Tanaka T

References (64)

Title : Aspergillus Hydrophobins: Physicochemical Properties, Biochemical Properties, and Functions in Solid Polymer Degradation - Tanaka_2022_Microorganisms_10_
Author(s) : Tanaka T , Terauchi Y , Yoshimi A , Abe K
Ref : Microorganisms , 10 : , 2022
Abstract : Hydrophobins are small amphipathic proteins conserved in filamentous fungi. In this review, the properties and functions of Aspergillus hydrophobins are comprehensively discussed on the basis of recent findings. Multiple Aspergillus hydrophobins have been identified and categorized in conventional class I and two non-conventional classes. Some Aspergillus hydrophobins can be purified in a water phase without organic solvents. Class I hydrophobins of Aspergilli self-assemble to form amphipathic membranes. At the air-liquid interface, RolA of Aspergillus oryzae self-assembles via four stages, and its self-assembled films consist of two layers, a rodlet membrane facing air and rod-like structures facing liquid. The self-assembly depends mainly on hydrophobin conformation and solution pH. Cys4-Cys5 and Cys7-Cys8 loops, disulfide bonds, and conserved Cys residues of RodA-like hydrophobins are necessary for self-assembly at the interface and for adsorption to solid surfaces. AfRodA helps Aspergillus fumigatus to evade recognition by the host immune system. RodA-like hydrophobins recruit cutinases to promote the hydrolysis of aliphatic polyesters. This mechanism appears to be conserved in Aspergillus and other filamentous fungi, and may be beneficial for their growth. Aspergilli produce various small secreted proteins (SSPs) including hydrophobins, hydrophobic surface-binding proteins, and effector proteins. Aspergilli may use a wide variety of SSPs to decompose solid polymers.
ESTHER : Tanaka_2022_Microorganisms_10_
PubMedSearch : Tanaka_2022_Microorganisms_10_
PubMedID: 35893556

Title : Phytochemical Analysis and Cholinesterase Inhibitory and Antioxidant Activities of Enhydra fluctuans Relevant in the Management of Alzheimer's Disease - Lopa_2021_Int.J.Food.Sci_2021_8862025
Author(s) : Lopa SS , Al-Amin MY , Hasan MK , Ahammed MS , Islam KM , Alam A , Tanaka T , Sadik MG
Ref : Int J Food Sci , 2021 :8862025 , 2021
Abstract : Enhydra fluctuans, a popular vegetable in Bangladesh, is used in folk medicine to treat diseases of the nervous system. The objective of this study was to investigate the phytochemical profile and cholinesterase inhibitory and antioxidant potential of the extracts of E. fluctuans. Among the four tested extracts, the chloroform extract was found to exert the highest inhibition against both the acetylcholinesterase and butyrylcholinesterase enzymes with the IC(50) (concentration required for 50% inhibition) values of 83.90 microg/mL and 48.14 microg/mL, respectively. Likewise, the chloroform extract showed the highest radical scavenging activity and reducing power. In DPPH radical scavenging assay, the IC(50) value was found to be 113.27 microg/mL, and in reducing power assay, the absorbance was found to be 1.916 at a concentration of 50 microg/mL. Phytochemical analyses revealed that the chloroform extract contained 19.16 mg gallic acid equivalent (GAE)/g extract of phenolics and 41.84 mg catechin equivalent (CE)/g extract of flavonoids, which appeared to be the highest among the extracts. A significant correlation was observed between phenolic content and butyrylcholinesterase inhibition and antioxidant activity, while a moderate correlation was seen between flavonoid content and cholinesterase inhibition and antioxidant activity. These findings suggest that E. fluctuans is a natural source of cholinesterase inhibitors and antioxidants, which could be utilized as functional foods for Alzheimer's disease management.
ESTHER : Lopa_2021_Int.J.Food.Sci_2021_8862025
PubMedSearch : Lopa_2021_Int.J.Food.Sci_2021_8862025
PubMedID: 33506005

Title : Cliniatines A-C, new Amaryllidaceae alkaloids from Clivia miniata, inhibiting Acetylcholinesterase - Hirasawa_2021_J.Nat.Med__
Author(s) : Hirasawa Y , Tanaka T , Hirasawa S , Wong CP , Uchiyama N , Kaneda T , Goda Y , Morita H
Ref : J Nat Med , : , 2021
Abstract : Cliniatines A-C (1-3), three new Amaryllidaceae alkaloids, consisting of 2,6-dimetylpyridine and lycorine-type and/or galanthamine-type were isolated from Clivia miniata (Lindl.) Bosse. The structures and absolute configurations of 1-3 were elucidated based on spectroscopic data and chemical correlation. Cliniatines A-C showed moderate inhibitory activity against acetylcholinesterase.
ESTHER : Hirasawa_2021_J.Nat.Med__
PubMedSearch : Hirasawa_2021_J.Nat.Med__
PubMedID: 34550553

Title : Identification of Polyphenolics from Loranthus globosus as Potential Inhibitors of Cholinesterase and Oxidative Stress for Alzheimer's Disease Treatment - Kundo_2021_Biomed.Res.Int_2021_9154406
Author(s) : Kundo NK , Manik MIN , Biswas K , Khatun R , Al-Amin MY , Alam A , Tanaka T , Sadik G
Ref : Biomed Res Int , 2021 :9154406 , 2021
Abstract : Mistletoes are considered to be the potential medicinal herbs due to their rich traditional uses. Loranthus globosus is a Bangladeshi mango mistletoe that has been reported as folk medicine for various ailments and diseases. In an attempt to explore its effectiveness in Alzheimer's disease (AD), we investigated the antioxidant and acetylcholinesterase inhibitory activity of L. globosus. We report that the crude methanol extract (CME) of the plant contains a good amount of polyphenolics and possesses antioxidant and cholinesterase inhibitory activity. Fractionation of CME with solvents of varying polarity revealed the highest activity and polyphenolic content in the ethylacetate fraction (EAF). Correlation analysis revealed a significant (P < 0.05) association of polyphenolics with the antioxidant and cholinesterase inhibitory properties. Using column chromatography with diaion resin, the polyphenolics (EAF-PP) were isolated from the EAF that displayed the potent antioxidant and cholinesterase inhibitory activities. Kinetic analysis showed that EAF-PP exhibited a competitive type of inhibition. A total of thirty-six compounds including catechin and its different derivatives were identified in the EAF-PP by LC/MS analysis. Bioactivity-guided separation approach afforded the isolation of the two major active compounds catechin and catechin dimer from the EAF-PP. Hence, EAF-PP represents a potential source of antioxidants and cholinesterase inhibitors, which can be used in the management of AD.
ESTHER : Kundo_2021_Biomed.Res.Int_2021_9154406
PubMedSearch : Kundo_2021_Biomed.Res.Int_2021_9154406
PubMedID: 34805409

Title : Evaluation of cholinesterase inhibitory and antioxidant activity of Wedelia chinensis and isolation of apigenin as an active compound - Islam_2021_BMC.Complement.Med.Ther_21_204
Author(s) : Islam MA , Zaman S , Biswas K , Al-Amin MY , Hasan MK , Alam A , Tanaka T , Sadik G
Ref : BMC Complement Med Ther , 21 :204 , 2021
Abstract : BACKGROUND: Wedelia chinensis has been reported as a folk medicine for the treatment of different diseases including neurodegenerative disease. Although the plant has been studied well for diverse biological activities, the effect of this plant in neurological disorder is largely unknown. The present study was undertaken to evaluate the cholinesterase inhibitory and antioxidant potential of W. chinensis. METHODS: The extract and fractions of the plant were evaluated for acetylcholinesterase and butyrylcholinesterase inhibitory activity by modified Ellman method. The antioxidant activity was assessed in several in vitro models/assays such as reducing power, total antioxidant capacity, total phenolic and flavonoid content, scavenging of 2,2'-diphenyl-1-picrylhydrazyl (DPPH) free radical and hydroxyl radical, and inhibition of brain lipid peroxidation. Chromatographic and spectroscopic methods were used to isolate and identify the active compound from the extract. RESULTS: Among the fractions, aqueous fraction (AQF) and ethylacetate fraction (EAF) exhibited high inhibition against acetylcholinesterase (IC(50): 40.02 +/- 0.16 microg/ml and 57.76 +/- 0.37 microg/ml) and butyrylcholinesterase (IC(50): 31.79 +/- 0.18 microg/ml and 48.41 +/- 0.05 microg/ml). Similarly, the EAF and AQF had high content of phenolics and flavonoids and possess strong antioxidant activity in several antioxidant assays including DPPH and hydroxyl radical scavenging, reducing power and total antioxidant activity. They effectively inhibited the peroxidation of brain lipid in vitro with IC(50) values of 45.20 +/- 0.10 microg/ml and 25.53 +/- 0.04 microg/ml, respectively. A significant correlation was observed between total flavonoids and antioxidant and cholinesterase inhibitory activity. Activity guided chromatographic separation led to the isolation of a major active compound from the EAF and its structure was elucidated as apigenin by spectral analysis. CONCLUSIONS: The potential ability of W. chinensis to inhibit the cholinesterase activity and peroxidation of lipids suggest that the plant might be useful for the management of AD.
ESTHER : Islam_2021_BMC.Complement.Med.Ther_21_204
PubMedSearch : Islam_2021_BMC.Complement.Med.Ther_21_204
PubMedID: 34315449

Title : Acetylcholinesterase Inhibitory and Antioxidant Activity of the Compounds Isolated from Vanda roxburghii - Ahammed_2021_Adv.Pharmacol.Pharm.Sci_2021_5569054
Author(s) : Ahammed S , Afrin R , Uddin N , Al-Amin Y , Hasan K , Haque U , Islam KMM , Alam A , Tanaka T , Sadik G
Ref : Advances in Pharmacology Pharm Sci , 2021 :5569054 , 2021
Abstract : Vanda roxburghii has been used in traditional medicine to treat nervous system disorders including Alzheimer's disease (AD). We reported earlier a high acetylcholinesterase inhibitory and antioxidant activity in the chloroform fraction of this plant. Therefore, this study was designed to explore the compounds with acetylcholinesterase inhibitory and antioxidant activities from the chloroform fraction of Vanda roxburghii. Phytochemical investigation led to the isolation for the first time of a fatty acid ester: methyl linoleate (1), and three phenolics: syringaldehyde (2), vanillin (3), and dihydroconiferyl dihydro-p-coumarate (4) along with the previously reported compound gigantol (5). Among the isolates, vanillin (3) and dihydroconiferyl dihydro-p-coumarate (4) were found to significantly inhibit the activity of acetylcholinesterase, scavenge the free radicals, exhibit the reducing power and total antioxidant activity, and effectively reduce the peroxidation of lipid. Gigantol (5) and syringaldehyde (2), despite lacking the activity against acetylcholinesterase, exhibited antioxidant activity. Among the compounds, gigantol (5) appeared to be the most potent antioxidant. These findings revealed that V. roxburghii contained compounds with potential acetylcholinesterase inhibitory and antioxidant activity, which support its traditional use in the treatment of AD.
ESTHER : Ahammed_2021_Adv.Pharmacol.Pharm.Sci_2021_5569054
PubMedSearch : Ahammed_2021_Adv.Pharmacol.Pharm.Sci_2021_5569054
PubMedID: 33855299

Title : The Role of Brain Methamidophos in Acephate Poisoning in Mice - Tanaka_2021_J.UOEH_43_197
Author(s) : Tanaka T , Sato H , Yoshida K , Kasai K
Ref : J UOEH , 43 :197 , 2021
Abstract : We gave mice a 540 mg/kg dose of LD50 acephate, followed by an assessment of acephate, methamidophos (MP), and choline esterase (ChE) activity for up to 4 hours (hr) in order to investigate the time course of acephate intoxication. At 1 hr, the blood acephate and MP levels were 428 +/- 90 microg/ml (mean +/- SEM) and 4.2 +/- 0.4 microg/ ml, respectively. The liver acephate levels were similar to those in the blood, but the liver MP levels were approximately 3.5 times that of the blood at 1 hr. The brain MP level tended to be higher than the blood MP at 1 hr. These levels decreased gradually over 4 hr, but the brain acephate and MP levels surpassed the blood levels significantly at 4 hr, and after 2 hr, respectively. Serum, liver, cerebrum, cerebellum, and brainstem cholinesterase activity (ChE) were inhibited at 1 hr, and remained inhibited in all but the cerebellum until the end of the experiment. The obtained data were applied to previously reported autopsy cases of acephate intake. Experimental data suggest that brain MP is involved in acute acephate-induced poisoning, even after a reduction in blood acephate. In autopsy cases with suspected acephate poisoning, the MP level in the brain should be considered in addition to the ChE activity to diagnose the cause of death.
ESTHER : Tanaka_2021_J.UOEH_43_197
PubMedSearch : Tanaka_2021_J.UOEH_43_197
PubMedID: 34092764

Title : Clinical and genetic investigation of 136 Japanese patients with congenital hypothyroidism - Tanaka_2020_J.Pediatr.Endocrinol.Metab_33_691
Author(s) : Tanaka T , Aoyama K , Suzuki A , Saitoh S , Mizuno H
Ref : J Pediatr Endocrinol Metab , 33 :691 , 2020
Abstract : Objectives Congenital hypothyroidism (CH) is the most common congenital endocrine disorder. Recent advances in genetic testing have revealed its causative mutations in some CH patients. However, the underlying etiology remains unknown in most patients. This study aimed to perform clinical and genetic investigation in Japanese CH patients to uncover genotype-phenotype correlations. Methods We enrolled 136 Japanese patients with transient or permanent CH between April 2015 and March 2017, and performed next-generation sequencing of 19 genes implicated in CH. Results We identified potentially pathogenic bi-allelic variants in DUOX2, TSHR, and TPO in 19, 5, and 1 patient, respectively (autosomal recessive), and a potentially pathogenic mono-allelic variant in NKX2-1 (autosomal dominant) in 1 patient. Molecular genetic diagnosis was highly suggested in 26 patients (19%) from 23 families. We also detected a potentially pathogenic mono-allelic variant in five recessive genes (DUOX2, TSHR, TG, DUOXA2, and TPO) in 31 unrelated patients (23%), although the pathogenicity of these variants remains inconclusive. Patients with bi-allelic DUOX2 variants showed a more severe clinical presentation in infancy than those with bi-allelic TSHR variants. However, this trend reversed beyond infancy. There were no statistical differences in initial thyroid stimulating hormone, free thyroxine, thyroglobulin, and levothyroxine dose as of March 2017 between patients with bi-allelic and mono-allelic DUOX2 variants. Conclusions The prevalence of potentially-pathogenic variants in Japanese CH patients was similar to that found by previous reports. Our study demonstrates a genotype-phenotype correlation in Japanese CH patients.
ESTHER : Tanaka_2020_J.Pediatr.Endocrinol.Metab_33_691
PubMedSearch : Tanaka_2020_J.Pediatr.Endocrinol.Metab_33_691
PubMedID: 32469330

Title : Interaction between Apolipoprotein E and Butyrylcholinesterase Genes on Risk of Alzheimer's Disease in a Prospective Cohort Study - Chuang_2020_J.Alzheimers.Dis__
Author(s) : Chuang YF , Varma V , An Y , Tanaka T , Davatzikos C , Resnick SM , Thambisetty M
Ref : J Alzheimers Dis , : , 2020
Abstract : BACKGROUND: An epistatic interaction between the varepsilon4 allele of apolipoprotein E (APOEvarepsilon4) gene and the K-variant of butyrylcholinesterase (BCHE-K) genes has been previously reported to increase risk of Alzheimer's disease (AD). However, these observations were largely from case-control studies with small sample sizes. OBJECTIVE: To examine the interaction between APOEvarepsilon4 and BCHE-K on: 1) the risk of incident AD and 2) rates of change in brain volumes and cognitive performance during the preclinical stages of AD in a prospective cohort study. METHODS: The study sample for survival analysis included 691 Caucasian participants (age at baseline, 58.4+/-9.9 years; follow-up time,16.9+/-9.7 years) from the Baltimore Longitudinal Study of Aging. The neuroimaging sample included 302 participants with 1,388 magnetic resonance imaging (MRI) scans. Cognitive performance was assessed in 703 participants over 4,908 visits. RESULTS: A total of 122 diagnoses (79 AD, 43 mild cognitive impairment [MCI]) were identified. Participants with both APOEvarepsilon4 and BCHE-K variants had a 3.7-fold greater risk of AD (Hazard ratio [HR] 95% CI=1.99-6.89, p < 0.001) compared to non-carriers of both genes (APOE varepsilon4 x BCHE-K interaction p = 0.025). There was no APOE varepsilon4-BCHE-K interaction effect on rate of cognitive decline and brain atrophy. CONCLUSION: The APOE and BCHE genes interact to influence risk of incident AD/MCI but not rates of brain atrophy and decline in cognitive performance before onset of cognitive impairment. This may suggest the epistatic interaction between APOE varepsilon4 and BCHE-K on AD risk is disease stage-dependent.
ESTHER : Chuang_2020_J.Alzheimers.Dis__
PubMedSearch : Chuang_2020_J.Alzheimers.Dis__
PubMedID: 32250307

Title : Biological Functions of alpha-Tocopheryl Succinate - Majima_2019_J.Nutr.Sci.Vitaminol.(Tokyo)_65_S104
Author(s) : Majima D , Mitsuhashi R , Fukuta T , Tanaka T , Kogure K
Ref : J Nutr Sci Vitaminol (Tokyo) , 65 :S104 , 2019
Abstract : alpha-Tocopheryl succinate (TS) is a succinic acid ester of a well-known natural antioxidant alpha-tocopherol (alpha-T). Physicochemical characteristics of TS are entirely different from the original compound alpha-T. TS becomes vesicles via forming a lamella structure. Furthermore, although the antioxidative activity of alpha-T is lacked by esterification of phenolic hydroxyl (OH) moiety with succinate, TS has versatile biological functions, such as inhibition of cholinesterase activity, inhibition of nuclear factor-kappa B (NF-kappaB) activation, enhancement of lipopolysaccharide-induced nitric oxide production, and anticancer effect. Especially, we expect TS as a novel anticancer agent. TS nanovesicle shows significant anticancer activity in vitro and in vivo. Nicotinamide adenine dinucleotide phosphate (NADPH) oxidase produces superoxide which mediates the anticancer activity of TS. Moreover, it suggests that TS activates protein kinase C via direct interaction. Based on the analysis of structure and activity relationship, it ensures that succinate moiety of TS plays a vital role in anticancer activity. This review introduces the detail and mechanism of versatile biological functions of TS.
ESTHER : Majima_2019_J.Nutr.Sci.Vitaminol.(Tokyo)_65_S104
PubMedSearch : Majima_2019_J.Nutr.Sci.Vitaminol.(Tokyo)_65_S104
PubMedID: 31619606

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

Title : Construction of a Pseudozyma antarctica strain without foreign DNA sequences (self-cloning strain) for high yield production of a biodegradable plastic-degrading enzyme - Sameshima-Yamashita_2019_Biosci.Biotechnol.Biochem__1
Author(s) : Sameshima-Yamashita Y , Watanabe T , Tanaka T , Tsuboi S , Yarimizu T , Morita T , Koike H , Suzuki K , Kitamoto H
Ref : Biosci Biotechnol Biochem , :1 , 2019
Abstract : The basidiomycetous yeast Pseudozyma antarctica GB-4(0) esterase (PaE) is a promising candidate for accelerating degradation of used biodegradable plastics (BPs). To increase safety and reduce costs associated with the use of PaE, we constructed a self-cloning strain with high-PaE productivity. A Lys12 gene (PaLYS12)-deleted lysine auxotroph strain GB4-(0)-L1 was obtained from GB-4(0) by ultraviolet mutagenesis and nystatin enrichment. Subsequently, the PaE gene (PaCLE1) expression cassette consisting of GB-4(0)-derived PaCLE1, under the control of a xylose-inducible xylanase promoter with PaLYS12, was randomly introduced into the GB4-(0)-L1 genome. A PaE high-producing strain, PGB474, was selected from among the transformants by high throughput double-screening based on its ability to degrade emulsified polybutylene succinate-co-adipate. Quantitative PCR revealed that four copies of the PaE gene expression cassette were introduced into the PGB474 genome. PGB474 produced 2.0 g/L of PaE by xylose-fed-batch cultivation using a 3-L jar fermentor for 72 h.
ESTHER : Sameshima-Yamashita_2019_Biosci.Biotechnol.Biochem__1
PubMedSearch : Sameshima-Yamashita_2019_Biosci.Biotechnol.Biochem__1
PubMedID: 30714483
Gene_locus related to this paper: psea2-s6bc01

Title : Viral infection induces different detoxification enzyme activities in insecticide-resistant and -susceptible brown planthopper Nilaparvata lugens strains - Yoshikawa_2018_J.Pestic.Sci_43_10
Author(s) : Yoshikawa K , Matsukawa M , Tanaka T
Ref : J Pestic Sci , 43 :10 , 2018
Abstract : This study aimed to describe the relationship between viral infection in Nilaparvata lugens (Stal), the brown planthopper (BPH), and different insecticide susceptibilities. BPH-resistant strains were selected using fenthion (an organophosphate) or etofenprox (a pyrethroid); a susceptible strain was used as the baseline colony before insecticide selection. All strains were infected with rice ragged stunt virus (RRSV) or rice grassy stunt virus (RGSV), after which the activities of three detoxification enzymes, cytochrome-P450-monooxygenase (P450), glutathione S-transferase (GST), and carboxylesterase (CE), were compared. Males of the strains selected for both insecticides showed high P450 and GST-CDNB activities. The activity of all enzymes was higher in males than in females, as a whole. However, males of the susceptible strain infected with RRSV showed decreased CE and GST-CDNB activities. BPH with low susceptibility to etofenprox showed a marked increase in P450 activity after RRSV infection; the GST-CDNB activity of females in the insecticide-resistant strain increased. RGSV infection induced high CE and P450 activities in etofenprox-selected females. The RRSV infection rate, but not the RGSV, decreased in etofenprox-selected strains.
ESTHER : Yoshikawa_2018_J.Pestic.Sci_43_10
PubMedSearch : Yoshikawa_2018_J.Pestic.Sci_43_10
PubMedID: 30363128

Title : Effects of donepezil on sleep disturbances in patients with dementia with Lewy bodies: An open-label study with actigraphy - Kazui_2017_Psychiatry.Res_251_312
Author(s) : Kazui H , Adachi H , Kanemoto H , Yoshiyama K , Wada T , Tokumasu Nomura K , Tanaka T , Ikeda M
Ref : Psychiatry Res , 251 :312 , 2017
Abstract : We investigated whether donepezil, a cholinesterase inhibitor, can be used to treat sleep disturbances in patients with dementia with Lewy bodies (DLB). Sleep disturbances were evaluated with the sleep disturbances item of the Neuropsychiatric inventory (NPI) and an actigraph in 16 DLB patients and 24 normal elderly control (NC) subjects. The presence/absence of nine kinds of sleep symptoms, such as dream enactment, were also evaluated in the DLB patients. The DLB patients were then given 5mg/day donepezil for 14 weeks and evaluated again. Eight of the 16 DLB patients had some sleep disturbances before taking donepezil. The actigraphy data indicated that average activity count per minute in sleep (AAC), which reflects body activity at night, was significantly higher and total sleep time was significantly longer in DLB patients than in NC subjects. The NPI sleep disturbances score significantly improved and the number of DLB patients who had sleep disturbances decreased after taking donepezil. The actigraphy results indicate that the sum of all wake epochs within the sleep period, which reflects the degree of fragmented sleep, and the AAC decreased in the DLB patients after donepezil treatment. These results indicate that donepezil treatment reduced sleep disturbances in DLB patients.
ESTHER : Kazui_2017_Psychiatry.Res_251_312
PubMedSearch : Kazui_2017_Psychiatry.Res_251_312
PubMedID: 28236784

Title : Potential anti-cholinesterase and beta-site amyloid precursor protein cleaving enzyme 1 inhibitory activities of cornuside and gallotannins from Cornus officinalis fruits - Bhakta_2017_Arch.Pharm.Res_40_836
Author(s) : Bhakta HK , Park CH , Yokozawa T , Tanaka T , Jung HA , Choi JS
Ref : Arch Pharm Res , 40 :836 , 2017
Abstract : Cholinesterase (ChE) and beta-site amyloid precursor protein cleaving enzyme 1 (BACE1) inhibitors are promising agents for the treatment of Alzheimer's disease (AD). In the present study, we examined the inhibitory activity of seven compounds isolated from the fruits of Cornus officinalis, cornuside, polymeric proanthocyanidins, 1,2,3-tri-O-galloyl-beta-D-glucose, 1,2,3,6-tetra-O-galloyl-beta-D-glucose, tellimagrandin I, tellimagrandin II, and isoterchebin, against acetylcholinesterase (AChE), butyrylcholinesterase (BChE), and BACE1. All of the compounds displayed concentration-dependent in vitro inhibitory activity toward the ChEs and BACE1. Among them, tellimagrandin II exhibited the best inhibitory activity toward ChEs, whereas the best BACE1 inhibitor was 1,2,3,6-tetra-O-galloyl-beta-D-glucose. Isoterchebin and polymeric proanthocyanidins were also significant ChE inhibitors. The kinetic and docking studies demonstrated that all compounds interacted with both the catalytic active sites and the peripheral anionic sites of the ChEs and BACE1. Tellimagrandin II, isoterchebin, and the polymeric proanthocyanidins exhibited concentration-dependent inhibition of peroxynitrite-mediated protein tyrosine nitration. In conclusion, we identified significant ChE and BACE1 inhibitors from Corni Fructus that could have value as new multi-targeted compounds for anti-AD agents.
ESTHER : Bhakta_2017_Arch.Pharm.Res_40_836
PubMedSearch : Bhakta_2017_Arch.Pharm.Res_40_836
PubMedID: 28589255

Title : Significance of preoperative butyrylcholinesterase level as an independent predictor of survival in patients with upper urinary tract urothelial carcinoma treated with nephroureterectomy - Noro_2017_Jpn.J.Clin.Oncol__1
Author(s) : Noro D , Koie T , Hashimoto Y , Tanaka T , Ohyama C , Tobisawa Y , Yoneyama T , Imai A , Hatakeyama S , Yamamoto H , Kitayama M , Hirota K
Ref : Japanese Journal of Clinical Oncology , :1 , 2017
Abstract : Objectives: Butyrylcholinesterase (BChE) is an alpha-glycoprotein synthesized in the liver. Its serum levels are reportedly correlated with disease activity in patients with cancer. The aim of this study was to estimate the potential prognostic significance of preoperative serum BChE levels in patients with upper urinary tract urothelial carcinoma (UTUC) undergoing radical nephroureterectomy (RNU). Methods: Of the 220 patients with UTUC who underwent RNU between 1995 and 2016 at Hirosaki University Hospital, 149 patients with available laboratory data were included for analysis. Covariates included age, sex, preoperative laboratory data, clinical T and N grades, tumor grade, tumor location and preoperative chemotherapy. Univariate and multivariate analyses were performed to identify clinical factors associated with overall survival (OS) and disease-free survival (DFS). Univariate analysis was performed using the Kaplan-Meier and log-rank methods, and the multivariate analysis was performed using a Cox proportional hazard model. Results: The median BChE level was 276 U/l and the optimal cut-off point for the serum BChE level was determined to be 218 IU/ml. The 5-year OS and DFS rates were 81.0% and 73.7%, respectively. The 5-year OS and DFS rates were significantly greater in the BChE >/= 218 than <218 U/l groups (86.6% vs. 53.7%, P < 0.001 and 76.4% vs. 58.3%, P = 0.049, respectively). In multivariate analysis, BChE levels were most significantly associated with OS, whereas BChE level and tumor grade were significantly associated with DFS. Conclusions: This study validated preoperative serum BChE levels as an independent prognostic factor for UTUC after RNU.
ESTHER : Noro_2017_Jpn.J.Clin.Oncol__1
PubMedSearch : Noro_2017_Jpn.J.Clin.Oncol__1
PubMedID: 29177431

Title : Impaired Mitophagy Plays a Role in Denervation of Neuromuscular Junctions in ALS Mice - Rogers_2017_Front.Neurosci_11_473
Author(s) : Rogers RS , Tungtur S , Tanaka T , Nadeau LL , Badawi Y , Wang H , Ni HM , Ding WX , Nishimune H
Ref : Front Neurosci , 11 :473 , 2017
Abstract : Motor neurons in amyotrophic lateral sclerosis (ALS) patients and animal models show degeneration from the nerve terminal, known as dying-back neuropathy. To investigate the mechanism underlying this neuropathy, we analyzed the neuromuscular junctions (NMJs) and motor neuron cell bodies in SOD1(G93A) mice using electron microscopy. NMJs of SOD1(G93A) mice exhibited significantly higher numbers of autophagosomes and degenerated mitochondria compared to wild-type controls. Mitophagosomes were identified in the NMJ presynaptic terminals of wild-type mice and SOD1(G93A) mice. However, the number of mitophagosomes did not increase significantly in SOD1(G93A) NMJs indicating a defect in mitophagy, the autophagic process to degrade mitochondria. Consistent with this, proteins essential for mitophagy, p62/SQSTM1, Bnip3, Pink1, and Parkin were down-regulated in motor neurons in SOD1(G93A) mice. Importantly, SQSTM1 is one of the genes mutated in familial ALS patients. We evaluated the effect of impaired mitophagy on motor neurons by analyzing the double knockout mice of Pink1 and Parkin, two genes responsible for sensing depolarized mitochondria and delivering degenerated mitochondria to mitophagosomes. The double knockout mice exhibited NMJ degeneration, including axon swelling and NMJ fragmentation at 4 months of age. These phenotypes were rarely observed in wild-type control mice of the same age. The protein level of ATP synthase beta subunit increased in the NMJ presynaptic terminals, suggesting the accumulation of mitochondria at NMJs of the double knockout mice. Importantly, NMJ denervation was observed in the double knockout mice. These data suggest that the reduced mitophagy function in motor neurons of SOD1(G93A) mice is one of the mechanisms causing degeneration of ALS NMJs.
ESTHER : Rogers_2017_Front.Neurosci_11_473
PubMedSearch : Rogers_2017_Front.Neurosci_11_473
PubMedID: 28890682

Title : Analysis of the ionic interaction between the hydrophobin RodA and two cutinases of Aspergillus nidulans obtained via an Aspergillus oryzae expression system - Tanaka_2017_Appl.Microbiol.Biotechnol_101_2343
Author(s) : Tanaka T , Nakayama M , Takahashi T , Nanatani K , Yamagata Y , Abe K
Ref : Applied Microbiology & Biotechnology , 101 :2343 , 2017
Abstract : Hydrophobins are amphipathic secretory proteins with eight conserved cysteine residues and are ubiquitous among filamentous fungi. In the fungus Aspergillus oryzae, the hydrophobin RolA and the polyesterase CutL1 are co-expressed when the sole available carbon source is the biodegradable polyester polybutylene succinate-co-adipate (PBSA). RolA promotes the degradation of PBSA by attaching to the particle surface, changing its structure and interacting with CutL1 to concentrate CutL1 on the PBSA surface. We previously reported that positively charged residues in RolA and negatively charged residues in CutL1 are cooperatively involved in the ionic interaction between RolA and CutL1. We also reported that hydrophobin RodA of the model fungus Aspergillus nidulans, which was obtained via an A. oryzae expression system, interacted via ionic interactions with CutL1. In the present study, phylogenetic and alignment analyses revealed that the N-terminal regions of several RolA orthologs contained positively charged residues and that the corresponding negatively charged residues on the surface of CutL1 that were essential for the RolA-CutL1 interaction were highly conserved in several CutL1 orthologs. A PBSA microparticle degradation assay, a pull-down assay using a dispersion of Teflon particles, and a kinetic analysis using a quartz crystal microbalance revealed that recombinant A. nidulans RodA interacted via ionic interactions with two recombinant A. nidulans cutinases. Together, these results imply that ionic interactions between hydrophobins and cutinases may be common among aspergilli and other filamentous fungi.
ESTHER : Tanaka_2017_Appl.Microbiol.Biotechnol_101_2343
PubMedSearch : Tanaka_2017_Appl.Microbiol.Biotechnol_101_2343
PubMedID: 27917435

Title : Asp30 of Aspergillus oryzae cutinase CutL1 is involved in the ionic interaction with fungal hydrophobin RolA - Terauchi_2017_Biosci.Biotechnol.Biochem_81_1363
Author(s) : Terauchi Y , Kim YK , Tanaka T , Nanatani K , Takahashi T , Abe K
Ref : Biosci Biotechnol Biochem , :1 , 2017
Abstract : Aspergillus oryzae hydrophobin RolA adheres to the biodegradable polyester polybutylene succinate-co-adipate (PBSA) and promotes PBSA degradation by interacting with A. oryzae polyesterase CutL1 and recruiting it to the PBSA surface. In our previous studies, we found that positively charged amino acid residues (H32, K34) of RolA and negatively charged residues (E31, D142, D171) of CutL1 are important for the cooperative ionic interaction between RolA and CutL1, but some other charged residues in the triple mutant CutL1-E31S/D142S/D171S are also involved. In the present study, on the basis of the 3D-structure of CutL1, we hypothesized that D30 is also involved in the CutL1-RolA interaction. We substituted D30 with serine and performed kinetic analysis of the interaction between wild-type RolA and the single mutant CutL1-D30S or quadruple mutant CutL1-D30S/E31S/D142S/D171S by using quartz crystal microbalance. Our results indicate that D30 is a novel residue involved in the ionic interaction between RolA and CutL1.
ESTHER : Terauchi_2017_Biosci.Biotechnol.Biochem_81_1363
PubMedSearch : Terauchi_2017_Biosci.Biotechnol.Biochem_81_1363
PubMedID: 28475418
Gene_locus related to this paper: aspor-cutas

Title : Serial Femtosecond Crystallography and Ultrafast Absorption Spectroscopy of the Photoswitchable Fluorescent Protein IrisFP - Colletier_2016_J.Phys.Chem.Lett_7_882
Author(s) : Colletier JP , Sliwa M , Gallat FX , Sugahara M , Guillon V , Schiro G , Coquelle N , Woodhouse J , Roux L , Gotthard G , Royant A , Uriarte LM , Ruckebusch C , Joti Y , Byrdin M , Mizohata E , Nango E , Tanaka T , Tono K , Yabashi M , Adam V , Cammarata M , Schlichting I , Bourgeois D , Weik M
Ref : J Phys Chem Lett , 7 :882 , 2016
Abstract : Reversibly photoswitchable fluorescent proteins find growing applications in cell biology, yet mechanistic details, in particular on the ultrafast photochemical time scale, remain unknown. We employed time-resolved pump-probe absorption spectroscopy on the reversibly photoswitchable fluorescent protein IrisFP in solution to study photoswitching from the nonfluorescent (off) to the fluorescent (on) state. Evidence is provided for the existence of several intermediate states on the pico- and microsecond time scales that are attributed to chromophore isomerization and proton transfer, respectively. Kinetic modeling favors a sequential mechanism with the existence of two excited state intermediates with lifetimes of 2 and 15 ps, the second of which controls the photoswitching quantum yield. In order to support that IrisFP is suited for time-resolved experiments aiming at a structural characterization of these ps intermediates, we used serial femtosecond crystallography at an X-ray free electron laser and solved the structure of IrisFP in its on state. Sample consumption was minimized by embedding crystals in mineral grease, in which they remain photoswitchable. Our spectroscopic and structural results pave the way for time-resolved serial femtosecond crystallography aiming at characterizing the structure of ultrafast intermediates in reversibly photoswitchable fluorescent proteins.
ESTHER : Colletier_2016_J.Phys.Chem.Lett_7_882
PubMedSearch : Colletier_2016_J.Phys.Chem.Lett_7_882
PubMedID: 26866390

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 : Acotiamide Hydrochloride, a Therapeutic Agent for Functional Dyspepsia, Enhances Acetylcholine-induced Contraction via Inhibition of Acetylcholinesterase Activity in Circular Muscle Strips of Guinea Pig Stomach - Ito_2016_Drug.Res.(Stuttg)_66_196
Author(s) : Ito K , Kawachi M , Matsunaga Y , Hori Y , Ozaki T , Nagahama K , Hirayama M , Kawabata Y , Shiraishi Y , Takei M , Tanaka T
Ref : Drug Res (Stuttg) , 66 :196 , 2016
Abstract : Acotiamide is a first-in-class prokinetic drug approved in Japan for the treatment of functional dyspepsia. Given that acotiamide enhances gastric motility in conscious dogs and rats, we assessed the in vitro effects of this drug on the contraction of guinea pig stomach strips and on acetylcholinesterase (AChE) activity in stomach homogenate following fundus removal. We also investigated the serotonin 5-HT4 receptor agonist mosapride, dopamine D2 receptor and AChE inhibitor itopride, and representative AChE inhibitor neostigmine. Acotiamide (0.3 and 1 muM) and itopride (1 and 3 muM) significantly enhanced the contraction of gastric body strips induced by electrical field stimulation (EFS), but mosapride (1 and 10 muM) did not. Acotiamide and itopride significantly enhanced the contraction of gastric body and antrum strips induced by acetylcholine (ACh), but not that induced by carbachol (CCh). Neostigmine also significantly enhanced the contraction of gastric body strips induced by ACh, but not that by CCh. In contrast, mosapride failed to enhance contractions induced by either ACh or CCh in gastric antrum strips. Acotiamide exerted mixed inhibition of AChE, and the percentage inhibition of acotiamide (100 muM) against AChE activity was markedly reduced after the reaction mixture was dialyzed. In contrast, itopride exerted noncompetitive inhibition on AChE activity. These results indicate that acotiamide enhances ACh-dependent contraction in gastric strips of guinea pigs via the inhibition of AChE activity, and that it exerts mixed and reversible inhibition of AChE derived from guinea pig stomach.
ESTHER : Ito_2016_Drug.Res.(Stuttg)_66_196
PubMedSearch : Ito_2016_Drug.Res.(Stuttg)_66_196
PubMedID: 26418413

Title : Ionic interaction of positive amino acid residues of fungal hydrophobin RolA with acidic amino acid residues of cutinase CutL1 - Takahashi_2015_Mol.Microbiol_96_14
Author(s) : Takahashi T , Tanaka T , Tsushima Y , Muragaki K , Uehara K , Takeuchi S , Maeda H , Yamagata Y , Nakayama M , Yoshimi A , Abe K
Ref : Molecular Microbiology , 96 :14 , 2015
Abstract : Hydrophobins are amphipathic proteins secreted by filamentous fungi. When the industrial fungus Aspergillus oryzae is grown in a liquid medium containing the polyester polybutylene succinate co-adipate (PBSA), it produces RolA, a hydrophobin, and CutL1, a PBSA-degrading cutinase. Secreted RolA attaches to the surface of the PBSA particles and recruits CutL1, which then condenses on the particles and stimulates the hydrolysis of PBSA. Here, we identified amino acid residues that are required for the RolA-CutL1 interaction by using site-directed mutagenesis. We quantitatively analyzed kinetic profiles of the interactions between RolA variants and CutL1 variants by using a quartz crystal microbalance (QCM). The QCM analyses revealed that Asp142, Asp171 and Glu31, located on the hydrophilic molecular surface of CutL1, and His32 and Lys34, located in the N-terminus of RolA, play crucial roles in the RolA-CutL1 interaction via ionic interactions. RolA immobilized on a QCM electrode strongly interacted with CutL1 (KD = 6.5 nM); however, RolA with CutL1 variants, or RolA variants with CutL1, showed markedly larger KD values, particularly in the interaction between the double variant RolA-H32S/K34S and the triple variant CutL1-E31S/D142S/D171S (KD = 78.0 nM). We discuss a molecular prototype model of hydrophobin-based enzyme recruitment at the solid-water interface.
ESTHER : Takahashi_2015_Mol.Microbiol_96_14
PubMedSearch : Takahashi_2015_Mol.Microbiol_96_14
PubMedID: 25588312
Gene_locus related to this paper: aspor-cutas

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

Title : In vitro acetylcholinesterase inhibitory activity and the antioxidant properties of Aegle marmelos leaf extract: implications for the treatment of Alzheimer's disease - Asaduzzaman_2014_Psychogeriatrics_14_1
Author(s) : Asaduzzaman M , Uddin MJ , Kader MA , Alam AH , Rahman AA , Rashid M , Kato K , Tanaka T , Takeda M , Sadik G
Ref : Psychogeriatrics , 14 :1 , 2014
Abstract : BACKGROUND: Alzheimer's disease (AD) is a progressive neurodegenerative disorder clinically characterized by loss of memory and cognition. The effective therapeutic options for AD are limited and thus there is a demand for new drugs. Aegle marmelos (Linn.) (A. marmelos) leaves have been used in traditional medicine to promote intellect and enhance memory. In this study, we evaluated A. marmelos for its acetylcholinesterase (AChE) inhibitory activity and antioxidant property in vitro in the treatment of AD.
METHODS: A crude methanol extract and four fractions (petroleum ether, chloroform, ethyl acetate and aqueous) were prepared from the leaves of A. marmelos. The preparations were assessed for AChE inhibitory activity by the Ellman method, and their antioxidant properties were assessed by several assays: reducing power, scavenging of 1,1-diphenyl-2-picrylhydrazyl free radical and hydroxyl radical, and inhibition of lipid peroxidation. Qualitative and quantitative analyses of endogenous substances in A. marmelos were performed by the standard phytochemical methods.
RESULTS: Among the different extracts tested, the ethyl acetate fraction exhibited the highest inhibition of AChE activity. In the same way, ethyl acetate fraction showed the highest reducing activity and radical scavenging ability towards the 1,1-diphenyl-2-picrylhydrazyl (half maximal inhibitory concentration = 3.84 mug/mL) and hydroxyl free radicals (half maximal inhibitory concentration = 5.68 mug/mL). The antiradical activity of the ethyl acetate fraction appeared to be similar to that of the reference standard butylated hydroxytoluene and catechin used in this study. In addition, the ethyl acetate fraction displayed higher inhibition of brain lipid peroxidation. Phytochemical screening of different extractives of A. marmelos showed the presence of phenols and flavonoids, alkaloid, saponin, glycoside, tannin and steroids. Quantitative analysis revealed higher contents of phenolics (58.79-mg gallic acid equivalent/g dried extract) and flavonoids (375.73-mg gallic acid equivalent/g dried extract) in the ethyl acetate fraction. CONCLUSION: The results suggest that the ethyl acetate fraction of A. marmelos is a significant source of polyphenolic compounds with potential AChE inhibitory property and antioxidant activity and, thus, may be useful in the treatment of AD.
ESTHER : Asaduzzaman_2014_Psychogeriatrics_14_1
PubMedSearch : Asaduzzaman_2014_Psychogeriatrics_14_1
PubMedID: 24646308

Title : Characterization of two putative prolinases (PepR1 and PepR2) from Lactobacillus plantarum WCFS1: Occurrence of two isozymes with structural similarity and different catalytic properties - Huang_2014_Biochim.Biophys.Acta_1854_91
Author(s) : Huang Y , Tanaka T
Ref : Biochimica & Biophysica Acta , 1854 :91 , 2014
Abstract : Two putative prolinases (PepR1 and PepR2) of Lactobacillus plantarum WCSF1 share 48.5% amino acid sequence identity (55.5% at the DNA level); however, PepR1 exhibits over 80% identity at the protein level with other lactobacilli prolinases while PepR2 exhibits only 51% or less identity. In this study, the putative genes were overexpressed in Escherichia coli, purified to gel electrophoretic homogeneity, and then characterized. Purified PepR1 and PepR2 hydrolyzed Pro-Xaa dipeptide substrates at similar rates, proving their nature as prolinases. Structural analyses using circular dichroism, dynamic light scattering, gel filtration, and molecular modelling revealed that the two prolinases have similar structural characteristics: high beta-sheet content, homotetrameric structure, and similar folding to the PepI/PepL/PepR peptidase family. However, kinetic and thermodynamic analyses of PepR1 and PepR2 indicated differences in many aspects: optimum temperatures (25 and 30 degrees C, respectively), optimum pH (pH7.5 and 8.0, respectively), substrate specificities (high stringency of PepR2), kinetic parameters, and thermal stability (29 and 48 degrees C, respectively). Also, these prolinases behaved differently towards inhibitor treatments, suggesting structural and/or functional differences in their active sites. Differences in the two prolinases would contribute to a diversity of catalytic activities, so that they work together cooperatively and complementarily to hydrolyze proline-containing peptides with broader specificity, working pH, working temperature, and higher efficiency, thus allowing adaptation to a wider range of environments.
ESTHER : Huang_2014_Biochim.Biophys.Acta_1854_91
PubMedSearch : Huang_2014_Biochim.Biophys.Acta_1854_91
PubMedID: 25463046

Title : Duplication of acetylcholinesterase gene in diamondback moth strains with different sensitivities to acephate - Sonoda_2014_Insect.Biochem.Mol.Biol_48_83
Author(s) : Sonoda S , Shi X , Song D , Liang P , Gao X , Zhang Y , Li J , Liu Y , Li M , Matsumura M , Sanada-Morimura S , Minakuchi C , Tanaka T , Miyata T
Ref : Insect Biochemistry & Molecular Biology , 48 :83 , 2014
Abstract : This study examined the acetylcholinesterase 1 gene (AChE1) in Plutella xylostella strains with different sensitivities to acephate. Multiple haplotypes of the gene were found in the field-collected strains including distinct haplotypes carrying one or both previously reported mutations (A298S and G324A). Moreover, sequencing results indicated the presence of duplicated copies of the gene in the field-collected strains. No correlation was found between copy numbers of AChE1 and levels of resistance to acephate suggesting that extensive AChE1 duplication is not a major resistance factor at least in some P. xylostella strains. Proportions of the A298S and G324A mutations showed no correlation with levels of resistance to acephate. This suggests that acephate resistance of P. xylostella is complex and cannot be evaluated based on the AChE1 copy number or proportions of the resistance mutations alone.
ESTHER : Sonoda_2014_Insect.Biochem.Mol.Biol_48_83
PubMedSearch : Sonoda_2014_Insect.Biochem.Mol.Biol_48_83
PubMedID: 24632376

Title : Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics - Sakai_2013_Plant.Cell.Physiol_54_e6
Author(s) : Sakai H , Lee SS , Tanaka T , Numa H , Kim J , Kawahara Y , Wakimoto H , Yang CC , Iwamoto M , Abe T , Yamada Y , Muto A , Inokuchi H , Ikemura T , Matsumoto T , Sasaki T , Itoh T
Ref : Plant Cell Physiol , 54 :e6 , 2013
Abstract : The Rice Annotation Project Database (RAP-DB, http://rapdb.dna.affrc.go.jp/) has been providing a comprehensive set of gene annotations for the genome sequence of rice, Oryza sativa (japonica group) cv. Nipponbare. Since the first release in 2005, RAP-DB has been updated several times along with the genome assembly updates. Here, we present our newest RAP-DB based on the latest genome assembly, Os-Nipponbare-Reference-IRGSP-1.0 (IRGSP-1.0), which was released in 2011. We detected 37,869 loci by mapping transcript and protein sequences of 150 monocot species. To provide plant researchers with highly reliable and up to date rice gene annotations, we have been incorporating literature-based manually curated data, and 1,626 loci currently incorporate literature-based annotation data, including commonly used gene names or gene symbols. Transcriptional activities are shown at the nucleotide level by mapping RNA-Seq reads derived from 27 samples. We also mapped the Illumina reads of a Japanese leading japonica cultivar, Koshihikari, and a Chinese indica cultivar, Guangluai-4, to the genome and show alignments together with the single nucleotide polymorphisms (SNPs) and gene functional annotations through a newly developed browser, Short-Read Assembly Browser (S-RAB). We have developed two satellite databases, Plant Gene Family Database (PGFD) and Integrative Database of Cereal Gene Phylogeny (IDCGP), which display gene family and homologous gene relationships among diverse plant species. RAP-DB and the satellite databases offer simple and user-friendly web interfaces, enabling plant and genome researchers to access the data easily and facilitating a broad range of plant research topics.
ESTHER : Sakai_2013_Plant.Cell.Physiol_54_e6
PubMedSearch : Sakai_2013_Plant.Cell.Physiol_54_e6
PubMedID: 23299411
Gene_locus related to this paper: orysa-Q0JK71 , orysj-q6yse8 , orysa-q6yzk1 , orysj-q2r2z8

Title : Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data - Kawahara_2013_Rice.(N.Y)_6_4
Author(s) : Kawahara Y , de la Bastide M , Hamilton JP , Kanamori H , McCombie WR , Ouyang S , Schwartz DC , Tanaka T , Wu J , Zhou S , Childs KL , Davidson RM , Lin H , Quesada-Ocampo L , Vaillancourt B , Sakai H , Lee SS , Kim J , Numa H , Itoh T , Buell CR , Matsumoto T
Ref : Rice (N Y) , 6 :4 , 2013
Abstract : BACKGROUND: Rice research has been enabled by access to the high quality reference genome sequence generated in 2005 by the International Rice Genome Sequencing Project (IRGSP). To further facilitate genomic-enabled research, we have updated and validated the genome assembly and sequence for the Nipponbare cultivar of Oryza sativa (japonica group). RESULTS: The Nipponbare genome assembly was updated by revising and validating the minimal tiling path of clones with the optical map for rice. Sequencing errors in the revised genome assembly were identified by re-sequencing the genome of two different Nipponbare individuals using the Illumina Genome Analyzer II/IIx platform. A total of 4,886 sequencing errors were identified in 321 Mb of the assembled genome indicating an error rate in the original IRGSP assembly of only 0.15 per 10,000 nucleotides. A small number (five) of insertions/deletions were identified using longer reads generated using the Roche 454 pyrosequencing platform. As the re-sequencing data were generated from two different individuals, we were able to identify a number of allelic differences between the original individual used in the IRGSP effort and the two individuals used in the re-sequencing effort. The revised assembly, termed Os-Nipponbare-Reference-IRGSP-1.0, is now being used in updated releases of the Rice Annotation Project and the Michigan State University Rice Genome Annotation Project, thereby providing a unified set of pseudomolecules for the rice community. CONCLUSIONS: A revised, error-corrected, and validated assembly of the Nipponbare cultivar of rice was generated using optical map data, re-sequencing data, and manual curation that will facilitate on-going and future research in rice. Detection of polymorphisms between three different Nipponbare individuals highlights that allelic differences between individuals should be considered in diversity studies.
ESTHER : Kawahara_2013_Rice.(N.Y)_6_4
PubMedSearch : Kawahara_2013_Rice.(N.Y)_6_4
PubMedID: 24280374
Gene_locus related to this paper: orysa-Q0JK71 , orysj-q6yse8 , orysa-q6yzk1 , orysa-q7xej4 , orysa-q7xem8 , orysa-q7xr64 , orysj-a0a0p0y6l9 , orysj-pla4 , orysj-pla1 , orysj-q2r2z8

Title : Acotiamide, a new orally active acetylcholinesterase inhibitor, stimulates gastrointestinal motor activity in conscious dogs - Nagahama_2012_Neurogastroenterol.Motil_24_566
Author(s) : Nagahama K , Matsunaga Y , Kawachi M , Ito K , Tanaka T , Hori Y , Oka H , Takei M
Ref : Neurogastroenterol Motil , 24 :566 , 2012
Abstract : UNLABELLED: BACKGROUND Acotiamide hydrochloride (acotiamide), a novel selective acetylcholinesterase (AChE) inhibitor, has proven significantly effective in treating functional dyspepsia (FD) in clinical trials, particularly in alleviating meal-related symptoms. In the present study, we examined the gastrointestinal prokinetic effects of acotiamide administered orally or intraduodenally in conscious dogs and investigated in vivo and ex vivo anti-AChE activity of acotiamide to clarify its mechanism of prokinetic action. METHODS: Gastrointestinal motility was measured in conscious dogs with chronically implanted force transducers. KEY RESULTS: Oral administration of acotiamide stimulated postprandial gastroduodenal and colonic motor activities. Measurement of gastrointestinal motility showed that acotiamide, like itopride and mosapride, enhanced gastric antral motility. Further, acotiamide markedly improved clonidine (an alpha(2) -adrenoceptor agonist)-induced hypomotility in a dog model of gastric motor dysfunction. The postprandial gastric antral motility enhanced by acotiamide was completely abolished on treatment with the muscarinic receptor antagonist atropine. Results of an in vivo experiment on anti-AChE activity showed clearly increased acetylcholine-induced gastric motility on intraduodenal administration of acotiamide, just as observed with the AChE inhibitor neostigmine. Further, in ex vivo experiment, intraduodenal administration of acotiamide significantly inhibited AChE activity in canine gastric antrum. CONCLUSIONS & INFERENCES: Our findings revealed that acotiamide administered through the alimentary tract exerts gastroprokinetic action via cholinergic pathways by inhibiting AChE activity. These results may also confirm the mechanism of action in clinical efficacy of acotiamide on FD.
ESTHER : Nagahama_2012_Neurogastroenterol.Motil_24_566
PubMedSearch : Nagahama_2012_Neurogastroenterol.Motil_24_566
PubMedID: 22429221

Title : Comprehensive sequence analysis of 24,783 barley full-length cDNAs derived from 12 clone libraries - Matsumoto_2011_Plant.Physiol_156_20
Author(s) : Matsumoto T , Tanaka T , Sakai H , Amano N , Kanamori H , Kurita K , Kikuta A , Kamiya K , Yamamoto M , Ikawa H , Fujii N , Hori K , Itoh T , Sato K
Ref : Plant Physiol , 156 :20 , 2011
Abstract : Full-length cDNA (FLcDNA) libraries consisting of 172,000 clones were constructed from a two-row malting barley cultivar (Hordeum vulgare 'Haruna Nijo') under normal and stressed conditions. After sequencing the clones from both ends and clustering the sequences, a total of 24,783 complete sequences were produced. By removing duplicates between these and publicly available sequences, 22,651 representative sequences were obtained: 17,773 were novel barley FLcDNAs, and 1,699 were barley specific. Highly conserved genes were found in the barley FLcDNA sequences for 721 of 881 rice (Oryza sativa) trait genes with 50% or greater identity. These FLcDNA resources from our Haruna Nijo cDNA libraries and the full-length sequences of representative clones will improve our understanding of the biological functions of genes in barley, which is the cereal crop with the fourth highest production in the world, and will provide a powerful tool for annotating the barley genome sequences that will become available in the near future.
ESTHER : Matsumoto_2011_Plant.Physiol_156_20
PubMedSearch : Matsumoto_2011_Plant.Physiol_156_20
PubMedID: 21415278
Gene_locus related to this paper: horvd-f2cta8 , horvd-f2cu28 , horvd-f2cu67 , horvd-f2cvb1 , horvd-f2d2e7 , horvd-f2d3b2 , horvd-f2d8w8 , horvd-f2dam1 , horvd-f2db20 , horvd-f2de38 , horvd-f2dey8 , horvd-f2djs2 , horvd-f2dlw1 , horvd-f2dnj9 , horvd-f2dnr0 , horvd-f2dq60 , horvd-f2dr75 , horvd-f2dvh4 , horvd-f2dwx9 , horvd-f2e2j6 , horvd-f2e3n3 , horvd-f2e504 , horvd-f2eb83 , horvd-f2ebk6 , horvd-f2ec44 , horvd-f2ecv3 , horvd-f2ee51 , horvd-f2eji1 , horvu-cp22 , orysa-q2qx94 , horvd-f2dey9 , horvd-f2djx2 , horvd-f2dln9 , horvd-f2dmr7 , horvd-f2dnv4 , horvd-f2drv9 , horvd-f2ds75 , horvd-f2dsx0 , horvd-f2e0a7 , horvd-f2e0u2 , horvd-f2e5v7 , horvd-f2d4p5 , horvd-m0vg59 , horvd-f2cqv0 , horvd-f2e1j3 , horvd-f2d241 , horvd-f2e8z5 , horvd-m0x298 , horvd-m0y280 , horvd-f2djb2 , horvd-f2dq90 , horvv-f2dwm7 , horvv-f2cwp1 , horvv-a0a287g9l8 , horvv-f2dfe3 , horvv-f2db09 , horvv-f2e0h1

Title : Acotiamide hydrochloride (Z-338) enhances gastric motility and emptying by inhibiting acetylcholinesterase activity in rats - Kawachi_2011_Eur.J.Pharmacol_666_218
Author(s) : Kawachi M , Matsunaga Y , Tanaka T , Hori Y , Ito K , Nagahama K , Ozaki T , Inoue N , Toda R , Yoshii K , Hirayama M , Kawabata Y , Takei M
Ref : European Journal of Pharmacology , 666 :218 , 2011
Abstract : In clinical trials, acotiamide hydrochloride (acotiamide: Z-338) has been reported to be useful in the treatment of functional dyspepsia. Here, we investigated the effects of acotiamide on gastric contraction and emptying activities in rats in comparison with itopride hydrochloride (itopride) and mosapride citrate (mosapride). We also examined in vitro the compound's inhibitory effect on acetylcholinesterase (AChE) activity derived from rat stomach. In in vivo studies, acotiamide (30 and 100mg/kg s.c.) and itopride (100mg/kg s.c.) markedly enhanced normal gastric antral motility in rats. In gastric motility dysfunction models, acotiamide (100mg/kg s.c.) and itopride (100mg/kg s.c.) improved both gastric antral hypomotility and the delayed gastric emptying induced by clonidine, an alpha(2)-adrenoceptor agonist. In contrast, mosapride (10mg/kg s.c.) had no effect on these models. Like the AChE inhibitors itopride (30 mg/kg s.c.) and neostigmine (10 mug/kg s.c.), acotiamide (10mg/kg s.c.) also clearly enhanced gastric body contractions induced by electrical stimulation of the vagus, which were abolished by atropine and hexamethonium, whereas mosapride (3 and 10mg/kg s.c.) did not. In in vitro studies, acotiamide concentration-dependently inhibited rat stomach-derived AChE activity (IC(50)=2.3 mumol/l). In addition, stomach tissue concentrations of acotiamide after administration at 10mg/kg s.c. were sufficient to produce inhibition of AChE activity in rat stomach. These results suggest that acotiamide stimulates gastric motility and improves gastric motility dysfunction in rats by inhibiting AChE activity, and may suggest a role for acotiamide in improving gastric motility dysfunction in patients with functional dyspepsia.
ESTHER : Kawachi_2011_Eur.J.Pharmacol_666_218
PubMedSearch : Kawachi_2011_Eur.J.Pharmacol_666_218
PubMedID: 21651906

Title : Different responses of a solitary (Meteorus pulchricornis) and a gregarious (Cotesia kariyai) endoparasitoid to four insecticides in the host Pseudaletia separata - Kanzaki_2010_J.Pestic.Sci_35_1
Author(s) : Kanzaki S , Tanaka T
Ref : Journal of Pesticide Science , 35 :1 , 2010
Abstract : This study clarified the difference in sensitivity of lepidopteran host larvae parasitized by a gregarious endoparasitoid Cotesia kariyai and a solitary endoparasitoid Meteorus pulchricornis to four insecticides, fenitrothion, cypermethrin, pyriproxyfen and pyridalyl, along with the growth and development of each parasitoid. It is well known that the physiological state of the host is regulated by endoparasitoid after parasitization. It was predicted from our previous report that the detoxification ability of the parasitized hosts was changed by parasitization. The effect of four insecticides on the growth and development of two parasitoids was examined with LD50 or LD95 values of unparasitized hosts. Fenitrothion and cypermethrin had an effect on the growth and development of host larvae parasitized by C. kariyai, but in M. pulchricornis caused low mortality on day 3 and later after parasitization. Pyriproxyfen had no effect on the growth and development of C. kariyai, but inhibited the adult eclosion of M. pulchricornis even when the parasitized hosts were treated with 50 ppm (less than LD10 to unparasitized hosts). Paraffin sections revealed developmental malformations in the abdomen during the pupal stage of M. pulchricornis endoparasitoid. Pyridalyl had a strong effect on larval emergence of C. kariyai from the host during early stages (until day 7 postparasitization), because parasitoid larvae did not grow as lepidopteran larvae became motionless after pyridalyl treatment and could not eat. On the other hand, pyridalyl at LD50 has a little effect on larval emergence and adult eclosion of M. pulchricornis. Gregarious and solitary endoparasitoids showed different sensitivity to four individual insecticides.
ESTHER : Kanzaki_2010_J.Pestic.Sci_35_1
PubMedSearch : Kanzaki_2010_J.Pestic.Sci_35_1

Title : The Rice Annotation Project Database (RAP-DB): 2008 update - Tanaka_2008_Nucleic.Acids.Res_36_D1028
Author(s) : Tanaka T , Antonio BA , Kikuchi S , Matsumoto T , Nagamura Y , Numa H , Sakai H , Wu J , Itoh T , Sasaki T , Aono R , Fujii Y , Habara T , Harada E , Kanno M , Kawahara Y , Kawashima H , Kubooka H , Matsuya A , Nakaoka H , Saichi N , Sanbonmatsu R , Sato Y , Shinso Y , Suzuki M , Takeda J , Tanino M , Todokoro F , Yamaguchi K , Yamamoto N , Yamasaki C , Imanishi T , Okido T , Tada M , Ikeo K , Tateno Y , Gojobori T , Lin YC , Wei FJ , Hsing YI , Zhao Q , Han B , Kramer MR , McCombie RW , Lonsdale D , O'Donovan CC , Whitfield EJ , Apweiler R , Koyanagi KO , Khurana JP , Raghuvanshi S , Singh NK , Tyagi AK , Haberer G , Fujisawa M , Hosokawa S , Ito Y , Ikawa H , Shibata M , Yamamoto M , Bruskiewich RM , Hoen DR , Bureau TE , Namiki N , Ohyanagi H , Sakai Y , Nobushima S , Sakata K , Barrero RA , Souvorov A , Smith-White B , Tatusova T , An S , An G , S OO , Fuks G , Messing J , Christie KR , Lieberherr D , Kim H , Zuccolo A , Wing RA , Nobuta K , Green PJ , Lu C , Meyers BC , Chaparro C , Piegu B , Panaud O , Echeverria M
Ref : Nucleic Acids Research , 36 :D1028 , 2008
Abstract : The Rice Annotation Project Database (RAP-DB) was created to provide the genome sequence assembly of the International Rice Genome Sequencing Project (IRGSP), manually curated annotation of the sequence, and other genomics information that could be useful for comprehensive understanding of the rice biology. Since the last publication of the RAP-DB, the IRGSP genome has been revised and reassembled. In addition, a large number of rice-expressed sequence tags have been released, and functional genomics resources have been produced worldwide. Thus, we have thoroughly updated our genome annotation by manual curation of all the functional descriptions of rice genes. The latest version of the RAP-DB contains a variety of annotation data as follows: clone positions, structures and functions of 31 439 genes validated by cDNAs, RNA genes detected by massively parallel signature sequencing (MPSS) technology and sequence similarity, flanking sequences of mutant lines, transposable elements, etc. Other annotation data such as Gnomon can be displayed along with those of RAP for comparison. We have also developed a new keyword search system to allow the user to access useful information. The RAP-DB is available at: http://rapdb.dna.affrc.go.jp/ and http://rapdb.lab.nig.ac.jp/.
ESTHER : Tanaka_2008_Nucleic.Acids.Res_36_D1028
PubMedSearch : Tanaka_2008_Nucleic.Acids.Res_36_D1028
PubMedID: 18089549
Gene_locus related to this paper: orysa-Q9FW17 , orysa-Q0JK71 , orysa-B9EWJ8 , orysa-Q5N7L1 , orysa-pir7a , orysa-q2qyj1 , orysj-q6yse8 , orysa-q6yzk1 , orysa-Q8S0U8 , orysa-q33aq0 , orysa-Q0J0A4 , orysi-a2z179 , orysi-a2zef2 , orysi-b8a7e6 , orysi-b8a7e7 , orysi-b8bfe5 , orysi-b8bhp9 , orysj-b9fi05 , orysj-b9fkb0 , orysj-cgep , orysj-q0djj0 , orysj-q0dud7 , orysj-q0jaf0 , orysj-q0jga1 , orysj-q5jl22 , orysj-q5jlw7 , orysj-q6h7q9 , orysj-q6yvk6 , orysj-q7f8x1 , orysj-q7xcx3 , orysj-q9fwm6 , orysj-q10j20 , orysj-q10ss2 , orysj-q69uw6 , orysj-q94d71 , orysj-q0iq98 , orysj-b9gbs4 , orysj-b9gbs1 , orysj-pla4 , orysj-pla1

Title : Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana - Itoh_2007_Genome.Res_17_175
Author(s) : Itoh T , Tanaka T , Barrero RA , Yamasaki C , Fujii Y , Hilton PB , Antonio BA , Aono H , Apweiler R , Bruskiewich R , Bureau T , Burr F , Costa de Oliveira A , Fuks G , Habara T , Haberer G , Han B , Harada E , Hiraki AT , Hirochika H , Hoen D , Hokari H , Hosokawa S , Hsing YI , Ikawa H , Ikeo K , Imanishi T , Ito Y , Jaiswal P , Kanno M , Kawahara Y , Kawamura T , Kawashima H , Khurana JP , Kikuchi S , Komatsu S , Koyanagi KO , Kubooka H , Lieberherr D , Lin YC , Lonsdale D , Matsumoto T , Matsuya A , McCombie WR , Messing J , Miyao A , Mulder N , Nagamura Y , Nam J , Namiki N , Numa H , Nurimoto S , O'Donovan C , Ohyanagi H , Okido T , Oota S , Osato N , Palmer LE , Quetier F , Raghuvanshi S , Saichi N , Sakai H , Sakai Y , Sakata K , Sakurai T , Sato F , Sato Y , Schoof H , Seki M , Shibata M , Shimizu Y , Shinozaki K , Shinso Y , Singh NK , Smith-White B , Takeda J , Tanino M , Tatusova T , Thongjuea S , Todokoro F , Tsugane M , Tyagi AK , Vanavichit A , Wang A , Wing RA , Yamaguchi K , Yamamoto M , Yamamoto N , Yu Y , Zhang H , Zhao Q , Higo K , Burr B , Gojobori T , Sasaki T
Ref : Genome Res , 17 :175 , 2007
Abstract : We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions were identified or inferred in 19,969 (70%) of the proteins, and 131 possible npRNAs (including 58 antisense transcripts) were found. Almost 5000 annotated protein-coding genes were found to be disrupted in insertional mutant lines, which will accelerate future experimental validation of the annotations. The rice loci were determined by using cDNA sequences obtained from rice and other representative cereals. Our conservative estimate based on these loci and an extrapolation suggested that the gene number of rice is approximately 32,000, which is smaller than previous estimates. We conducted comparative analyses between rice and Arabidopsis thaliana and found that both genomes possessed several lineage-specific genes, which might account for the observed differences between these species, while they had similar sets of predicted functional domains among the protein sequences. A system to control translational efficiency seems to be conserved across large evolutionary distances. Moreover, the evolutionary process of protein-coding genes was examined. Our results suggest that natural selection may have played a role for duplicated genes in both species, so that duplication was suppressed or favored in a manner that depended on the function of a gene.
ESTHER : Itoh_2007_Genome.Res_17_175
PubMedSearch : Itoh_2007_Genome.Res_17_175
PubMedID: 17210932
Gene_locus related to this paper: orysa-Q7XTC5 , orysa-Q852M6 , orysa-Q8GSE8 , orysa-Q9FYP7 , orysa-Q5ZA26 , orysa-Q5JLP6 , orysa-Q8H5P5 , orysa-Q7F1Y5 , orysa-cbp3 , orysa-cbpx , orysa-Q6YSZ8 , orysa-Q9FW17 , orysa-Q84QZ6 , orysa-Q0JK71 , orysa-B9EWJ8 , orysa-Q6ZDG6 , orysa-Q6ZDG5 , orysa-Q658B2 , orysa-Q5N7L1 , orysa-Q8RYV9 , orysa-Q8H3R3 , orysa-Q5SNH3 , orysa-pir7a , orysa-q2qnj4 , orysa-q2qyj1 , orysa-q2r077 , orysa-Q4VWY7 , orysa-q5smv5 , orysa-q5z901 , orysa-Q5ZBI5 , orysa-q6atz0 , orysa-q6i5q3 , orysa-q6j657 , orysa-q6k4q2 , orysj-q6yse8 , orysa-q6yy42 , orysa-q6yzk1 , orysa-q6z8b1 , orysa-q6z995 , orysa-q6zjq6 , orysa-q7x7y5 , orysa-Q7XC50 , orysa-q7xr62 , orysa-q7xr63 , orysa-q7xsg1 , orysa-q7xsq2 , orysa-q7xts6 , orysa-q7xv53 , orysa-Q8LQS5 , orysa-Q8RZ79 , orysa-Q8S0U8 , orysa-Q8W3C6 , orysa-Q9LHX5 , orysa-q53m20 , orysa-q53nd8 , orysa-q60e79 , orysa-q67iz2 , orysa-q67iz3 , orysa-q67iz7 , orysa-q67iz8 , orysa-q67j02 , orysa-q67j05 , orysa-q67j09 , orysa-q67j10 , orysa-q67tr6 , orysa-q67tv0 , orysa-q69j38 , orysa-q69y21 , orysa-q75hy1 , orysa-q75hy2 , orysa-Q0J0A4 , orysa-q651a8 , orysa-q652g4 , orysa-q688m8 , orysa-Q6H8G1 , orysi-a2z179 , orysi-a2zef2 , orysi-b8a7e6 , orysi-b8a7e7 , orysi-b8bfe5 , orysi-b8bhp9 , orysj-b9fi05 , orysj-q0djj0 , orysj-q0jaf0 , orysj-q0jga1 , orysj-q0jhi5 , orysj-q5jl22 , orysj-q5jlw7 , orysj-q6h7q9 , orysj-q6yvk6 , orysj-q7f8x1 , orysj-q7xcx3 , orysj-q9fwm6 , orysj-q10j20 , orysj-q10ss2 , orysj-q69uw6 , orysj-q94d71 , orysj-q0iq98 , orysj-b9gbs4 , orysj-b9gbs1

Title : CGI-58 facilitates lipolysis on lipid droplets but is not involved in the vesiculation of lipid droplets caused by hormonal stimulation - Yamaguchi_2007_J.Lipid.Res_48_1078
Author(s) : Yamaguchi T , Omatsu N , Morimoto E , Nakashima H , Ueno K , Tanaka T , Satouchi K , Hirose F , Osumi T
Ref : J Lipid Res , 48 :1078 , 2007
Abstract : A lipid droplet (LD)-associated protein, perilipin, is a critical regulator of lipolysis in adipocytes. We previously showed that Comparative Gene Identification-58 (CGI-58), a product of the causal gene of Chanarin-Dorfman syndrome, interacts with perilipin on LDs. In this study, we investigated the function of CGI-58 using RNA interference. Notably, CGI-58 knockdown caused an abnormal accumulation of LDs in both 3T3-L1 preadipocytes and Hepa1 hepatoma cells. CGI-58 knockdown did not influence the differentiation of 3T3-L1 adipocytes but reduced the activity of both basal and cAMP-dependent protein kinase-stimulated lipolysis. In vitro studies showed that CGI-58 itself does not have lipase/esterase activity, but it enhanced the activity of adipose triglyceride lipase. Upon lipolytic stimulation, endogenous CGI-58 was rapidly dispersed from LDs into the cytosol along with small particulate structures. This shift in localization depends on the phosphorylation of perilipin, because phosphorylated perilipin lost the ability to bind CGI-58. During lipolytic activation, LDs in adipocytes vesiculate into micro-LDs. Using coherent anti-Stokes Raman scattering microscopy, we pursued the formation of micro-LDs in single cells, which seemed to occur in cytoplasmic regions distant from the large central LDs. CGI-58 is not required for this process. Thus, CGI-58 facilitates lipolysis in cooperation with perilipin and other factors, including lipases.
ESTHER : Yamaguchi_2007_J.Lipid.Res_48_1078
PubMedSearch : Yamaguchi_2007_J.Lipid.Res_48_1078
PubMedID: 17308334

Title : Lupane-type saponins from leaves of Acanthopanax sessiliflorus and their inhibitory activity on pancreatic lipase - Yoshizumi_2006_J.Agric.Food.Chem_54_335
Author(s) : Yoshizumi K , Hirano K , Ando H , Hirai Y , Ida Y , Tsuji T , Tanaka T , Satouchi K , Terao J
Ref : Journal of Agricultural and Food Chemistry , 54 :335 , 2006
Abstract : Three known saponins, chiisanoside, 11-deoxyisochiisanoside, and isochiisanoside, and one novel saponin, 3,4-seco-4(23),20(29)-lupadiene-3,28-dioic acid 28-O-alpha-l-rhamnopyranosyl (1-->4)-beta-d-glucopyranosyl (1-->6)-beta-d-glucopyranoside, referred to as sessiloside, were isolated from a hot water extract of Acanthopanax sessiliflorus leaves. All of these saponins were lupane-type triterpene triglycosides, and their concentrations were 4.1, 1.0, 0.5, and 0.4% (w/w) of the total extract, respectively. Sessiloside and chiisanoside inhibited pancreatic lipase activity in vitro, and addition of the saponin-rich fraction to a high-fat diet suppressed the body weight gain of mice. The possibility of application of the lupane-type saponins from A. sessiliflorus leaves to the treatment of obesity is discussed.
ESTHER : Yoshizumi_2006_J.Agric.Food.Chem_54_335
PubMedSearch : Yoshizumi_2006_J.Agric.Food.Chem_54_335
PubMedID: 16417288

Title : Parasitization by Cotesia plutellae enhances detoxifying enzyme activity in Plutella xylostella - Takeda_2006_Pestic.Biochem.Physiol_86_15
Author(s) : Takeda T , Nakamatsu Y , Tanaka T
Ref : Pesticide Biochemistry and Physiology , 86 :15 , 2006
Abstract : Insecticidal tests using diazinon showed that the mortality of Plutella xylostella larvae parasitized by Cotesia plutellae was reduced by 4.6-fold compared to that of the nonparasitized hosts. The use of chemicals with synergistic effect to insecticides in toxicity assay helps to elucidate the kind of enzyme involved in lowering insect mortality. Synergism of diethyl maleate and piperonyl butoxide with diazinon resulted to 2.4- and 1.9-fold increase, respectively, in susceptibility of parasitized larvae compared to those of nonparasitized larvae. These results indicated the possibility that the decrease in susceptibility to diazinon was due to the elevated activities of glutathione-S-transferase (GST) and cytochrome P450 monooxygenase (CYP), respectively. The GST activities in parasitized larvae were significantly higher than those of nonparasitized ones starting from three days post-parasitization until emergence of parasitoid larva. High GST activities during late parasitism could be attributed to both enzyme activities toward diazinon of parasitized P. xylostella larva itself and C. plutellae larva inside larval host. High GST activity one day after parasitization, although statistical significance was not detected, was caused by polydnavirus (PDV) and the venom of C. plutellae not by parasitoid larvae. Artificial injection of PDV plus venom demonstrated that the resulting increase in GST activity is similar to the increase brought by parasitization. High CYP activity after 3 days post-parasitization in parasitized larva was attributed mainly to the activity of parasitoid larva. Carboxylesterase activity in the parasitized host remained at a high level, while that in the nonparasitized host decreased slightly as pupation approaches. On the other hand, acetylcholinesterase activity also remained constant after parasitization until larval emergence, while that of the nonparasitized hosts decreased gradually as the host larvae approach pupation. These results were supported by inhibition tests using diazoxon in vitro.
ESTHER : Takeda_2006_Pestic.Biochem.Physiol_86_15
PubMedSearch : Takeda_2006_Pestic.Biochem.Physiol_86_15

Title : The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information - Ohyanagi_2006_Nucleic.Acids.Res_34_D741
Author(s) : Ohyanagi H , Tanaka T , Sakai H , Shigemoto Y , Yamaguchi K , Habara T , Fujii Y , Antonio BA , Nagamura Y , Imanishi T , Ikeo K , Itoh T , Gojobori T , Sasaki T
Ref : Nucleic Acids Research , 34 :D741 , 2006
Abstract : With the completion of the rice genome sequencing, a standardized annotation is necessary so that the information from the genome sequence can be fully utilized in understanding the biology of rice and other cereal crops. An annotation jamboree was held in Japan with the aim of annotating and manually curating all the genes in the rice genome. Here we present the Rice Annotation Project Database (RAP-DB), which has been developed to provide access to the annotation data. The RAP-DB has two different types of annotation viewers, BLAST and BLAT search, and other useful features. By connecting the annotations to other rice genomics data, such as full-length cDNAs and Tos17 mutant lines, the RAP-DB serves as a hub for rice genomics. All of the resources can be accessed through http://rapdb.lab.nig.ac.jp/.
ESTHER : Ohyanagi_2006_Nucleic.Acids.Res_34_D741
PubMedSearch : Ohyanagi_2006_Nucleic.Acids.Res_34_D741
PubMedID: 16381971
Gene_locus related to this paper: orysa-Q9FW17 , orysa-Q0JK71 , orysa-B9EWJ8 , orysa-Q5N7L1 , orysa-Q5N7J6 , orysa-pir7a , orysa-q2qyi1 , orysa-q2qyj1 , orysa-q2rbb3 , orysj-q6yse8 , orysa-q6yzk1 , orysa-Q8S0U8 , orysa-Q84ZY8 , orysa-Q0J0A4 , orysi-a2z179 , orysi-a2zef2 , orysi-b8a7e6 , orysi-b8a7e7 , orysi-b8bfe5 , orysi-b8bhp9 , orysj-b9fi05 , orysj-q0d4u5 , orysj-q0djj0 , orysj-q0jaf0 , orysj-q0jga1 , orysj-q0jhi5 , orysj-q5jl22 , orysj-q5jlw7 , orysj-q6h7q9 , orysj-q6yvk6 , orysj-q7f8x1 , orysj-q7xcx3 , orysj-q9fwm6 , orysj-q10j20 , orysj-q10ss2 , orysj-q69uw6 , orysj-q94d71 , orysj-q0iq98 , orysj-b9gbs4 , orysj-b9gbs1

Title : Acephate in biological fluids of two autopsy cases after ingestion of the chemical - Tanaka_2005_J.Forensic.Sci_50_933
Author(s) : Tanaka T , Tanaka N , Kita T , Kasai K , Sato H
Ref : J Forensic Science , 50 :933 , 2005
Abstract : Two autopsy cases, where the individuals were suspected of having ingested acephate, an organophosphorous insecticide, are reported. Acephate and its active metabolite, methamidophos (MP), were analyzed in the biological fluids by GC/MS, using the salting out method with liquid-liquid extraction columns. The first case was that of a 70-year-old man whose blood acephate was 149 microg/mL, and MP was 3.0 microg/mL. Serum pseudocholinesterase (ChE) activity was inhibited. No remarkable finding of injury or disease was determined as the cause of his death, but acute poisoning by acephate was mostly suspected. The second case was that of a 60-year-old man. A deep gash in the left neck injured the left common carotid artery in addition to the severely ischemic state of the primary organs. His blood acephate was 46 microg/mL, and MP was not detected. ChE activity was in the normal range. Hemorrhage was mainly suspected as the cause of his death. The concentrations of acephate and MP in human blood after oral ingestion are first reported here, and the acute toxic level of acephate is discussed.
ESTHER : Tanaka_2005_J.Forensic.Sci_50_933
PubMedSearch : Tanaka_2005_J.Forensic.Sci_50_933
PubMedID: 16078501

Title : Genes involved in SkfA killing factor production protect a Bacillus subtilis lipase against proteolysis - Westers_2005_Appl.Environ.Microbiol_71_1899
Author(s) : Westers H , Braun PG , Westers L , Antelmann H , Hecker M , Jongbloed JD , Yoshikawa H , Tanaka T , van Dijl JM , Quax WJ
Ref : Applied Environmental Microbiology , 71 :1899 , 2005
Abstract : Small lipases of Bacillus species, such as LipA from Bacillus subtilis, have a high potential for industrial applications. Recent studies showed that deletion of six AT-rich islands from the B. subtilis genome results in reduced amounts of extracellular LipA. Here we demonstrate that the reduced LipA levels are due to the absence of four genes, skfABCD, located in the prophage 1 region. Intact skfABCD genes are required not only for LipA production at wild-type levels by B. subtilis 168 but also under conditions of LipA overproduction. Notably, SkfA has bactericidal activity and, probably, requires the SkfB to SkfD proteins for its production. The present results show that LipA is more prone to proteolytic degradation in the absence of SkfA and that high-level LipA production can be improved significantly by employing multiple protease-deficient B. subtilis strains. In conclusion, our findings imply that SkfA protects LipA, directly or indirectly, against proteolytic degradation. Conceivably, SkfA could act as a modulator in LipA folding or as a protease inhibitor.
ESTHER : Westers_2005_Appl.Environ.Microbiol_71_1899
PubMedSearch : Westers_2005_Appl.Environ.Microbiol_71_1899
PubMedID: 15812018

Title : Genome sequencing and analysis of Aspergillus oryzae - Machida_2005_Nature_438_1157
Author(s) : Machida M , Asai K , Sano M , Tanaka T , Kumagai T , Terai G , Kusumoto K , Arima T , Akita O , Kashiwagi Y , Abe K , Gomi K , Horiuchi H , Kitamoto K , Kobayashi T , Takeuchi M , Denning DW , Galagan JE , Nierman WC , Yu J , Archer DB , Bennett JW , Bhatnagar D , Cleveland TE , Fedorova ND , Gotoh O , Horikawa H , Hosoyama A , Ichinomiya M , Igarashi R , Iwashita K , Juvvadi PR , Kato M , Kato Y , Kin T , Kokubun A , Maeda H , Maeyama N , Maruyama J , Nagasaki H , Nakajima T , Oda K , Okada K , Paulsen I , Sakamoto K , Sawano T , Takahashi M , Takase K , Terabayashi Y , Wortman JR , Yamada O , Yamagata Y , Anazawa H , Hata Y , Koide Y , Komori T , Koyama Y , Minetoki T , Suharnan S , Tanaka A , Isono K , Kuhara S , Ogasawara N , Kikuchi H
Ref : Nature , 438 :1157 , 2005
Abstract : The genome of Aspergillus oryzae, a fungus important for the production of traditional fermented foods and beverages in Japan, has been sequenced. The ability to secrete large amounts of proteins and the development of a transformation system have facilitated the use of A. oryzae in modern biotechnology. Although both A. oryzae and Aspergillus flavus belong to the section Flavi of the subgenus Circumdati of Aspergillus, A. oryzae, unlike A. flavus, does not produce aflatoxin, and its long history of use in the food industry has proved its safety. Here we show that the 37-megabase (Mb) genome of A. oryzae contains 12,074 genes and is expanded by 7-9 Mb in comparison with the genomes of Aspergillus nidulans and Aspergillus fumigatus. Comparison of the three aspergilli species revealed the presence of syntenic blocks and A. oryzae-specific blocks (lacking synteny with A. nidulans and A. fumigatus) in a mosaic manner throughout the genome of A. oryzae. The blocks of A. oryzae-specific sequence are enriched for genes involved in metabolism, particularly those for the synthesis of secondary metabolites. Specific expansion of genes for secretory hydrolytic enzymes, amino acid metabolism and amino acid/sugar uptake transporters supports the idea that A. oryzae is an ideal microorganism for fermentation.
ESTHER : Machida_2005_Nature_438_1157
PubMedSearch : Machida_2005_Nature_438_1157
PubMedID: 16372010
Gene_locus related to this paper: aspor-Q2U722 , aspfn-b8mvx2 , aspfn-b8mwk1 , aspfn-b8n1a4 , aspfn-b8n5l3 , aspfn-b8n7y0 , aspfn-b8n829 , aspfn-b8ncj5 , aspfn-b8nhj9 , aspfn-b8njx6 , aspfn-b8nsk2 , aspfu-q4wj61 , aspor-axe1 , aspor-CPI , aspor-cutas , aspor-cuti2 , aspor-DPPIV , aspor-faec , aspor-MDLB , aspor-ppme1 , aspor-q2tw11 , aspor-q2tw16 , aspor-q2tw28 , aspor-q2twc4 , aspor-q2twg0 , aspor-q2twj3 , aspor-q2twv2 , aspor-q2twv4 , aspor-q2tx21 , aspor-q2txq8 , aspor-q2tya1 , aspor-q2tyh6 , aspor-q2tyn9 , aspor-q2typ0 , aspor-q2tyq4 , aspor-q2tyv8 , aspor-q2tz03 , aspor-q2tzh3 , aspor-q2tzr5 , aspor-q2tzv9 , aspor-q2u0k7 , aspor-q2u0q2 , aspor-q2u0r6 , aspor-q2u1a5 , aspor-q2u1a6 , aspor-q2u1k0 , aspor-q2u1k8 , aspor-q2u1m8 , aspor-q2u2a1 , aspor-q2u2a4 , aspor-q2u3a3 , aspor-q2u3a6 , aspor-q2u3k5 , aspor-q2u3l6 , aspor-q2u4a0 , aspor-q2u4e0 , aspor-q2u4f6 , aspor-q2u4g6 , aspor-q2u4h9 , aspor-q2u4w9 , aspor-q2u4y8 , aspor-q2u5f5 , aspor-q2u5n3 , aspor-q2u5y8 , aspor-q2u6h7 , aspor-q2u6j5 , aspor-q2u6m8 , aspor-q2u6m9 , aspor-q2u6n6 , aspor-q2u7i2 , aspor-q2u7v0 , aspor-q2u8j8 , aspor-q2u8r1 , aspor-q2u8r4 , aspor-q2u8t5 , aspor-q2u8z3 , aspor-q2u9a1 , aspor-q2u9n5 , aspor-q2u144 , aspor-q2u161 , aspor-q2u185 , aspor-q2u199 , aspor-q2u212 , aspor-q2u331 , aspor-q2u348 , aspor-q2u400 , aspor-q2u453 , aspor-q2u489 , aspor-q2u704 , aspor-q2u728 , aspor-q2u798 , aspor-q2u822 , aspor-q2u854 , aspor-q2u875 , aspor-q2u908 , aspor-q2ua10 , aspor-q2ua48 , aspor-q2uab6 , aspor-q2uak9 , aspor-q2uaq4 , aspor-q2ub32 , aspor-q2ub76 , aspor-q2uba1 , aspor-q2ubd6 , aspor-q2ubm2 , aspor-q2ubr2 , aspor-q2uc28 , aspor-q2uc65 , aspor-q2uc77 , aspor-q2uc98 , aspor-q2uck0 , aspor-q2ucy7 , aspor-q2ud03 , aspor-q2ud06 , aspor-q2ud08 , aspor-q2ud23 , aspor-q2udn5 , aspor-q2udr0 , aspor-q2uec1 , aspor-q2uef3 , aspor-q2uf10 , aspor-q2uf27 , aspor-q2uf48 , aspor-q2ufd8 , aspor-q2ufe5 , aspor-q2ufm4 , aspor-q2ufr3 , aspor-q2ufz8 , aspor-q2ug78 , aspor-q2ugd6 , aspor-q2uge1 , aspor-q2ugg7 , aspor-q2ugi2 , aspor-q2ugl2 , aspor-q2ugy9 , aspor-q2uh24 , aspor-q2uh73 , aspor-q2uhe4 , aspor-q2uhf0 , aspor-q2uhj6 , aspor-q2uhn1 , aspor-q2uhq0 , aspor-q2ui56 , aspor-q2uib2 , aspor-q2uib5 , aspor-q2uie9 , aspor-q2uih1 , aspor-q2uii1 , aspor-q2uik9 , aspor-q2uiq0 , aspor-q2uiu1 , aspor-q2uix9 , aspor-q2uiy5 , aspor-q2uiz4 , aspor-q2uj89 , aspor-q2uja2 , aspor-q2uju3 , aspor-q2uk31 , aspor-q2uk42 , aspor-q2ukb6 , aspor-q2ukq7 , aspor-q2ul81 , aspor-q2uli9 , aspor-q2ulr2 , aspor-q2ulv7 , aspor-q2umf3 , aspor-q2umv2 , aspor-q2umx6 , aspor-q2unw5 , aspor-q2up23 , aspor-q2up89 , aspor-q2upe6 , aspor-q2upi1 , aspor-q2upl1 , aspor-q2upw4 , aspor-q2uq56 , aspor-q2uqb4 , aspor-q2uqm7 , aspor-q2ur58 , aspor-q2ur64 , aspor-q2ur80 , aspor-q2ur83 , aspor-q2ure7 , aspor-q2urf3 , aspor-q2urg5 , aspor-q2urq0 , aspor-q2urt4 , aspor-q2uru5 , aspor-q2usi0 , aspor-q2usp7 , aspor-q2usq8 , aspor-q2usv6 , aspor-q2uta5 , aspor-q2uu89 , aspor-q2uub4 , aspor-q2uux8 , aspor-q2uv29 , aspor-TGLA , aspor-q2ue03 , aspor-q2uj83 , aspno-a0a0l1j1c9

Title : Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae - Galagan_2005_Nature_438_1105
Author(s) : Galagan JE , Calvo SE , Cuomo C , Ma LJ , Wortman JR , Batzoglou S , Lee SI , Basturkmen M , Spevak CC , Clutterbuck J , Kapitonov V , Jurka J , Scazzocchio C , Farman M , Butler J , Purcell S , Harris S , Braus GH , Draht O , Busch S , d'Enfert C , Bouchier C , Goldman GH , Bell-Pedersen D , Griffiths-Jones S , Doonan JH , Yu J , Vienken K , Pain A , Freitag M , Selker EU , Archer DB , Penalva MA , Oakley BR , Momany M , Tanaka T , Kumagai T , Asai K , Machida M , Nierman WC , Denning DW , Caddick M , Hynes M , Paoletti M , Fischer R , Miller B , Dyer P , Sachs MS , Osmani SA , Birren BW
Ref : Nature , 438 :1105 , 2005
Abstract : The aspergilli comprise a diverse group of filamentous fungi spanning over 200 million years of evolution. Here we report the genome sequence of the model organism Aspergillus nidulans, and a comparative study with Aspergillus fumigatus, a serious human pathogen, and Aspergillus oryzae, used in the production of sake, miso and soy sauce. Our analysis of genome structure provided a quantitative evaluation of forces driving long-term eukaryotic genome evolution. It also led to an experimentally validated model of mating-type locus evolution, suggesting the potential for sexual reproduction in A. fumigatus and A. oryzae. Our analysis of sequence conservation revealed over 5,000 non-coding regions actively conserved across all three species. Within these regions, we identified potential functional elements including a previously uncharacterized TPP riboswitch and motifs suggesting regulation in filamentous fungi by Puf family genes. We further obtained comparative and experimental evidence indicating widespread translational regulation by upstream open reading frames. These results enhance our understanding of these widely studied fungi as well as provide new insight into eukaryotic genome evolution and gene regulation.
ESTHER : Galagan_2005_Nature_438_1105
PubMedSearch : Galagan_2005_Nature_438_1105
PubMedID: 16372000
Gene_locus related to this paper: emeni-axe1 , emeni-BST1 , emeni-c8vrl3 , emeni-CUTI3 , emeni-faec , emeni-ppme1 , emeni-q5aqv0 , emeni-q5ara9 , emeni-q5av79 , emeni-q5avd3 , emeni-q5awc7 , emeni-q5awq3 , emeni-q5awu9 , emeni-q5aww7 , emeni-q5ax50 , emeni-q5ay37 , emeni-q5ay57 , emeni-q5ayk9 , emeni-q5az32 , emeni-q5azl2 , emeni-q5azp1 , emeni-q5b1v2 , emeni-q5b2c1 , emeni-q5b3d2 , emeni-q5b5j7 , emeni-q5b7i6 , emeni-q5b8p6 , emeni-q5b9e7 , emeni-q5b246 , emeni-q5b446 , emeni-q5b602 , emeni-q5b938 , emeni-q5ba78 , emeni-q5bad3 , emeni-q5bar0 , emeni-q5bcd1 , emeni-q5bcd2 , emeni-q5bcf8 , emeni-q5bdr0 , emeni-q5beh9 , emeni-q5bgk7 , emeni-q7si80 , emeni-q5bdv9 , emeni-c8vu15 , 9euro-a0a3d8t644 , emeni-q5b719 , emeni-q5ax97 , emeni-tdia , emeni-afoc , emeni-dbae

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 : Dissection of the host range of the fungal plant pathogen Alternaria alternata by modification of secondary metabolism - Ito_2004_Mol.Microbiol_52_399
Author(s) : Ito K , Tanaka T , Hatta R , Yamamoto M , Akimitsu K , Tsuge T
Ref : Molecular Microbiology , 52 :399 , 2004
Abstract : The filamentous fungus Alternaria alternata contains seven pathogenic variants (pathotypes), which produce different host-specific toxins and cause diseases on different plants. The strawberry pathotype produces host-specific AF-toxin and causes Alternaria black spot of strawberry. This pathotype is also pathogenic to Japanese pear cultivars susceptible to the Japanese pear pathotype that produces AK-toxin. The strawberry pathotype produces two related molecular species, AF-toxins I and II: toxin I is toxic to both strawberry and pear, and toxin II is toxic only to pear. Previously, we isolated a cosmid clone pcAFT-1 from the strawberry pathotype that contains three genes involved in AF-toxin biosynthesis. Here, we have identified a new gene, designated AFTS1, from pcAFT-1. AFTS1 encodes a protein with similarity to enzymes of the aldo-ketoreductase superfamily. Targeted mutation of AFTS1 diminished the host range of the strawberry pathotype: Delta aftS1 mutants were pathogenic to pear, but not to strawberry, as is the Japanese pear pathotype. These mutants were found to produce AF-toxin II, but not AF-toxin I. These data represent a novel example of how the host range of a plant pathogenic fungus can be restricted by modification of secondary metabolism.
ESTHER : Ito_2004_Mol.Microbiol_52_399
PubMedSearch : Ito_2004_Mol.Microbiol_52_399
PubMedID: 15066029
Gene_locus related to this paper: altal-aft8 , altal-amt4

Title : Comparison of kinetic properties of a hydrophilic form of acetylcholinesterase purified from strains susceptible and resistant to carbamate and organophosphorus insecticides of green rice leafhopper (Nephotettix cincticeps Uhler) - Kato_2004_Pestic.Biochem.Physiol_79_64
Author(s) : Kato Y , Tanaka T , Miyata T
Ref : Pesticide Biochemistry and Physiology , 79 :64 , 2004
Abstract : A hydrophilic form of acetylcholinesterase (AChE) was purified from N-methyl carbamate susceptible (SA) and highly N-methyl carbamate-resistant (N3D) strains of the green rice leafhopper (GRLH), Nephotettix cincticeps Uhler. Both of purified AChE from SA and N3D strains displayed the highest activities toward acetylthiocholine (ATCh) at pH 8.5. In the SA strain, the optimum concentrations for ATCh, propionylthiocholine (PTCh), and butyrylthiocholine (BTCh) were about 1 x 10-3, 2.5 x 10-3, and 1 x 10-3 M, respectively. However, in the N3D strain, substrate inhibition was not identified for ATCh, PTCh, and BTCh to 1 ? 10-2 M. The Km value in the SA strain was 51.1, 39.1, and 41.6 [mu]M and that in the N3D strain was 91.8, 88.1, and 85.2 [mu]M for ATCh, PTCh, and BTCh, respectively. The Km value in the N3D strain indicated about 1.80-, 2.25-, and 2.05-fold lower affinity than that of the SA strain for ATCh, PTCh, and BTCh, respectively. The Vmax value in the SA strain was 70.2, 30.5, and 4.6 U/mg protein and that in the N3D strain was 123.0, 27.0, and 14.5 U/mg protein for ATCh, PTCh, and BTCh, respectively. The Vmax value in the N3D strain was 1.75- and 3.15-fold higher for ATCh and BTCh than that in the N3D strain. However, it was 1.13-fold lower for PTCh. The increased activity of AChE in the N3D strain is due to the qualitatively modified enzyme with a higher catalytic efficiency. The bimolecular rate constant (ki) for propoxur was 27.1 x 10e4 and 0.51 x 10e4 M-1 min-1 in the SA and N3D strain and that for monocrotophos was 0.031 x 10e4 and 2.0 x 10e4 M-1 min-1 in the SA and N3D strain. AChE from the N3D strain was 53-fold less sensitive than SA strain to inhibition by propoxur. In contrast, AChE from the N3D strain was 65-fold more sensitive to inhibition by monocrotophos than AChE from the SA strain. This indicated negatively correlated cross-insensitivity of AChE to propoxur and monocrotophos.
ESTHER : Kato_2004_Pestic.Biochem.Physiol_79_64
PubMedSearch : Kato_2004_Pestic.Biochem.Physiol_79_64
Gene_locus related to this paper: nepci-ACHE

Title : Phenobarbital induction of permethrin detoxification and phenobarbital metabolism in susceptible and resistant strains of the beet armyworm Spodoptera exigua (Hubner) - Natsuhara_2004_Pestic.Biochem.Physiol_79_33
Author(s) : Natsuhara K , Shimada K , Tanaka T , Miyata T
Ref : Pesticide Biochemistry and Physiology , 79 :33 , 2004
Abstract : The permethrin resistant strain (TR-strain) of the beet armyworm, Spodoptera exigua (Hbner), has 92.5-fold resistance to permethrin (at LD50 level) compared to the permethrin susceptible strain (TS-strain). Bioassay involving permethrin mixed with piperonyl butoxide, an inhibitor of microsomal cytochrome P450s, significantly reduced the resistance ratio from 92.5- to 7.9-fold. However, S,S,S-tributylphosphorotrithioate and diethylmaleate which are inhibitors of esterases and glutathione S-transferase, respectively, did not affect the resistance level. These results indicate that the detoxification of permethrin in the TR-strain was primarily due to the cytochrome P450 monooxygenases. LD50 for permethrin was increased to 4.5-fold by the pre-treatment of phenobarbital in the TS-strain. The effect of induction by phenobarbital was almost completely overcome by the piperonyl butoxide treatment. However, it was observed that phenobarbital treatment did not cause any change in the toxicity of permethrin to TR strain. Since this result deviated from the expectation that the metabolism of phenobarbital in the TR-strain should be greater than that in the TS-strain, it was deemed necessary to compare the metabolism of phenobarbital between the TS- and TR-strains. Comparison was made based on the concentration of phenobarbital in the hemolymph and whole body. The results showed no significant difference in phenobarbital treatment between the two strains used in this study suggesting the possibility that the induction system in TS-strain is different from the TR-strain.
ESTHER : Natsuhara_2004_Pestic.Biochem.Physiol_79_33
PubMedSearch : Natsuhara_2004_Pestic.Biochem.Physiol_79_33

Title : A conditionally dispensable chromosome controls host-specific pathogenicity in the fungal plant pathogen Alternaria alternata - Hatta_2002_Genetics_161_59
Author(s) : Hatta R , Ito K , Hosaki Y , Tanaka T , Tanaka A , Yamamoto M , Akimitsu K , Tsuge T
Ref : Genetics , 161 :59 , 2002
Abstract : The filamentous fungus Alternaria alternata contains seven pathogenic variants (pathotypes), which produce host-specific toxins and cause diseases on different plants. Previously, the gene cluster involved in host-specific AK-toxin biosynthesis of the Japanese pear pathotype was isolated, and four genes, named AKT genes, were identified. The AKT homologs were also found in the strawberry and tangerine pathotypes, which produce AF-toxin and ACT-toxin, respectively. This result is consistent with the fact that the toxins of these pathotypes share a common 9,10-epoxy-8-hydroxy-9-methyl-decatrienoic acid structural moiety. In this study, three of the AKT homologs (AFT1-1, AFTR-1, and AFT3-1) were isolated on a single cosmid clone from strain NAF8 of the strawberry pathotype. In NAF8, all of the AKT homologs were present in multiple copies on a 1.05-Mb chromosome. Transformation-mediated targeting of AFT1-1 and AFT3-1 in NAF8 produced AF-toxin-minus, nonpathogenic mutants. All of the mutants lacked the 1.05-Mb chromosome encoding the AFT genes. This chromosome was not essential for saprophytic growth of this pathogen. Thus, we propose that a conditionally dispensable chromosome controls host-specific pathogenicity of this pathogen.
ESTHER : Hatta_2002_Genetics_161_59
PubMedSearch : Hatta_2002_Genetics_161_59
PubMedID: 12019223
Gene_locus related to this paper: altal-aft8

Title : No evidence of PEG1\/MEST gene mutations in Silver-Russell syndrome patients - Kobayashi_2001_Am.J.Med.Genet_104_225
Author(s) : Kobayashi S , Uemura H , Kohda T , Nagai T , Chinen Y , Naritomi K , Kinoshita EI , Ohashi H , Imaizumi K , Tsukahara M , Sugio Y , Tonoki H , Kishino T , Tanaka T , Yamada M , Tsutsumi O , Niikawa N , Kaneko-Ishino T , Ishino F
Ref : American Journal of Medicine Genet , 104 :225 , 2001
Abstract : Silver-Russell syndrome (SRS) is characterized by prenatal and postnatal growth retardation with morphologic anomalies. Maternal uniparental disomy 7 has been reported in some SRS patients. PEG1/MEST is an imprinted gene on chromosome 7q32 that is expressed only from the paternal allele and is a candidate gene for SRS. To clarify its biological function and role in SRS, we screened PEG1/MEST abnormalities in 15 SRS patients from various standpoints. In the lymphocytes of SRS patients, no aberrant expression patterns of two splice variants (alpha and beta) of PEG1/MEST were detected when they were compared with normal samples. Direct sequence analysis failed to detect any mutations in the PEG1/MEST alpha coding region, and there were no significant mutations in the 5'-flanking upstream region containing the predicted promoter and the highly conserved human/mouse genomic region. Differential methylation patterns of the CpG island for PEG1/MEST alpha were normally maintained and resulted in the same pattern as in the normal control, suggesting that there was no loss of imprinting. These findings suggest that PEG1/MEST can be excluded as a major determinant of SRS.
ESTHER : Kobayashi_2001_Am.J.Med.Genet_104_225
PubMedSearch : Kobayashi_2001_Am.J.Med.Genet_104_225
PubMedID: 11754049

Title : Complete genome sequence of an aerobic thermoacidophilic crenarchaeon, Sulfolobus tokodaii strain7 - Kawarabayasi_2001_DNA.Res_8_123
Author(s) : Kawarabayasi Y , Hino Y , Horikawa H , Jin-no K , Takahashi M , Sekine M , Baba S , Ankai A , Kosugi H , Hosoyama A , Fukui S , Nagai Y , Nishijima K , Otsuka R , Nakazawa H , Takamiya M , Kato Y , Yoshizawa T , Tanaka T , Kudoh Y , Yamazaki J , Kushida N , Oguchi A , Aoki K , Masuda S , Yanagii M , Nishimura M , Yamagishi A , Oshima T , Kikuchi H
Ref : DNA Research , 8 :123 , 2001
Abstract : The complete genomic sequence of an aerobic thermoacidophilic crenarchaeon, Sulfolobus tokodaii strain7 which optimally grows at 80 degrees C, at low pH, and under aerobic conditions, has been determined by the whole genome shotgun method with slight modifications. The genomic size was 2,694,756 bp long and the G + C content was 32.8%. The following RNA-coding genes were identified: a single 16S-23S rRNA cluster, one 5S rRNA gene and 46 tRNA genes (including 24 intron-containing tRNA genes). The repetitive sequences identified were SR-type repetitive sequences, long dispersed-type repetitive sequences and Tn-like repetitive elements. The genome contained 2826 potential protein-coding regions (open reading frames, ORFs). By similarity search against public databases, 911 (32.2%) ORFs were related to functional assigned genes, 921 (32.6%) were related to conserved ORFs of unknown function, 145 (5.1%) contained some motifs, and remaining 849 (30.0%) did not show any significant similarity to the registered sequences. The ORFs with functional assignments included the candidate genes involved in sulfide metabolism, the TCA cycle and the respiratory chain. Sequence comparison provided evidence suggesting the integration of plasmid, rearrangement of genomic structure, and duplication of genomic regions that may be responsible for the larger genomic size of the S. tokodaii strain7 genome. The genome contained eukaryote-type genes which were not identified in other archaea and lacked the CCA sequence in the tRNA genes. The result suggests that this strain is closer to eukaryotes among the archaea strains so far sequenced. The data presented in this paper are also available on the internet homepage (http:\/\/www.bio.nite.go.jp\/E-home\/genome_list-e.html\/).
ESTHER : Kawarabayasi_2001_DNA.Res_8_123
PubMedSearch : Kawarabayasi_2001_DNA.Res_8_123
PubMedID: 11572479
Gene_locus related to this paper: sulto-ST0002 , sulto-ST0071 , sulto-ST0672 , sulto-ST0779 , sulto-ST1414 , sulto-ST1737 , sulto-ST1745 , sulto-ST2026 , sulto-ST2099 , sulto-ST2511

Title : [A case of carbamate poisoning in which GCMS was useful to identify causal substance and to decide the appropriate treatment] - Kinoshita_2001_Chudoku.Kenkyu_14_343
Author(s) : Kinoshita H , Hirose Y , Tanaka T , Hori Y , Nakajima M , Fujisawa M , Oseki M
Ref : Chudoku Kenkyu , 14 :343 , 2001
Abstract : We often have cases of insecticide poisoning where the patient is unconscious and the causal substances are unknown We report an 83-year-old unconscious man who had apparently ingested several agricultural chemicals possibly organophosphate or carbamate According to his family there were three kinds of containers of agricultural chemicals with their caps opened around him When he was transferred to our hospital he presented hypertension hypersalivation and muscle fasciculation His pupils were markedly miotic In order to identify the substances ingested we used a gas chromatographymass spectrometer GCMS using his gastric content Within 30 minutes we were able to identify the causal substance as methomyl one of the popular carbamates thereby eliminating the need to use pralidoxime PAM GCMS makes it possible to identify unknown substances quickly and accurately and is therefore extremely useful in deciding the appropriate treatment
ESTHER : Kinoshita_2001_Chudoku.Kenkyu_14_343
PubMedSearch : Kinoshita_2001_Chudoku.Kenkyu_14_343
PubMedID: 11806102

Title : A 38 kb segment containing the cdc2 gene from the left arm of fission yeast chromosome II: sequence analysis and characterization of the genomic DNA and cDNAs encoded on the segment - Machida_2000_Yeast_16_71
Author(s) : Machida M , Yamazaki S , Kunihiro S , Tanaka T , Kushida N , Jinnno K , Haikawa Y , Yamazaki J , Yamamoto S , Sekine M , Oguchi A , Nagai Y , Sakai M , Aoki K , Ogura K , Kudoh Y , Kikuchi H , Zhang MQ , Yanagida M
Ref : Yeast , 16 :71 , 2000
Abstract : A genomic 38 kbp segment on the c1750 cosmid clone containing the cdc2 gene, located in the left arm of chromosome II from Schizosaccharomyces pombe, was sequenced. The segment was found to have five previously known genes, pht1, cdc2, his3, act1 and mei4. Among 11 coding sequences (CDSs) predicted by the gene finding software INTRON.PLOT., four CDSs, pi007, pi010, pi014 and pi016, had considerable similarity to 40S ribosomal protein, glycosyltransferase, cdc2-related protein kinase and alpha-1, 2-mannosyltransferase, respectively. Another unusually huge open reading frame (ORF) (pi011), consisting of 2233 amino acids, existed, having significant homology to alpha-amylase, granule-bound glycogen synthase and the Sz. pombe YS 1110 clone product at the N-terminal, middle and C-terminal regions, respectively. All the predicted 11 CDSs were experimentally analysed by RACE PCR. The sequencing of the RACE products revealed that there were two small overlaps at the 3' untranslated regions (UTRs) between pi004 and pi005 (17 bp) and between pi007 and pi008 (2 bp). The distances between 5' end of the 5'UTR and the putative translation initiation codon varied from 10 to 302 nucleotides (nt) among the nine CDSs successfully analysed by 5'-RACE. The expression level of each CDS on this clone was determined. Among the 16 genes on this clone, the previously determined genes, pht1, cdc2, his3 and act1, were found to be most highly expressed. Finally, cDNAs of all the newly identified genes were detected by RACE, proving the actual expression of these genes. The nucleotide sequence has been submitted to the EMBL database under Accession No. AB004534.
ESTHER : Machida_2000_Yeast_16_71
PubMedSearch : Machida_2000_Yeast_16_71
PubMedID: 10620777
Gene_locus related to this paper: schpo-be46

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

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

Title : Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3 - Kawarabayasi_1998_DNA.Res_5_55
Author(s) : Kawarabayasi Y , Sawada M , Horikawa H , Haikawa Y , Hino Y , Yamamoto S , Sekine M , Baba S , Kosugi H , Hosoyama A , Nagai Y , Sakai M , Ogura K , Otsuka R , Nakazawa H , Takamiya M , Ohfuku Y , Funahashi T , Tanaka T , Kudoh Y , Yamazaki J , Kushida N , Oguchi A , Aoki K , Kikuchi H
Ref : DNA Research , 5 :55 , 1998
Abstract : The complete sequence of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3, has been determined by assembling the sequences of the physical map-based contigs of fosmid clones and of long polymerase chain reaction (PCR) products which were used for gap-filling. The entire length of the genome was 1,738,505 bp. The authenticity of the entire genome sequence was supported by restriction analysis of long PCR products, which were directly amplified from the genomic DNA. As the potential protein-coding regions, a total of 2061 open reading frames (ORFs) were assigned, and by similarity search against public databases, 406 (19.7%) were related to genes with putative function and 453 (22.0%) to the sequences registered but with unknown function. The remaining 1202 ORFs (58.3%) did not show any significant similarity to the sequences in the databases. Sequence comparison among the assigned ORFs in the genome provided evidence that a considerable number of ORFs were generated by sequence duplication. By similarity search, 11 ORFs were assumed to contain the intein elements. The RNA genes identified were a single 16S-23S rRNA operon, two 5S rRNA genes and 46 tRNA genes including two with the intron structure. All the assigned ORFs and RNA coding regions occupied 91.25% of the whole genome. The data presented in this paper are available on the internet at http:@www.nite.go.jp.
ESTHER : Kawarabayasi_1998_DNA.Res_5_55
PubMedSearch : Kawarabayasi_1998_DNA.Res_5_55
PubMedID: 9679194
Gene_locus related to this paper: pyrho-PH0594 , pyrho-PH0863 , pyrho-PH1262

Title : The complete genome sequence of the gram-positive bacterium Bacillus subtilis - Kunst_1997_Nature_390_249
Author(s) : Kunst F , Ogasawara N , Moszer I , Albertini AM , Alloni G , Azevedo V , Bertero MG , Bessieres P , Bolotin A , Borchert S , Borriss R , Boursier L , Brans A , Braun M , Brignell SC , Bron S , Brouillet S , Bruschi CV , Caldwell B , Capuano V , Carter NM , Choi SK , Cordani JJ , Connerton IF , Cummings NJ , Daniel RA , Denziot F , Devine KM , Dusterhoft A , Ehrlich SD , Emmerson PT , Entian KD , Errington J , Fabret C , Ferrari E , Foulger D , Fritz C , Fujita M , Fujita Y , Fuma S , Galizzi A , Galleron N , Ghim SY , Glaser P , Goffeau A , Golightly EJ , Grandi G , Guiseppi G , Guy BJ , Haga K , Haiech J , Harwood CR , Henaut A , Hilbert H , Holsappel S , Hosono S , Hullo MF , Itaya M , Jones L , Joris B , Karamata D , Kasahara Y , Klaerr-Blanchard M , Klein C , Kobayashi Y , Koetter P , Koningstein G , Krogh S , Kumano M , Kurita K , Lapidus A , Lardinois S , Lauber J , Lazarevic V , Lee SM , Levine A , Liu H , Masuda S , Mauel C , Medigue C , Medina N , Mellado RP , Mizuno M , Moestl D , Nakai S , Noback M , Noone D , O'Reilly M , Ogawa K , Ogiwara A , Oudega B , Park SH , Parro V , Pohl TM , Portelle D , Porwollik S , Prescott AM , Presecan E , Pujic P , Purnelle B , Rapoport G , Rey M , Reynolds S , Rieger M , Rivolta C , Rocha E , Roche B , Rose M , Sadaie Y , Sato T , Scanlan E , Schleich S , Schroeter R , Scoffone F , Sekiguchi J , Sekowska A , Seror SJ , Serror P , Shin BS , Soldo B , Sorokin A , Tacconi E , Takagi T , Takahashi H , Takemaru K , Takeuchi M , Tamakoshi A , Tanaka T , Terpstra P , Togoni A , Tosato V , Uchiyama S , Vandebol M , Vannier F , Vassarotti A , Viari A , Wambutt R , Wedler H , Weitzenegger T , Winters P , Wipat A , Yamamoto H , Yamane K , Yasumoto K , Yata K , Yoshida K , Yoshikawa HF , Zumstein E , Yoshikawa H , Danchin A
Ref : Nature , 390 :249 , 1997
Abstract : Bacillus subtilis is the best-characterized member of the Gram-positive bacteria. Its genome of 4,214,810 base pairs comprises 4,100 protein-coding genes. Of these protein-coding genes, 53% are represented once, while a quarter of the genome corresponds to several gene families that have been greatly expanded by gene duplication, the largest family containing 77 putative ATP-binding transport proteins. In addition, a large proportion of the genetic capacity is devoted to the utilization of a variety of carbon sources, including many plant-derived molecules. The identification of five signal peptidase genes, as well as several genes for components of the secretion apparatus, is important given the capacity of Bacillus strains to secrete large amounts of industrially important enzymes. Many of the genes are involved in the synthesis of secondary metabolites, including antibiotics, that are more typically associated with Streptomyces species. The genome contains at least ten prophages or remnants of prophages, indicating that bacteriophage infection has played an important evolutionary role in horizontal gene transfer, in particular in the propagation of bacterial pathogenesis.
ESTHER : Kunst_1997_Nature_390_249
PubMedSearch : Kunst_1997_Nature_390_249
PubMedID: 9384377
Gene_locus related to this paper: bacsu-CAH , bacsu-cbxnp , bacsu-lip , bacsu-LIPB , bacsu-PKSR , bacsu-pnbae , bacsu-PPSE , bacsu-srf4 , bacsu-srfac , bacsu-YBAC , bacsu-YBDG , bacsu-ybfk , bacsu-ycgS , bacsu-yczh , bacsu-YDEN , bacsu-ydjp , bacsu-yfhM , bacsu-yisY , bacsu-YITV , bacsu-yjau , bacsu-YJCH , bacsu-MHQD , bacsu-yqjl , bacsu-yqkd , bacsu-YRAK , bacsu-YTAP , bacsu-YTMA , bacsu-YTPA , bacsu-ytxm , bacsu-yugF , bacsu-YUII , bacsu-YUKL , bacsu-YVAK , bacsu-YvaM , bacsu-RsbQ

Title : A new Bacillus subtilis gene, med, encodes a positive regulator of comK - Ogura_1997_J.Bacteriol_179_6244
Author(s) : Ogura M , Ohshiro Y , Hirao S , Tanaka T
Ref : Journal of Bacteriology , 179 :6244 , 1997
Abstract : Bacillus subtilis degR, a positive regulator of the production of degradative enzymes, is negatively regulated by the competence transcription factor ComK which is overproduced in mecA null mutants. We used transposon Tn10 to search for a mutation that reduced the repression level of degR caused by a mecA mutation. A new gene exerting positive regulation on comK was obtained and designated med (suppressor of mecA effect on degR). Sequence determination, Northern analysis, and primer extension analyses revealed that the med gene contained an open reading frame (ORF) composed of 317 codons and was transcribed into an approximately 1,250-nucleotide mRNA together with its short downstream gene. The expression of comK is positively regulated by factors such as ComK itself, ComS (SrfA)-MecA, DegU, SinR, and AbrB. Quantitative analyses using comK'-'lacZ, srfA-lacZ, degU'-'lacZ, and sinR'-'lacZ fusions showed that disruption of med caused a significant decrease in comK expression in both mecA+ and mecA strains, while expression of srfA, sinR, and degU was not affected by the mutation. An epistatic analysis revealed that overproduction of ComK resulted in alteration of med expression, suggesting a regulatory loop between comK and med. Several possible mechanisms for positive regulation of comK by Med are discussed.
ESTHER : Ogura_1997_J.Bacteriol_179_6244
PubMedSearch : Ogura_1997_J.Bacteriol_179_6244
PubMedID: 9335269
Gene_locus related to this paper: bacsu-yjau

Title : Biochemical and molecular characterization of the polyhydroxybutyrate depolymerase of Comamonas acidovorans YM1609, isolated from freshwater - Kasuya_1997_Appl.Environ.Microbiol_63_4844
Author(s) : Kasuya K , Inoue Y , Tanaka T , Akehata T , Iwata T , Fukui T , Doi Y
Ref : Applied Environmental Microbiology , 63 :4844 , 1997
Abstract : Comamonas acidovorans YM1609 secreted a polyhydroxybutyrate (PHB) depolymerase into the culture supernatant when it was cultivated on poly(3-hydroxybutyrate) [P(3HB)] or poly(3-hydroxybutyrate-co-3-hydroxyvalerate) [P(3HB-co-3HV)] as the sole carbon source. The PHB depolymerase was purified from culture supernatant of C. acidovorans by two chromatographic methods, and its molecular mass was determined as 45,000 Da by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. The enzyme was stable at temperatures below 37 degrees C and at pH values of 6 to 10, and its activity was inhibited by diisopropyl fluorophosphonate. The liquid chromatography analysis of water-soluble products revealed that the primary product of enzymatic hydrolysis of P(3HB) was a dimer of 3-hydroxybutyric acid. Kinetics of enzymatic hydrolysis of P(3HB) film were studied. In addition, a gene encoding the PHB depolymerase was cloned from the C. acidovorans genomic library. The nucleotide sequence of this gene was found to encode a protein of 494 amino acids (M(r), 51,018 Da). Furthermore, by analysis of the N-terminal amino acid sequence of the purified enzyme, the molecular mass of the mature enzyme was calculated to be 48,628 Da. Analysis of the deduced amino acid sequence suggested a domain structure of the protein containing a catalytic domain, fibronectin type III module as linker, and a putative substrate-binding domain. Electron microscopic visualization of the mixture of P(3HB) single crystals and a fusion protein of putative substrate-binding domain with glutathione S-transferase demonstrated that the fusion protein adsorbed strongly and homogeneously to the surfaces of P(3HB) single crystals.
ESTHER : Kasuya_1997_Appl.Environ.Microbiol_63_4844
PubMedSearch : Kasuya_1997_Appl.Environ.Microbiol_63_4844
PubMedID: 9406404
Gene_locus related to this paper: comac-PHAZCAC

Title : Human butyrylcholinesterase L330I mutation belongs to a fluoride-resistant gene, by expression in human fetal kidney cells - Sudo_1997_Biochem.Biophys.Res.Commun_240_372
Author(s) : Sudo K , Maekawa M , Akizuki S , Magara T , Ogasawara H , Tanaka T
Ref : Biochemical & Biophysical Research Communications , 240 :372 , 1997
Abstract : We noticed a Japanese male showed low serum butyrylcholinesterase (BCHE) activity on health examination. The phenotyping analysis revealed a reduced dibucaine number (DN) and an especially low fluoride number (FN), similar to an FS phenotype. A homozygous missense mutation, a T to A transversion at nucleotide 988, was identified in his BCHE gene. This mutation resulted in the replacement of leucine by isoleucine at codon 330 (L330I). DN and FN of recombinant BCHE(L330I) secreted by human fetal kidney cells were compared to recombinant wild-type(usual gene) BCHE and normal serum BCHE. These results showed this amino acid substitution of BCHE, Leu330 to Ile, really caused the abnormal DN and FN. We conclude that the BCHE L330I mutation is a fluoride-resistant gene, a Japanese type fluoride-resistant gene.
ESTHER : Sudo_1997_Biochem.Biophys.Res.Commun_240_372
PubMedSearch : Sudo_1997_Biochem.Biophys.Res.Commun_240_372
PubMedID: 9388484
Gene_locus related to this paper: human-BCHE

Title : Direct association of adenosine deaminase with a T cell activation antigen, CD26 - Kameoka_1993_Science_261_466
Author(s) : Kameoka J , Tanaka T , Nojima Y , Schlossman SF , Morimoto C
Ref : Science , 261 :466 , 1993
Abstract : CD26, the T cell activation molecule dipeptidyl peptidase IV (DPPIV), associates with a 43-kilodalton protein. Amino acid sequence analysis and immunoprecipitation studies demonstrated that this 43-kilodalton protein was adenosine deaminase (ADA). ADA was coexpressed with CD26 on the Jurkat T cell lines, and an in vitro binding assay showed that the binding was through the extracellular domain of CD26. ADA deficiency causes severe combined immunodeficiency disease (SCID) in humans. Thus, ADA and CD26 (DPPIV) interact on the T cell surface, and this interaction may provide a clue to the pathophysiology of SCID caused by ADA deficiency.
ESTHER : Kameoka_1993_Science_261_466
PubMedSearch : Kameoka_1993_Science_261_466
PubMedID: 8101391

Title : Comparison of the pharmacokinetics of E2020, a new compound for Alzheimer's disease, in healthy young and elderly subjects - Ohnishi_1993_J.Clin.Pharmacol_33_1086
Author(s) : Ohnishi A , Mihara M , Kamakura H , Tomono Y , Hasegawa J , Yamazaki K , Morishita N , Tanaka T
Ref : Journal of Clinical Pharmacology , 33 :1086 , 1993
Abstract : E2020, a central-acting cholinesterase inhibitor, is now under clinical development as a potential therapeutic agent for senile dementia of Alzheimer type. In the current study, the authors compared the pharmacokinetics of this drug after single oral administration in 12 healthy young volunteers (20-27 years of age) and 6 elderly volunteers (65-82 years of age). The subjects received a single 2-mg oral dose of E2020 after a meal. Blood samples for determination of the drug level were collected over 168 hours after drug administration and were measured by specific high-pressure liquid chromatography methods with ultraviolet detection. E2020 was generally well tolerated by all subjects of both groups. The plasma elimination half-life of the beta-phase (t 1/2 beta) and time to maximum peak plasma concentration (tmax) were significantly longer in the elderly than in the young: t 1/2 beta, 103.8 +/- 40.6 versus 59.7 +/- 16.1 hours; and tmax, 5.2 +/- 2.8 versus 3.4 +/- 1.5 hours, respectively. There were no statistically significant differences in maximum peak plasma concentration and area under the curve between the two groups. The mean (+/- standard deviation) oral clearance (Cl/F) in the elderly (9.1 +/- 2.4 L/h) was similar to that in the young (10.6 +/- 2.7 L/h). The volume of distribution in the steady state (Vdss/F) was significantly larger in the elderly than that in the young: 1217.2 +/- 223.2 versus 852.5 +/- 147.7 L, respectively. These results suggested that the drug was absorbed more slowly and distributed more widely and thoroughly, but that its clearance from the body is essentially unaffected by age.(ABSTRACT TRUNCATED AT 250 WORDS)
ESTHER : Ohnishi_1993_J.Clin.Pharmacol_33_1086
PubMedSearch : Ohnishi_1993_J.Clin.Pharmacol_33_1086
PubMedID: 8300891

Title : Cloning and functional expression of the T cell activation antigen CD26 -
Author(s) : Tanaka T
Ref : J Immunol , 150 :2090 , 1993
PubMedID: 8094732
Gene_locus related to this paper: human-DPP4

Title : Cloning and functional expression of the T cell activation antigen CD26 - Tanaka_1992_J.Immunol_149_481
Author(s) : Tanaka T , Camerini D , Seed B , Torimoto Y , Dang NH , Kameoka J , Dahlberg HN , Schlossman SF , Morimoto C
Ref : J Immunol , 149 :481 , 1992
Abstract : A cDNA encoding the T cell activation Ag CD26 was isolated from human PHA-activated T cells by using an expression cloning method. The nucleotide sequence obtained predicts a protein of 766 amino acids of type II membrane topology, with six amino acids in the cytoplasmic region. The predicted amino acid sequence of the Ag was 85% homologous to that of the dipeptidyl peptidase IV enzyme isolated from rat liver. Derivatives of the human leukemic T cell line Jurkat transfected with a CD26 expression plasmid were established. Characterization of the CD26 Ag expressed by the transfected Jurkat cells revealed that the Ag could be immunoprecipitated as a 110-kDa molecule similar to that found on peripheral blood T cells and that the Ag had dipeptidyl peptidase IV activity. Functional analysis of these Jurkat transfectants showed that cross-linking of the CD26 and CD3 Ag with their respective antibodies resulted in enhanced intracellular calcium mobilization and IL-2 production. These results provide direct evidence that the CD26 Ag plays a role in T cell activation.
ESTHER : Tanaka_1992_J.Immunol_149_481
PubMedSearch : Tanaka_1992_J.Immunol_149_481
PubMedID: 1352530
Gene_locus related to this paper: human-DPP4

Title : [Clinical assessment of myocardial protection with blood-GIK solution] - Koyama_1989_Rinsho.Kyobu.Geka_9_169
Author(s) : Koyama N , Watanabe Y , Yoshihara K , Tokuhiro K , Horikoshi J , Tanaka T , Shiono N , Kawamura K , Takanashi Y , Komatsu H
Ref : Rinsho Kyobu Geka , 9 :169 , 1989
Abstract : Since Jan, 1984, three different types of myocardial protection have been tried in coronary bypass surgery. These are GIK (1984. 1-1984. 12), Young+GIK (1985. 1-1986. 8), and blood GIK (1986. 9-until present). In this study we tried to demonstrate the advantage of myocardial protection induced with blood GIK solution in comparison with that with GIK alone or Young + GIK. (Materials and methods) Eighty-three patients undergone coronary bypass surgery in that period, were evaluated and divided into three groups: Group I had myocardial protection with GIK alone in 24 patients, group II had myocardial protection with Young + GIK in 28 patients, and group III had myocardial protection with Young + blood GIK in 31 patients. Among these groups, the changes of serum enzymes and hemodynamics in postoperative period were compared. (Results) In the hemodynamic changes, cardiac index at 24 hours after operation in group III, was higher than that in the other two groups (p < 0.05). The peak value of MB-CPK in all groups appeared 12 hours after operation, however, 21.9 +/- 19.72 IU/ml in group III was significantly lower than 33.4 +/- 25.5 in group I, or 36.9 +/- 26.8 in group II (p < 0.01). The results demonstrates that the myocardial protection induced with blood GIK are superior to these with the other two method.
ESTHER : Koyama_1989_Rinsho.Kyobu.Geka_9_169
PubMedSearch : Koyama_1989_Rinsho.Kyobu.Geka_9_169
PubMedID: 9301914