominantly expressed in epithelial cells of C. elegans. This study demonstrates that PAF-AH (II) is essential for epithelial morphogenesis.
ESTHER : Inoue_2004_Proc.Natl.Acad.Sci.U.S.A_101_13233
PubMedSearch : Inoue_2004_Proc.Natl.Acad.Sci.U.S.A_101_13233
PubMedID: 15340150
Gene_locus related to this paper: caeel-pafa , caeel-W03G9.6

Title : Vesicular acetylcholine transporter can be a morphological marker for the reinnervation to muscle of regenerating motor axons - Maeda_2004_Neurosci.Res_48_305
Author(s) : Maeda M , Ohba N , Nakagomi S , Suzuki Y , Kiryu-Seo S , Namikawa K , Kondoh W , Tanaka A , Kiyama H
Ref : Neurosci Res , 48 :305 , 2004
Abstract : This study was designed to evaluate whether the vesicular acetylcholine transporter (VAChT), which packages acetylcholine into synaptic vesicles, can be used as a marker for regenerating motor axon terminal. We examined motor axon regeneration in the tongue after hypoglossal nerve axotomy, using an anterograde tracer biotin-dextran (BD), retrograde tracer Fluoro-Gold (FG), electron microscopic (EM) observation, and VAChT immunocytochemistry. BD study demonstrated that outgrowth of thin regenerating axons into the frontal area of the tongue was firstly observed at 14 post-operative days, and presynaptic formation of neuromuscular junction (NMJ) was observed from 21 post-operative days. Under electron microscopic observation, reconstruction of new NMJs was observed within the interval between 21 and 28 days. VAChT-immunoreactive nerve terminals disappeared by 3 days after axotomy, slightly appeared at 14 post-operative days, and thereafter gradually increased in number from 21 to 28 post-operative days. The re-expression of VAChT positive presynaptic terminal was almost the same as those obtained in BD, FG and EM studies. Regenerating axons tip in the crush model of the hypoglossal nerve exhibited prominent VAChT immunoreactivity in growing tip of regenerating axons. These indicate that VAChT is an excellent morphological indicator for regenerating nerve terminals of motor neurons.
ESTHER : Maeda_2004_Neurosci.Res_48_305
PubMedSearch : Maeda_2004_Neurosci.Res_48_305
PubMedID: 15154676

Title : Correlation between structure of the lactones and substrate specificity in enzyme-catalyzed polymerization for the synthesis of polyesters - Suzuki_2003_Biomacromolecules_4_537
Author(s) : Suzuki Y , Taguchi S , Hisano T , Toshima K , Matsumura S , Doi Y
Ref : Biomacromolecules , 4 :537 , 2003
Abstract : Small-size (4-membered) and medium-size (5-, 6-, and 7-membered) unsubstituted lactones as well as unsubstituted macrolides (12 and 13 membered) were subjected to the ring-opening polymerization using the extracellular PHB depolymerase from Alcaligenes faecalis T1 (PhaZ(Afa)). The characteristic reactivities of the lactones were discussed based on a tertiary structure model of the active site of the PhaZ(Afa). With respect to the ring-size of the lactones, the 4-membered beta-propiolactone and 6-membered delta-valerolactone (delta-VL) showed the highest polymerization activity, and delta-VL seemed to be the upper size limit for the molecular recognition of the narrow active site cleft of PhaZ(Afa). On the other hand, epsilon-caprolactone, 11-undecanolide, and 12-dodecanolide, which showed excellent polymerization activities by lipases, were scarcely polymerized by PhaZ(Afa). This was ascribed to the difference in the recognition sites between PhaZ(Afa) and lipase. In addition, the effect of the substrate-binding domain of PhaZ(Afa) and the enantioselective ring-opening polymerization of (R,S)-beta-butyrolactone ((R,S)-beta-BL) were studied. The substrate-binding domain lacking PhaZ(Afa) showed higher reactivities than PhaZ(Afa) for the polymerization of the lactones and that a significant enantioselectivity was observed at the early stage of the polymerization of (R,S)-beta-BL to produce the (R)-enriched optically active poly(3-hydroxybutyrate).
ESTHER : Suzuki_2003_Biomacromolecules_4_537
PubMedSearch : Suzuki_2003_Biomacromolecules_4_537
PubMedID: 12741767

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

Title : Cholinergic inhibition of electrogenic sodium absorption in the guinea pig distal colon - Hayashi_2003_Am.J.Physiol.Gastrointest.Liver.Physiol_284_G617
Author(s) : Hayashi H , Suzuki T , Yamamoto T , Suzuki Y
Ref : American Journal of Physiology Gastrointest Liver Physiol , 284 :G617 , 2003
Abstract : Submucosal cholinergic and noncholinergic neurons in intestines have been shown to be involved in regulating epithelial transport functions, particularly stimulating Cl(-) secretion. This study investigates the role of submucosal cholinergic neurons in regulating electrogenic Na(+) absorption in distal colon. Amiloride-sensitive short-circuit current (I(sc)) and (22)Na(+) flux were measured in mucosal and mucosal-submucosal preparations mounted in Ussing chambers. In the mucosal preparation, carbachol (CCh) added to the serosal side inhibited amiloride-sensitive I(sc) and amiloride-sensitive (22)Na(+) absorption. The inhibitory effect of CCh was observed at approximately 0.1 microM, and maximum inhibition of approximately 70% was attained at approximately 30 microM (IC(50) = approximately 1 microM). CCh-induced inhibition of amiloride-sensitive I(sc) was almost totally abolished by 10 microM atropine. Treatment of the tissue with ionomycin markedly reduced amiloride-sensitive I(sc), but a subsequent addition of CCh further decreased it. Also, CCh still had an inhibitory effect, although significantly attenuated, after the tissue had been incubated with a low-Ca(2+) solution containing ionomycin and BAPTA-AM. Applying electrical field stimulation to submucosal neurons in the mucosal-submucosal preparation resulted in inhibition of amiloride-sensitive I(sc), approximately 33% of this inhibition being atropine sensitive. Physostigmine inhibited amiloride-sensitive I(sc), this effect being abolished by atropine. In conclusion, submucosal cholinergic and noncholinergic neurons were involved in inhibiting electrogenic Na(+) absorption in colon. This inhibition by cholinergic neurons was mediated by muscarinic receptor activation.
ESTHER : Hayashi_2003_Am.J.Physiol.Gastrointest.Liver.Physiol_284_G617
PubMedSearch : Hayashi_2003_Am.J.Physiol.Gastrointest.Liver.Physiol_284_G617
PubMedID: 12444010

Title : Two enzymatic reaction pathways in the formation of pyropheophorbide a - Suzuki_2002_Photosynth.Res_74_225
Author(s) : Suzuki Y , Doi M , Shioi Y
Ref : Photosynth Res , 74 :225 , 2002
Abstract : The demethoxycarbonyl reaction of pheophorbide a in plants and algae was investigated. Two types of enzyme that catalyze alternative reactions in the formation of pyropheophorbide a were found. One enzyme, designated 'pheophorbidase (Phedase)', was purified nearly to homogeneity from cotyledons of radish (Raphanus sativus). This enzyme catalyzes the conversion of pheophorbide a to a precursor of pyropheophorbide a, C-13(2)-carboxylpyropheophorbide a, by demethylation, and then the precursor is decarboxylated non-enzymatically to yield pyropheophorbide a. The activity of Phedase was inhibited by the reaction product, methanol. The other enzyme, termed 'pheophorbide demethoxycarbonylase (PDC)', was highly purified from the Chl b-less mutant NL-105 of Chlamydomonas reinhardtii. This enzyme had produced no intermediate as shown in the Phedase reaction, indicating that it converts pheophorbide a directly into pyropheophorbide a, probably by nucleophilic reaction. Phedase and PDC consisted of both senescence-induced and constitutive enzymes. The molecular weight of both Phedases was 113 000 and of senescence-induced PDC was 170 000. The K (m) values against pheophorbide a for both Phedases were 14-15 muM and 283 muM for senescence-induced PDC. The activity of both Phedases was inhibited by the reaction product, methanol, whereas methanol had no specific effect on senescence-induced PDC. Phenylmethylsulfonic fluoride and N-ethylmaleimide inhibited the senescence-induced Phedase and PDC, respectively. Among the 23 species from 15 different families tested, Phedase activity was found in 10 species from three families. PDC activity was not detected in plants lacking Phedase activity, except for Chlamydomonas. Based on these findings, a likely conclusion is that at least two alternative pathways that are catalyzed by two different enzymes, Phedase and PDC, exist for the formation of pyropheophorbide a.
ESTHER : Suzuki_2002_Photosynth.Res_74_225
PubMedSearch : Suzuki_2002_Photosynth.Res_74_225
PubMedID: 16228561
Gene_locus related to this paper: rapsa-q2v0w1

Title : Innervation of NADPH diaphorase-containing neurons correlated with acetylcholinesterase, tyrosine hydroxylase, and neuropeptides in the pigeon cloaca - Atoji_2001_J.Anat_198_181
Author(s) : Atoji Y , Yamamoto Y , Suzuki Y
Ref : Journal of Anatomy , 198 :181 , 2001
Abstract : The motility of the avian cloaca is under neural control, but little is known about the neural network that accomplishes this function. This present study was designed to determine the distribution of nitric oxide-synthesising neurons in the pigeon cloaca by enzyme histochemistry for reduced nicotinamide adenine dinucleotide phosphate-diaphorase (NADPH-d). NADPH-d-positive staining was seen in the neurons and fibres in the cloaca. The highest density of nerve fibres was noted in the coprodeum and the lowest in the proctodeum. In the coprodeum, NADPH-d neurons were found singly, formed small groups of 2-10 neurons, or were seen in plexuses in the muscle layer, lamina propria, or around the arterioles. Several NADPH-d-positive neurons were also observed in the ganglia of the cloaca. NADPH-d fibres ran in the muscle layer, lamina muscularis mucosae and lamina propria, or surrounded blood vessels. The distribution pattern of acetylcholinesterase (AChE)-stained neurons and fibres in the cloaca was similar to that of NADPH-d. Double staining for NADPH-d and AChE showed colocalisation of the 2 enzymes in many neurons of the cloaca. Tyrosine hydroxylase (TH)-immunoreactive nerve fibres originating outside the cloaca were also noted. In the urodeum and proctodeum, neurons or fibres positive for NADPH-d, AChE or TH were scattered in the lamina propria. Nerve fibres immunoreactive for calcitonin-gene related peptide, galanin, methionine-enkephalin, substance P, and vasoactive intestinal peptide were found sparsely in the cloaca. Our results demonstrate that nitrergic neurons constitute a subpopulation which is closely associated with the cholinergic system in the pigeon cloaca.
ESTHER : Atoji_2001_J.Anat_198_181
PubMedSearch : Atoji_2001_J.Anat_198_181
PubMedID: 11273043

Title : Innervation of the pigeon oviduct: correlation of NADPH diaphorase with acetylcholinesterase, tyrosine hydroxylase, and neuropeptides - Atoji_2000_Auton.Neurosci_84_1
Author(s) : Atoji Y , Mizutani K , Yamamoto Y , Suzuki Y
Ref : Auton Neurosci , 84 :1 , 2000
Abstract : The motility of the avian oviduct is controlled by hormones and neurons, but little is microscopically known about a neural network in the oviduct. The present study was investigated to determine the distribution of nitric oxide-synthesizing neurons in the oviduct of the pigeon by histochemistry for nicotinamide adenine dinucleotide phosphate-diaphorase (NADPH-d). The NADPH-d reaction was seen in the neurons and fibers. NADPH-d neurons were mainly distributed around the arterioles of the intermuscular tissue in the upper oviduct (infundibulum, magnum, and isthmus); in addition, NADPH-d neurons were also seen in the smooth muscle layers and lamina propria in the lower oviduct (uterus and vagina). NADPH-d neurons were found singly or in small groups of two-eight cell bodies. The number of NADPH-d neurons was smallest in the infundibulum, gradually increased toward the vagina. NADPH-d was also shown to be strongly positive in many neurons in the ganglia of the vaginal adventitia. Bundles of NADPH-d fibers ran in the smooth muscle layer, surrounded blood vessels, or connected with small groups of NADPH-d neurons by forming strands. Thin fibers branched from these bundles and constituted a finer network in the smooth muscle layer and lamina propria. Acetylcholinesterase staining in neurons and fibers showed a similar pattern of NADPH-d distribution in the oviduct. By double staining, 70 approximately 77% of neurons showed colocalization of NADPH-d and acetylcholinesterase in the uterus and vagina. Tyrosine hydroxylase immunoreactivity stained only nerve fibers and were distributed largely around blood vessels in the oviduct. Nerve fibers immunoreactive for calcitonin-gene related peptide, galanin, methionine-enkephalin, substance P, or vasoactive intestinal peptide were found sparsely in the oviduct. These results demonstrate that nitrergic neurons make up a large subpopulation of intrinsic neurons that are closely associated with a cholinergic system in the pigeon oviduct, thus suggesting that nitric oxide and acetylcholine could be used to modify the relaxation of the avian oviduct.
ESTHER : Atoji_2000_Auton.Neurosci_84_1
PubMedSearch : Atoji_2000_Auton.Neurosci_84_1
PubMedID: 11109984

Title : Effects of Desacetyl-alpha-MSH on Lipid Mobilization in the Rainbow Trout, Oncorhynchus mykiss - Yada_2000_Zoolog.Sci_17_1123
Author(s) : Yada T , Azuma T , Takahashi A , Suzuki Y , Hirose S
Ref : Zoolog Sci , 17 :1123 , 2000
Abstract : Effects of melanocyte-stimulating hormone (MSH) and beta-endorphin on lipid mobilization were examined in the rainbow trout (Oncorhynchus mykiss). Plasma levels of fatty acid (FA) were measured after intra-arterial administration of alpha-MSH, desacetyl-alpha-MSH, beta-MSH, or beta-endorphin through a cannula in the dorsal aorta. Desacetyl-alpha-MSH at 1 ng/g body weight resulted in an increase in plasma FA levels 1-3 hr after the injection, whereas the other three peptides showed no significant effect at the same dose. There was no significant change in plasma levels of cortisol after administration of any of the peptides. Lipolytic enzyme activity in the liver was significantly increased in a dose-related manner 1 hr after single intra-peritoneal injection of desacetyl-alpha-MSH. The direct effect of desacetyl-alpha-MSH on lipolysis was examined in liver slices incubated in vitro. Lipase activity in the liver slice was stimulated in the medium containing desacetyl-alpha-MSH in a dose-related manner. The results indicate that desacetyl-alpha-MSH is a potent stimulator of lipid mobilization in the rainbow trout.
ESTHER : Yada_2000_Zoolog.Sci_17_1123
PubMedSearch : Yada_2000_Zoolog.Sci_17_1123
PubMedID: 18522468

Title : Evaluation of liver function parameters by Tc-99m-GSA using multivariate analysis: a study of 47 clinical cases - Suzuki_1999_Acta.Med.Okayama_53_225
Author(s) : Suzuki Y , Kohno Y , Takeda Y , Hiraki Y
Ref : Acta Med Okayama , 53 :225 , 1999
Abstract : To investigate the correlation between nuclear medicine parameters determined by technetium-99m-DTPA-galactosyl-human serum albumin (Tc-99m-GSA) and liver function tests, canonical correlation analysis was performed. Tc-99m-GSA studies were performed on 47 patients with hepatocellular carcinoma (HCC) who had undergone transcatheter arterial embolization (TAE). The nuclear medicine parameters LU15, HH15 and LHL15, which are results of nuclear imaging tests, were chosen in combination with the following liver function tests: the serum bilirubin level (T.Bil), the serum albumin level (Alb), serum cholinesterase activity (Ch-E), the clearance rate of indocyanine green (KICG), the hepaplastin test (HPT) and the prothrombin time (PT). The canonical correlation coefficient was 0.7345 and the upper tail probability was 0.00167. A significant correlation was observed between the two sets of variables. The high structural coefficients of Ch-E, KICG and HPT indicated a close relationship with the nuclear medicine parameters, supporting the notion that these nuclear medicine parameters are useful for the estimation of liver damage. The structural coefficients of the nuclear medicine parameters were also high, with LU15 being a parameter as useful as both HH15 and LHL15. T.Bil may evaluate a liver function that is not measured by nuclear imaging techniques, so we should take T.Bil results into account before considering TAE.
ESTHER : Suzuki_1999_Acta.Med.Okayama_53_225
PubMedSearch : Suzuki_1999_Acta.Med.Okayama_53_225
PubMedID: 10561731

Title : Construction and characterization of a full length-enriched and a 5'-end-enriched cDNA library - Suzuki_1997_Gene_200_149
Author(s) : Suzuki Y , Yoshitomo-Nakagawa K , Maruyama K , Suyama A , Sugano S
Ref : Gene , 200 :149 , 1997
Abstract : Using 'oligo-capped' mRNA [Maruyama, K., Sugano, S., 1994. Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. Gene 138, 171-174], whose cap structure was replaced by a synthetic oligonucleotide, we constructed two types of cDNA library. One is a 'full length-enriched cDNA library' which has a high content of full-length cDNA clones and the other is a '5'-end-enriched cDNA library', which has a high content of cDNA clones with their mRNA start sites. The 5'-end-enriched library was constructed especially for isolating the mRNA start sites of long mRNAs. In order to characterize these libraries, we performed one-pass sequencing of randomly selected cDNA clones from both libraries (84 clones for the full length-enriched cDNA library and 159 clones for the 5'-end-enriched cDNA library). The cDNA clones of the polypeptide chain elongation factor 1 alpha were most frequently (nine clones) isolated, and more than 80% of them (eight clones) contained the mRNA start site of the gene. Furthermore, about 80% of the cDNA clones of both libraries whose sequence matched with known genes had the known 5' ends or sequences upstream of the known 5' ends (28 out of 35 for the full length-enriched library and 51 out of 62 for the 5'-end-enriched library). The longest full-length clone of the full length-enriched cDNA library was about 3300 bp (among 28 clones). In contrast, seven clones (out of the 51 clones with the mRNA start sites) from the 5'-end-enriched cDNA library came from mRNAs whose length is more than 3500 bp. These cDNA libraries may be useful for generating 5' ESTs with the information of the mRNA start sites that are now scarce in the EST database.
ESTHER : Suzuki_1997_Gene_200_149
PubMedSearch : Suzuki_1997_Gene_200_149
PubMedID: 9373149
Gene_locus related to this paper: human-ACOT2 , human-LIPF , human-LPL , human-PLA1A , human-PLA2G15

Title : [Intravenous neostigmine enhances the analgesic effect of epidural anesthesia] - Shirasaka_1997_Masui_46_1246
Author(s) : Shirasaka T , Suzuki Y , Ono Y , Takasaki M
Ref : Masui , 46 :1246 , 1997
Abstract : A single-blind trial of the intravenous neostigmine on epidural anesthesia was carried out on 75 patients undergoing lower limb or lower abdominal surgery. They were allocated to three groups of 25: patients of group C received 2 ml of 0.9% saline, patients of group AN 1 ml (0.5 mg) of atropine and 2 ml (1 mg) of neostigmine, and patients of group N 2 ml (1 mg) of neostigmine, intravenously 5 min before epidural injection of 15 ml of 2% mepivacaine solution without epinephrine. We assessed the onset and spread of cold sensory block and analgesia, and the degree of motor block and sedation. The onset time of analgesia at T 11 was significantly shorter in group N [6.2 +/- 2.0 (SD) min] than in groups C (8.5 +/- 2.6 min) and AN (8.7 +/- 2.4 min). The segmental spread of analgesia 10 and 20 min after epidural injection was significantly larger in group N (10.8 +/- 3.9 and 15.4 +/- 2.7 seg, respectively) than in groups C (7.6 +/- 3.4 and 12.8 +/- 3.5 seg, respectively) and AN (7.8 +/- 3.6 and 13 +/- 3.4 seg, respectively). There were no differences in the onset and spread of cold sensory block, and the degree of motor block and sedation among the three groups. The incidence of bradycardia and fecal incontinence was significantly higher in group N than in groups C and AN. These results demonstrate that intravenous neostigmine potentiates the analgesic effect of epidural anesthesia mediated by a cholinergic muscarinic mechanism. However, in clinical practice, it does not seem to be useful, because of the side effects.
ESTHER : Shirasaka_1997_Masui_46_1246
PubMedSearch : Shirasaka_1997_Masui_46_1246
PubMedID: 9311220

Title : Protective protein gene mutations in galactosialidosis - Shimmoto_1993_J.Clin.Invest_91_2393
Author(s) : Shimmoto M , Fukuhara Y , Itoh K , Oshima A , Sakuraba H , Suzuki Y
Ref : J Clinical Investigation , 91 :2393 , 1993
Abstract : Four different protective protein cDNA mutations, 146A-->G (Q49R), 193T-->C (W65R), 268-269TC-->CT (S90L), and 1184A-->G (Y395C), were identified in six Japanese galactosialidosis patients with various phenotypic manifestations, and another mutation, 746T-->A (Y249N), in a patient of French-German origin with an atypical clinical course. Y395C was a common mutation in four Japanese patients in infancy and childhood; two juvenile patients were compound heterozygotes of Y395C and another common mutation, SpDEx7, and the other two infants were compound heterozygotes of Y395C and mutant alleles other than SpDEx7. We confirmed these mutations in genomic DNA by direct-sequence analysis or restriction-site analysis. The mutant cDNA clones, transiently expressed in a transformed galactosialidosis cell line, did not restore the secondarily deficient beta-galactosidase or alpha-neuraminidase activity except for the Y249N mutation that expressed some carboxypeptidase activity and restored the two lysosomal enzyme activities. Pulse-chase analysis detected a small amount of the mature form, as well as the precursor, in the cells transfected with the Y249N cDNA. Only precursor proteins were detected, mature proteins not appearing for the other mutant cDNAs.
ESTHER : Shimmoto_1993_J.Clin.Invest_91_2393
PubMedSearch : Shimmoto_1993_J.Clin.Invest_91_2393
PubMedID: 8514852
Gene_locus related to this paper: human-CTSA

Title : A new point mutation of protective protein gene in two Japanese siblings with juvenile galactosialidosis. -
Author(s) : Fukuhara Y , Takano T , Shimmoto M , Oshima A , Takeda E , Kuroda Y , Sakuraba H , Suzuki Y
Ref : Brain Dysfunction , 5 :319 , 1992
PubMedID:
Gene_locus related to this paper: human-CTSA

Title : Galactosialidosis: clinical and molecular analysis of 19 Japanese patients. -
Author(s) : Takano T , Shimmoto M , Fukuhara Y , Itoh K , Kase R , Takiyama N , Kobayashi T , Oshima A , Sakuraba H , Suzuki Y
Ref : Brain Dysfunction , 4 :271 , 1991
PubMedID:
Gene_locus related to this paper: human-CTSA

Title : Japanese-type adult galactosialidosis: a unique and common splice junction mutation causing exon skipping in the protective protein\/carboxypeptidase gene -
Author(s) : Shimmoto M , Takano T , Fukuhara Y , Oshima A , Sakuraba H , Suzuki Y
Ref : Proc Jpn Acad , 66B :217 , 1990
PubMedID:
Gene_locus related to this paper: human-CTSA

Title : Galactosialidosis: simultaneous deficiency of esterase, carboxy-terminal deamidase and acid carboxypeptidase activities - Kase_1990_Biochem.Biophys.Res.Commun_172_1175
Author(s) : Kase R , Itoh K , Takiyama N , Oshima A , Sakuraba H , Suzuki Y
Ref : Biochemical & Biophysical Research Communications , 172 :1175 , 1990
Abstract : Esterase and deamidase activities at pH 7.0 and carboxypeptidase activity at pH 5.7 were markedly low or deficient in seven galactosialidosis fibroblast strains with deficient activity of "protective protein" for lysosomal beta-galactosidase and neuraminidase. No simultaneous deficiency of these three enzyme activities was observed in other lysosomal disease fibroblasts examined in this study. This result strongly suggests that "protective protein" is identical with a multifunctional protein with esterase/deamidase/carboxypeptidase activities and its mutation in galactosialidosis results in deficiency of these three enzyme activities.
ESTHER : Kase_1990_Biochem.Biophys.Res.Commun_172_1175
PubMedSearch : Kase_1990_Biochem.Biophys.Res.Commun_172_1175
PubMedID: 2244901
Gene_locus related to this paper: human-CTSA

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 : Galactosialidosis: a direct evidence that a 46-kilodalton protein restores deficient enzyme activities in fibroblasts - Nanba_1987_Biochem.Biophys.Res.Commun_144_138
Author(s) : Nanba E , Tsuji A , Omura K , Suzuki Y
Ref : Biochemical & Biophysical Research Communications , 144 :138 , 1987
Abstract : The intracellular function of a specific protein to protect lysosomal beta-galactosidase and neuraminidase activities against proteases in human fibroblasts was studied. Beta-Galactosidase was purified from human placenta to different degrees; a preparation (A) contained also two concomitant proteins, and a highly purified preparation (B) contained only the mature beta-galactosidase. The protein concentrate of the culture medium of normal fibroblasts restored the activities of the deficient enzymes, beta-galactosidase and neuraminidase, in galactosialidosis cells. This effect was inhibited only by the anti-A anti-serum, and not by the anti-B antiserum. A 46-kilodalton protein, secreted from fibroblasts cultured in the presence of ammonium chloride, was detected again only by the anti-A antiserum, and not by the anti-B antiserum. It was concluded that this protein has a function to restore their activities in fibroblasts from galactosialidosis patients after being endocytosed from the culture medium.
ESTHER : Nanba_1987_Biochem.Biophys.Res.Commun_144_138
PubMedSearch : Nanba_1987_Biochem.Biophys.Res.Commun_144_138
PubMedID: 3107551
Gene_locus related to this paper: human-CTSA

Title : Galactosialidosis: low beta-galactosidase activity in serum after long-term clotting - Sakuraba_1985_Ann.Neurol_18_261
Author(s) : Sakuraba H , Iimori Y , Suzuki Y , Kint JA , Akagi M
Ref : Annals of Neurology , 18 :261 , 1985
Abstract : Serum beta-galactosidase activity was found to be markedly increased in clotting blood from normal subjects, but patients with galactosialidosis showed only a slight increase of this enzyme activity. Consequently, the beta-galactosidase activity was low in serum after long-term clotting in patients with this disease. The mechanism of the enzyme activation is unknown. The use of anticoagulants completely inhibited the activation.
ESTHER : Sakuraba_1985_Ann.Neurol_18_261
PubMedSearch : Sakuraba_1985_Ann.Neurol_18_261
PubMedID: 3929673
Gene_locus related to this paper: human-CTSA

Title : Beta-galactosidase-neuraminidase deficiency: restoration of beta-galactosidase activity by protease inhibitors - Suzuki_1981_J.Biochem_90_271
Author(s) : Suzuki Y , Sakuraba H , Hayashi K , Suzuki K , Imahori K
Ref : J Biochem , 90 :271 , 1981
Abstract : Beta-Galactosidase was partially restored by protease inhibitors, leupeptin, chymostatin and E-64 in cultured fibroblasts from three patients with beta-galactosidase-neuraminidase deficiency. Pepstatin did not activate this enzyme. Neuraminidase was not affected by any of these compounds in the culture medium. It was concluded that the activating effect was produced by a specific inhibition of thiol proteases.
ESTHER : Suzuki_1981_J.Biochem_90_271
PubMedSearch : Suzuki_1981_J.Biochem_90_271
PubMedID: 6793566
Gene_locus related to this paper: human-CTSA

Title : beta-Galactosidase-neuraminidase deficiency in adults: deficiency of a freeze-labile neuraminidase in leukocytes and fibroblasts - Suzuki_1981_Hum.Genet_58_387
Author(s) : Suzuki Y , Sakuraba H , Potier M , Akagi M , Sakai M , Beppu H
Ref : Hum Genet , 58 :387 , 1981
Abstract : 4-methylumbelliferyl neuraminidase activity was studied in fibroblasts, leukocytes, and frozen tissues from adult patients with beta-galactosidase-neuraminidase deficiency and specific clinical manifestations. This enzyme was almost completely deficient in fibroblasts, but the residual activity was relatively high (20% of the control mean) in the leukocytes from the patients. The frozen liver from one patient showed the enzyme activity as high as controls. This enzyme consisted of two components, freeze-labile and freeze-stable, and it was demonstrated that only the labile enzyme was deficient in fibroblasts and leukocytes. The apparently normal activity of neuraminidase in frozen autopsy tissues of a patient may be explained by the loss of the labile component in control tissues after a long-term freezing. The neuraminidase activity was variable in parents and no definite conclusion was drawn on the hereditary nature of the disease.
ESTHER : Suzuki_1981_Hum.Genet_58_387
PubMedSearch : Suzuki_1981_Hum.Genet_58_387
PubMedID: 7327559
Gene_locus related to this paper: human-CTSA

Title : beta-Galactosidase deficiency in juvenile and adult patients. Report of six Japanese cases and review of literature - Suzuki_1977_Hum.Genet_36_219
Author(s) : Suzuki Y , Nakamura N , Fukuoka K , Shimada Y , Uono M
Ref : Hum Genet , 36 :219 , 1977
Abstract : Six juvenile and adult patients with progressive neurological diseases and beta-galactosidase deficiency were reported. Any diseases known to date were denied. These cases together with ten case reports in the literature were reviewed and were classified into three groups from clinical and biochemical points. Group 1 patients were characterized by progressive ataxia and myoclonus with gargoyl changes and macular cherry-red spots. In this syndrome beta-galactosidase activity seems to be secondarily affected by other biochemical defects. A group 2 patient showed similar neurological manifestations without gargoyle changes or macular cherry-red spots. Patients with these clinical features not associated with beta-galactosidase deficiency have also been described in the literature. Group 3 patients had progressive pyramidal and extrapyramidal disease without gargoyl changes or macular cherry-red spots. These cases may represent juvenile and adult type GM1-gangliosidosis. Accumulation of GM1 has not yet been demonstrated.
ESTHER : Suzuki_1977_Hum.Genet_36_219
PubMedSearch : Suzuki_1977_Hum.Genet_36_219
PubMedID: 404231
Gene_locus related to this paper: human-CTSA

Title : Macular cherry-red spots and beta-galactosidase deficiency in an adult. An autopsy case with progressive cerebellar ataxia, myoclonus, thrombocytopathy, and accumulation of polysaccharide in liver - Suzuki_1977_Arch.Neurol_34_157
Author(s) : Suzuki Y , Nakamura N , Shimada Y , Yotsumoto H , Endo H , Nagashima K
Ref : Archives of Neurology , 34 :157 , 1977
Abstract : An adult patient with macular cherry-red spots, a gargoyle-like physical appearance, cerebellar ataxia, myoclonus, convulsive seizures, and pyramidal tract signs showed a profound deficiency of beta-galactosidase in liver and brain. Thrombocytopathy of undetermined etiology was evident since childhood, and the patient died of intracranial bleeding at age 22. Cerebral ganglioside pattern was normal. Hepatic mucopolysaccharides were not increased. GM1-gangliosidosis and mucopolysaccharidosis were ruled out by those analytical data. However, a large amount of amylopectin-like polysaccharide was found to be accumulated in liver. Hepatocyte contained numerous inclusion bodies with granulofibrillary structure similar to Lafora bodies, corpora amylacea, and inclusion bodies in glycogenosis type IV. This case seems to represent a new inborn metabolic disease closely related to GM1-gangliosidosis and mucopolysaccharidosis. The primary metabolic defect is not known at present.
ESTHER : Suzuki_1977_Arch.Neurol_34_157
PubMedSearch : Suzuki_1977_Arch.Neurol_34_157
PubMedID: 402903
Gene_locus related to this paper: human-CTSA

Title : Atropinesterase and cocainesterase of rabbit serum: localization of the enzyme activity in isozymes - Stormont_1970_Science_167_200
Author(s) : Stormont C , Suzuki Y
Ref : Science , 167 :200 , 1970
Abstract : Zymograms reveal a multiplicity of esterase isozymes in rabbit serum. Most of the staining activity is concentrated in a region of the gels just anodal to the albumins where six phenotypes (A, AF, F, M, P, and S) are distinguished. The atropinesterase activity is associated with phenotypes A and AF and appears to be restricted to a single isozyme, zone A. Cocainesterase activity is limited to isozyme S, a zone common to all phenotypes except M.
ESTHER : Stormont_1970_Science_167_200
PubMedSearch : Stormont_1970_Science_167_200
PubMedID: 5409647

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