Yamada C

References (6)

Title : Fatal Poisoning with Both Dichlorvos and Phenthoate - Nara_2018_J.Forensic.Sci_63_1928
Author(s) : Nara A , Yamada C , Kodama T , Saka K , Takagi T
Ref : J Forensic Science , 63 :1928 , 2018
Abstract : Organophosphates are widely used as pesticides. However, organophosphates are occasionally orally ingested to commit suicide. In this case, a man in his late 80s committed suicide by ingesting both dichlorvos and phenthoate. Autopsy findings revealed a characteristic volatile odor from his mouth, stomach, lungs, liver, and kidneys. The esophageal mucosa was denatured and had lost elasticity. Serum cholinesterase activity was 9 IU/L. Toxicological analyses performed using high-performance liquid chromatography-tandem mass spectrometry revealed that dichlorvos concentrations in the left and right cardiac blood samples were 11.6 and 4.6 mug/mL, respectively. Phenthoate concentrations in the left and right cardiac blood samples were 5.8 and 0.51 mug/mL, respectively. The total amounts of dichlorvos and phenthoate in the stomach were 7.35 and 4.55 g, respectively. The case history, autopsy findings, and toxicological analyses indicated that the cause of death was acute fatal poisoning after oral ingestion of both dichlorvos and phenthoate.
ESTHER : Nara_2018_J.Forensic.Sci_63_1928
PubMedSearch : Nara_2018_J.Forensic.Sci_63_1928
PubMedID: 29601635

Title : Isolation and characterization of a thermostable lipase from Bacillus thermoamylovorans NB501 - Yamada_2017_J.Gen.Appl.Microbiol_62_313
Author(s) : Yamada C , Sawano K , Iwase N , Matsuoka M , Arakawa T , Nishida S , Fushinobu S
Ref : J Gen Appl Microbiol , 62 :313 , 2017
Abstract : Two thermophilic bacterial strains, Bacillus thermoamylovorans NB501 and NB502, were isolated from a high-temperature aerobic fermentation reactor system that processes tofu refuse (okara) in the presence of used soybean oil. We cloned a lipase gene from strain NB501, which secretes a thermophilic lipase. The biochemical characteristics of the recombinant enzyme (Lip501r) were elucidated. Lip501r is monomeric in solution with an apparent molecular mass of 38 kDa on SDS-PAGE. The optimal pH and apparent optimal temperature of Lip501r were 8 and 60 degrees C, respectively. Supplementation of 5 mM Ca(2+) enhanced the thermostability, and the enzyme retained 56% of its activity for 30 min at 50 degrees C. Lip501r was active on a wide range of substrates with different lengths of p-nitrophenyl (pNP) esters, and showed a remarkably higher activity with pNP-myristate. The Km and Vmax values for pNP-butyrate in the presence of 5 mM CaCl2 were 1.8 mM and 220 units/mg, respectively. The possible industrial use of the thermophilic lipase in modifying edible oil was explored by examining the degradation of soybean oil. A TLC analysis of the degraded products indicated that Lip501r is an 1,3-position specific lipase. A homology modeling study revealed that helix alpha6 in the lid domain of NB501 lipase was shorter than that of lipases from the Geobacillus group.
ESTHER : Yamada_2017_J.Gen.Appl.Microbiol_62_313
PubMedSearch : Yamada_2017_J.Gen.Appl.Microbiol_62_313
PubMedID: 27885194
Gene_locus related to this paper: 9baci-c4t9i5

Title : Crystal structure of a feruloyl esterase belonging to the tannase family: A disulfide bond near a catalytic triad - Suzuki_2014_Proteins_82_2857
Author(s) : Suzuki K , Hori A , Kawamoto K , Thangudu RR , Ishida T , Igarashi K , Samejima M , Yamada C , Arakawa T , Wakagi T , Koseki T , Fushinobu S
Ref : Proteins , 82 :2857 , 2014
Abstract : Feruloyl esterase (FAE) catalyzes the hydrolysis of the ferulic and diferulic acids present in plant cell wall polysaccharides, and tannase catalyzes the hydrolysis of tannins to release gallic acid. The fungal tannase family in the ESTHER database contains various enzymes, including FAEs and tannases. Despite the importance of FAEs and tannases in bioindustrial applications, three-dimensional structures of the fungal tannase family members have been unknown. Here, we determined the crystal structure of FAE B from Aspergillus oryzae (AoFaeB), which belongs to the fungal tannase family, at 1.5 A resolution. AoFaeB consists of a catalytic alpha/beta-hydrolase fold domain and a large lid domain, and the latter has a novel fold. To estimate probable binding models of substrates in AoFaeB, an automated docking analysis was performed. In the active site pocket of AoFaeB, residues responsible for the substrate specificity of the FAE activity were identified. The catalytic triad of AoFaeB comprises Ser203, Asp417, and His457, and the serine and histidine residues are directly connected by a disulfide bond of the neighboring cysteine residues, Cys202 and Cys458. This structural feature, the "CS-D-HC motif," is unprecedented in serine hydrolases. A mutational analysis indicated that the novel structural motif plays essential roles in the function of the active site. Proteins 2014; 82:2857-2867. (c) 2014 Wiley Periodicals, Inc.
ESTHER : Suzuki_2014_Proteins_82_2857
PubMedSearch : Suzuki_2014_Proteins_82_2857
PubMedID: 25066066
Gene_locus related to this paper: aspor-q2up89

Title : Thyroglobulin gene mutations producing defective intracellular transport of thyroglobulin are associated with increased thyroidal type 2 iodothyronine deiodinase activity - Kanou_2007_J.Clin.Endocrinol.Metab_92_1451
Author(s) : Kanou Y , Hishinuma A , Tsunekawa K , Seki K , Mizuno Y , Fujisawa H , Imai T , Miura Y , Nagasaka T , Yamada C , Ieiri T , Murakami M , Murata Y
Ref : J Clinical Endocrinology Metab , 92 :1451 , 2007
Abstract : CONTEXT: Most patients with defective synthesis and/or secretion of thyroglobulin (Tg) present relatively high serum free T3 (FT3) concentrations with disproportionately low free T4 (FT4) resulting in a high FT3/FT4 ratio. The mechanism of this change in FT3/FT4 ratio remains unknown. OBJECTIVE: We hypothesize that increased type 2 iodothyronine deiodinase (D2) activity in the thyroid gland may explain the higher FT3/FT4 ratio that is frequently observed in patients with abnormal Tg synthesis. DESIGN: We recently identified a compound heterozygous patient (patient A) with a Tg G2356R mutation and one previously described (C1245R) that is known to cause a defect in intracellular transport of Tg. In the current study, after determining the abnormality caused by G2356R, we measured D2 activity as well as its mRNA level in the thyroid gland. We also measured the thyroidal D2 activity in three patients with Tg transport defect and in normal thyroid tissue. RESULTS: Morphological and biochemical analysis of the thyroid gland from patient A, complemented by a pulse-chase experiment, revealed that G2356R produces a defect in intracellular Tg transport. D2 activity but not type 1 deiodinase in thyroid glands of patients with abnormal Tg transport was significantly higher than in normal thyroid glands, whereas D2 mRNA level in patient A was comparable with that in normal thyroid glands. Furthermore, there was a positive correlation between D2 activity and FT3/FT4 ratios. CONCLUSION: Increased thyroidal D2 activity in the thyroid gland is responsible for the higher FT3/FT4 ratios in patients with defective intracellular Tg transport..
ESTHER : Kanou_2007_J.Clin.Endocrinol.Metab_92_1451
PubMedSearch : Kanou_2007_J.Clin.Endocrinol.Metab_92_1451
PubMedID: 17244789

Title : Isolation of a bacterium that degrades urethane compounds and characterization of its urethane hydrolase - Akutsu-Shigeno_2006_Appl.Microbiol.Biotechnol_70_422
Author(s) : Akutsu-Shigeno Y , Adachi Y , Yamada C , Toyoshima K , Nomura N , Uchiyama H , Nakajima-kambe T
Ref : Applied Microbiology & Biotechnology , 70 :422 , 2006
Abstract : A bacterium which degrades urethane compounds was isolated and identified as Rhodococcus equi strain TB-60. Strain TB-60 degraded toluene-2,4-dicarbamic acid dibutyl ester (TDCB) and accumulated toluene diamine as the degradation product. The enzyme which cleaves urethane bond in TDCB was strongly induced by acetanilide. The purified enzyme (urethane hydrolase) was found to be homogeneous on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The molecular weight was estimated to be 55 kDa. The optimal temperature and pH were 45 degrees C and 5.5, respectively. The enzyme hydrolyzed aliphatic urethane compound as well as aromatic ones. The activity was inhibited by HgCl(2), p-chrolomercuribenzoic acid, and phenylmethylsulfonyl fluoride, suggesting that cysteine and/or serine residues play an important role in the activity. The enzyme catalyzed the hydrolysis of anilides, amides, and esters as well as TDCB. It was characterized as a novel amidase/esterase, differing in some properties from other known amidases/esterases.
ESTHER : Akutsu-Shigeno_2006_Appl.Microbiol.Biotechnol_70_422
PubMedSearch : Akutsu-Shigeno_2006_Appl.Microbiol.Biotechnol_70_422
PubMedID: 16041575

Title : Annotation of the Drosophila melanogaster euchromatic genome: a systematic review - Misra_2002_Genome.Biol_3_RESEARCH0083
Author(s) : Misra S , Crosby MA , Mungall CJ , Matthews BB , Campbell KS , Hradecky P , Huang Y , Kaminker JS , Millburn GH , Prochnik SE , Smith CD , Tupy JL , Whitfied EJ , Bayraktaroglu L , Berman BP , Bettencourt BR , Celniker SE , de Grey AD , Drysdale RA , Harris NL , Richter J , Russo S , Schroeder AJ , Shu SQ , Stapleton M , Yamada C , Ashburner M , Gelbart WM , Rubin GM , Lewis SE
Ref : Genome Biol , 3 :RESEARCH0083 , 2002
Abstract : BACKGROUND: The recent completion of the Drosophila melanogaster genomic sequence to high quality and the availability of a greatly expanded set of Drosophila cDNA sequences, aligning to 78% of the predicted euchromatic genes, afforded FlyBase the opportunity to significantly improve genomic annotations. We made the annotation process more rigorous by inspecting each gene visually, utilizing a comprehensive set of curation rules, requiring traceable evidence for each gene model, and comparing each predicted peptide to SWISS-PROT and TrEMBL sequences.
RESULTS: Although the number of predicted protein-coding genes in Drosophila remains essentially unchanged, the revised annotation significantly improves gene models, resulting in structural changes to 85% of the transcripts and 45% of the predicted proteins. We annotated transposable elements and non-protein-coding RNAs as new features, and extended the annotation of untranslated (UTR) sequences and alternative transcripts to include more than 70% and 20% of genes, respectively. Finally, cDNA sequence provided evidence for dicistronic transcripts, neighboring genes with overlapping UTRs on the same DNA sequence strand, alternatively spliced genes that encode distinct, non-overlapping peptides, and numerous nested genes.
CONCLUSIONS: Identification of so many unusual gene models not only suggests that some mechanisms for gene regulation are more prevalent than previously believed, but also underscores the complex challenges of eukaryotic gene prediction. At present, experimental data and human curation remain essential to generate high-quality genome annotations.
ESTHER : Misra_2002_Genome.Biol_3_RESEARCH0083
PubMedSearch : Misra_2002_Genome.Biol_3_RESEARCH0083
PubMedID: 12537572
Gene_locus related to this paper: drome-a1z6g9 , drome-abhd2 , drome-ACHE , drome-CG8058 , drome-CG8093 , drome-CG8233 , drome-CG8425 , drome-CG9059 , drome-CG9186 , drome-CG9542 , drome-CG10982 , drome-CG11309 , drome-CG11406 , drome-CG11598 , drome-CG17097 , drome-glita , drome-KRAKEN , drome-nrtac , drome-OME , drome-q7k274 , drome-q9vux3