Jin J

References (30)

Title : StructuralDPPIV: a novel deep learning model based on atom-structure for predicting dipeptidyl peptidase-IV inhibitory peptides - Wang_2024_Bioinformatics__
Author(s) : Wang D , Jin J , Li Z , Wang Y , Fan M , Liang S , Su R , Wei L
Ref : Bioinformatics , : , 2024
Abstract : MOTIVATION: Diabetes is a chronic metabolic disorder that has been a major cause of blindness, kidney failure, heart attacks, stroke, and lower limb amputation across the world. To alleviate the impact of diabetes, researchers have developed the next generation of anti-diabetic drugs, known as dipeptidyl peptidase IV inhibitory peptides (DPP-IV-IPs). However, the discovery of these promising drugs has been restricted due to the lack of effective peptide-mining tools. RESULTS: Here, we presented StructuralDPPIV, a deep learning model designed for DPP-IV-IP identification, which takes advantage of both molecular graph features in amino acid and sequence information. Experimental results on the independent test dataset and two wet experiment datasets show that our model outperforms the other state-of-art methods. Moreover, to better study what StructuralDPPIV learns, we used CAM technology and perturbation experiment to analyze our model, which yielded interpretable insights into the reasoning behind prediction results. AVAILABILITY: The project code is available at https://github.com/WeiLab-BioChem/Structural-DPP-IV. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
ESTHER : Wang_2024_Bioinformatics__
PubMedSearch : Wang_2024_Bioinformatics__
PubMedID: 38305458

Title : Fabrication of immobilized lipases from Candida rugosa on hierarchical mesoporous silica for enzymatic enrichment of -3 polyunsaturated fatty acids by selective hydrolysis - Dong_2024_Food.Chem.X_22_101434
Author(s) : Dong Z , Jin J , Wei W , Wang X , Wu G , Jin Q
Ref : Food Chem X , 22 :101434 , 2024
Abstract : In this study, lipase from Candida rugosa was immobilized on hydrophobic hierarchical porous hollow silica microsphere (HPHSM-C3) via adsorption. The prepared biocatalyst HPHSM-C3@CRL exhibited higher activity, thermal and pH stability. HPHSM-C3@CRL remained 70.2% of initial activity after 30 days of storage at 24 degreesC and 50.4% of initial activity after 10 cycles. Moreover, HPHSM-C3@CRL was utilized in enzymatic enrichment of omega-3 polyunsaturated fatty acids (omega-3 PUFAs) in glycerides, achieving omega-3 PUFAs content of 53.42% with the hydrolysis rate of 48.78% under optimal condition. The K(m) and V(max) value of HPHSM-C3@CRL was 42.2% lower and 63.5% higher than those of CRL, respectively. The 3D structure analysis of CRL, substrates and pore structure of HPHSM-C3 suggested that the hierarchical pore improved activity and selectivity of immobilized lipase. This result demonstrated that HPHSM-C3@CRL may be an effective biocatalyst for the enzymatic enrichment of omega-3 PUFAs in food industries.
ESTHER : Dong_2024_Food.Chem.X_22_101434
PubMedSearch : Dong_2024_Food.Chem.X_22_101434
PubMedID: 38779499

Title : Comprehensive analysis of the immune implication of EPHX4 gene in laryngeal squamous cell carcinoma - Shen_2024_Braz.J.Otorhinolaryngol_90_101411
Author(s) : Shen N , Gao G , Lu X , Jin J , Lin L , Qian M , Qin Y
Ref : Braz J Otorhinolaryngol , 90 :101411 , 2024
Abstract : OBJECTIVES: The role of Epoxide Hydrolase-4 (EPHX4), a member of epoxide hydrolase family, has not been investigated in cancer. The purpose of this article is to explore the application value of EPHX4 in laryngeal cancer and its relationship with immune infiltration. METHODS: We observed that EPHX4 expression and its survival assays in laryngeal cancer specimens based on The Cancer Genome Atlas (TCGA) cohorts. We also analyzed the correlation between immune cell infiltration levels and EPHX4 gene copy number in laryngeal cancer. Finally, we conducted in vitro assay to evaluate the functions of EPHX4 in laryngeal cancer cell line. RESULTS: EPHX4 is highly expressed in laryngeal cancer specimens and has a poor prognosis. EPHX4 related immune cell analysis showed that it participated in NK Natural killer cell mediated cytotoxicity. Finally, Cell experiments indicate that EPHX4 could promote laryngeal cancer cell line proliferation, colony formation and invasion. CONCLUSIONS: Our research results suggest that EPHX4 may be a potential immunotherapy target for laryngeal cancer. The nominated immune signature is a helpful and promising prognostic indicator in laryngeal cancer. LEVELS OF EVIDENCE: Level 3.
ESTHER : Shen_2024_Braz.J.Otorhinolaryngol_90_101411
PubMedSearch : Shen_2024_Braz.J.Otorhinolaryngol_90_101411
PubMedID: 38663041

Title : Metagenomic exploration of microbial and enzymatic traits involved in microplastic biodegradation - Hu_2023_Chemosphere_348_140762
Author(s) : Hu X , Gu H , Sun X , Wang Y , Liu J , Yu Z , Li Y , Jin J , Wang G
Ref : Chemosphere , 348 :140762 , 2023
Abstract : Agricultural mulch films are frequently applied to achieve high yield, resulting in large quantities of microplastic (MP) pollution in agroecosystem. However, studies focusing specifically on the diversity of MP-degrading enzymes and related microbial communities have yet to be conducted. Here, we established a soil microcosmic incubation with addition of 5% (w/w) conventional (low-density polyethylene (LDPE)) and biodegradable (blend of polylactic acid (PLA) and polybutylene adipate terephthalate (PBAT)) MPs for incubation 90 days. The DNA samples extracted from soils and plastisphere of MPs were examined by metagenomics and genome binning methods, specifically targeting carbohydrate-active enzymes (CAZymes) and plastic-degrading enzymes (PDZymes). The results revealed that plastisphere of MPs exhibited significantly distinct patterns of CAZymes and PDZymes from soils, and abundances of all examined exoenzymes were higher in plastisphere than those in soils. Plastisphere of LDPE-MPs selectively enriched proteases and alkane monooxygenase (alkB), and required families of carbohydrate-binding module (CBM) to increase the binding of CAZymes with MPs. Dissimilarly, diverse CAZymes with high abundances were observed in the plastisphere of PBAT-PLA MPs and esterases were important indicative PDZymes for PBAT-PLA degradation. The enriched exoenzymes in plastisphere of LDPE-MPs were mainly assigned to Actinobacteria while Proteobacteria with higher abundance in plastisphere of PBAT-PLA MPs containing most indicative exoenzymes. Moreover, a high-quality genome classified as Amycolatopsis japonica was reconstructed and found to contain one or more gene copies of indicative exoenzymes for polyethylene. Two novel genomes classified as Sphingomonas were selectively enriched in plastisphere of PBAT-PLA MPs and contained diverse genes encoding degrading exoenzymes. Taken together, our study highlighted the CAZymes and PDZymes can be exploited as potent microbial strategies for solving MPs pollution in croplands.
ESTHER : Hu_2023_Chemosphere_348_140762
PubMedSearch : Hu_2023_Chemosphere_348_140762
PubMedID: 38006912

Title : Kinetics, Thermodynamics and Mechanism of Enzymatic Degradation of Zearalenone in Degummed Corn Oil - Zhao_2022_Toxins.(Basel)_15_
Author(s) : Zhao C , Xie P , Jin J , Jin Q , Wang X
Ref : Toxins (Basel) , 15 : , 2022
Abstract : The kinetics and thermodynamics of the enzymatic degradation of zearalenone (ZEN) in degummed corn oil were investigated by analyzing the impacts of temperature, pH, ZEN hydrolase dosage and ZEN concentration on the initial reaction rate. The kinetic study found that the maximum reaction rate was 0.97 micromol x kg1 min1, the Michaelis constant (Km) was 11,476 micromol x kg1 and the Michaelis equation was V = 0.97[S]/(11,476 + [S]). The thermodynamic study showed that the activation energy (Ea) was 70.37 kJ.mol1, the activation enthalpy change of the reaction (deltaH) > 0, the free energy of activation (deltaG) > 0 and the activation entropy change (deltaS) < 0, indicating the reaction could not be spontaneous. The reaction mechanism of ZEN was studied by a hybrid quadrupole orbitrap mass spectrometer. It was found that ZEN first generated the intermediate G/L/D/W-ZEN+H2O, followed by generating the intermediate W-ZEN-H2O under the action of a degrading enzyme. Then, the lactone bond was opened to produce C18H24O6, and finally the decarboxylation product C17H24O4 formed automatically.
ESTHER : Zhao_2022_Toxins.(Basel)_15_
PubMedSearch : Zhao_2022_Toxins.(Basel)_15_
PubMedID: 36668839

Title : Removal of Zearalenone from Degummed Corn Oil by Hydrolase on a Batch-Refining Unit - Zhao_2022_Foods_11_
Author(s) : Zhao C , Xie P , Jin J , Jin Q , Wang X
Ref : Foods , 11 : , 2022
Abstract : The removal of zearalenone (ZEN) from degummed corn oil (DCO) using hydrolase on a batch-refining unit was studied. According to single-factor and response surface experiments, the optimum technological conditions for reaching the maximum degradation rate were a temperature of 39.01 degreesC, a pH of 8.08, a time of 3.9 h, and an enzyme dosage of 44.7 mg/kg, whereby the rate of ZEN degradation can reach 94.66%. Different effects on the removal of ZEN were observed at different initial ZEN contents under the optimal technological conditions, of which the decrease was rapid for high ZEN content and slow for low ZEN content.
ESTHER : Zhao_2022_Foods_11_
PubMedSearch : Zhao_2022_Foods_11_
PubMedID: 36496603

Title : Comparative transcriptome analysis of Chinese grass shrimp (Palaemonetes sinensis) hepatopancreas under ectoparasitic isopod (Tachaea chinensis) infection - Yu_2021_Fish.Shellfish.Immunol__
Author(s) : Yu C , Xu W , Li X , Jin J , Zhao X , Wang S , Zhang Z , Wei Y , Chen Q , Li Y
Ref : Fish Shellfish Immunol , : , 2021
Abstract : Tachaea chinensis, a parasitic isopod, negatively affects the production of several commercially important shrimp species. To better understand the interaction between shrimp immunity and isopod infection, we performed a transcriptome analysis of the hepatopancreas of Palaemonetes sinensis challenged with T. chinensis. After assembly and annotation, 75,980 high-quality unigenes were obtained using RNA-seq data. Dierential gene expression analysis revealed 896 signicantly dierently expressed genes (DEGs) after infection, with 452 and 444 upregulated and downregulated genes, respectively. Specifically, expression levels of genes involved in detoxification, such as the interferon regulatory factor, venom carboxylesterase-6, serine proteinase inhibitor, and cytochrome P450, were upregulated. Furthermore, expression levels of genes corresponding to retinol dehydrogenase, triosephosphate isomerase, variant ionotropic glutamate receptor, and phosphoenolpyruvate carboxykinase were significantly upregulated after isopod parasitization, indicating that the shrimp's visual system was influenced by isopod parasitization. Moreover, quantitative real-time PCR of 10 DEGs helped validate the RNA-seq findings. These results provide a valuable basis for future studies on the elucidation of immune responses of P. sinensis to T. chinensis infection.
ESTHER : Yu_2021_Fish.Shellfish.Immunol__
PubMedSearch : Yu_2021_Fish.Shellfish.Immunol__
PubMedID: 34303835

Title : Toxic effects of fluridone on early developmental stages of Japanese Medaka (Oryzias latipes) - Jin_2019_Sci.Total.Environ_700_134495
Author(s) : Jin J , Kurobe T , Hammock BG , Lam CH , Lin L , Teh SJ
Ref : Sci Total Environ , 700 :134495 , 2019
Abstract : The herbicide fluridone is intensively applied to control invasive aquatic plants globally, including in the Sacramento and San Joaquin Delta (the Delta), California, USA. Our previous study revealed that the adult stage of Delta Smelt showed acute and sub-lethal adverse effects following 6h of exposure to environmentally relevant concentrations of fluridone. To further investigate mechanisms of toxicity of fluridone and to assess its toxicity to early life stages of fish, we performed additional exposures using the fish model Japanese Medaka (Oryzias latipes). Male and female Medaka embryos were exposed to concentrations of fluridone for 14 d and showed reduced hatching success in a dose dependent manner. The half maximal effective concentration for the hatching success was 2.3mgL(-1). In addition, male and female Medaka larvae were acute exposed to fluridone for 6h to assess their swimming behavior and gene expression patterns. Fish exposed to fluridone at 4.2mgL(-1) or higher became lethargic and showed abnormal swimming behavior. The response to the stimuli was significantly impaired by fluridone at 21mgL(-1) and above in males, and at 104mgL(-1) in females. Transcriptome analysis identified a total of 799 genes that were significantly differentially expressed, comprising 555 up-regulated and 244 down-regulated genes in males exposed to 21mg L(-1) of fluridone. The gene set enrichment analysis indicated a number of biological processes altered by fluridone. Among the genes involved in those biological processes, the expression of the genes, acetylcholinesterase, retinoic acid receptor, insulin receptor substrate, glutathione reductase, and glutathione S transferase, exhibited dose- and sex-dependent responses to fluridone. The study indicated that fluridone exposure led to detrimental toxic effects at early developmental stages of fish, by disturbing the biological processes of growth and development, and the nervous system, inducing oxidative stress and endocrine disruption.
ESTHER : Jin_2019_Sci.Total.Environ_700_134495
PubMedSearch : Jin_2019_Sci.Total.Environ_700_134495
PubMedID: 31693955

Title : The red bayberry genome and genetic basis of sex determination - Jia_2019_Plant.Biotechnol.J_17_397
Author(s) : Jia HM , Jia HJ , Cai QL , Wang Y , Zhao HB , Yang WF , Wang GY , Li YH , Zhan DL , Shen YT , Niu QF , Chang L , Qiu J , Zhao L , Xie HB , Fu WY , Jin J , Li XW , Jiao Y , Zhou CC , Tu T , Chai CY , Gao JL , Fan LJ , van de Weg E , Wang JY , Gao ZS
Ref : Plant Biotechnol J , 17 :397 , 2019
Abstract : Morella rubra, red bayberry, is an economically important fruit tree in south China. Here, we assembled the first high-quality genome for both a female and a male individual of red bayberry. The genome size was 313-Mb, and 90% sequences were assembled into eight pseudo chromosome molecules, with 32 493 predicted genes. By whole-genome comparison between the female and male and association analysis with sequences of bulked and individual DNA samples from female and male, a 59-Kb region determining female was identified and located on distal end of pseudochromosome 8, which contains abundant transposable element and seven putative genes, four of them are related to sex floral development. This 59-Kb female-specific region was likely to be derived from duplication and rearrangement of paralogous genes and retained non-recombinant in the female-specific region. Sex-specific molecular markers developed from candidate genes co-segregated with sex in a genetically diverse female and male germplasm. We propose sex determination follow the ZW model of female heterogamety. The genome sequence of red bayberry provides a valuable resource for plant sex chromosome evolution and also provides important insights for molecular biology, genetics and modern breeding in Myricaceae family.
ESTHER : Jia_2019_Plant.Biotechnol.J_17_397
PubMedSearch : Jia_2019_Plant.Biotechnol.J_17_397
PubMedID: 29992702
Gene_locus related to this paper: 9rosi-a0a6a1wtm7

Title : Sub-lethal effects of herbicides penoxsulam, imazamox, fluridone and glyphosate on Delta Smelt (Hypomesus transpacificus) - Jin_2018_Aquat.Toxicol_197_79
Author(s) : Jin J , Kurobe T , Ramirez-Duarte WF , Bolotaolo MB , Lam CH , Pandey PK , Hung TC , Stillway ME , Zweig L , Caudill J , Lin L , Teh SJ
Ref : Aquat Toxicol , 197 :79 , 2018
Abstract : Concerns regarding non-target toxicity of new herbicides used to control invasive aquatic weeds in the San Francisco Estuary led us to compare sub-lethal toxicity of four herbicides (penoxsulam, imazamox, fluridone, and glyphosate) on an endangered fish species Delta Smelt (Hypomesus transpacificus). We measured 17beta-estradiol (E2) and glutathione (GSH) concentrations in liver, and acetylcholinesterase (AChE) activity in brain of female and male fish after 6h of exposure to each of the four herbicides. Our results indicate that fluridone and glyphosate disrupted the E2 concentration and decreased glutathione concentration in liver, whereas penoxsulam, imazamox, and fluridone inhibited brain AChE activity. E2 concentrations were significantly increased in female and male fish exposed to 0.21muM of fluridone and in male fish exposed to 0.46, 4.2, and 5300muM of glyphosate. GSH concentrations decreased in males exposed to fluridone at 2.8muM and higher, and glyphosate at 4.2muM. AChE activity was significantly inhibited in both sexes exposed to penoxsulam, imazamox, and fluridone, and more pronounced inhibition was observed in females. The present study demonstrates the potential detrimental effects of these commonly used herbicides on Delta Smelt.
ESTHER : Jin_2018_Aquat.Toxicol_197_79
PubMedSearch : Jin_2018_Aquat.Toxicol_197_79
PubMedID: 29448126

Title : Elucidation of pressure-induced lid movement and catalysis behavior of Rhizopus chinensis lipase - Chen_2017_Int.J.Biol.Macromol_103_360
Author(s) : Chen G , Tang J , Miao M , Jiang B , Jin J , Feng B
Ref : Int J Biol Macromol , 103 :360 , 2017
Abstract : The changes of lid movement and catalysis behavior of Rhizopus chinensis lipase under high hydrostatic pressure treatment was studied. Molecular dynamics simulation showed that the lipase lid under pressure was partially opened at below 200MPa but got more closed at over 400MPa. The interfacial activation changed little at pressure below 400MPa but became marginal with the pressure increased to 500MPa. The lipase hydrolysis ability by high pressure treatment underwent a course of initial increasing then reducing with maximum activity obtained at 200MPa and 40 degrees C. At moderate given pressure, the pressure treatment lowered the volume between the reactants and the transition state. Km decreased from 0.592 to 0.441mmol/L with pressure increasing from 0.1 to 200MPa. Meanwhile, vmax and Kcat increased 24.2% and 20% respectively. The change trend of reaction kinetic parameters under 400-500MPa was contrary to that under 0.1-200MPa.
ESTHER : Chen_2017_Int.J.Biol.Macromol_103_360
PubMedSearch : Chen_2017_Int.J.Biol.Macromol_103_360
PubMedID: 28472692

Title : O-Linked N-acetylglucosamine transferase 1 regulates global histone H4 acetylation via stabilization of the nonspecific lethal protein NSL3 - Wu_2017_J.Biol.Chem_292_10014
Author(s) : Wu D , Zhao L , Feng Z , Yu C , Ding J , Wang L , Wang F , Liu D , Zhu H , Xing F , Conaway JW , Conaway RC , Cai Y , Jin J
Ref : Journal of Biological Chemistry , 292 :10014 , 2017
Abstract : The human males absent on the first (MOF)-containing histone acetyltransferase nonspecific lethal (NSL) complex comprises nine subunits including the O-linked N-acetylglucosamine (O-GlcNAc) transferase, isoform 1 (OGT1). However, whether the O-GlcNAc transferase activity of OGT1 controls histone acetyltransferase activity of the NSL complex and whether OGT1 physically interacts with the other NSL complex subunits remain unclear. Here, we demonstrate that OGT1 regulates the activity of the NSL complex by mainly acetylating histone H4 Lys-16, Lys-5, and Lys-8 via O-GlcNAcylation and stabilization of the NSL complex subunit NSL3. Knocking down or overexpressing OGT1 in human cells remarkably affected the global acetylation of histone H4 residues Lys-16, Lys-5, and Lys-8. Because OGT1 is a subunit of the NSL complex, we also investigated the function of OGT1 in this complex. Co-transfection/co-immunoprecipitation experiments combined with in vitro O-GlcNAc transferase assays confirmed that OGT1 specifically binds to and O-GlcNAcylates NSL3. In addition, wheat germ agglutinin affinity purification verified the occurrence of O-GlcNAc modification on NSL3 in cells. Moreover, O-GlcNAcylation of NSL3 by wild-type OGT1 (OGT1-WT) stabilized NSL3. This stabilization was lost after co-transfection of NSL3 with an OGT1 mutant, OGT1(C964A), that lacks O-GlcNAc transferase activity. Furthermore, stabilization of NSL3 by OGT1-WT significantly increased the global acetylation levels of H4 Lys-5, Lys-8, and Lys-16 in cells. These results suggest that OGT1 regulates the activity of the NSL complex by stabilizing NSL3.
ESTHER : Wu_2017_J.Biol.Chem_292_10014
PubMedSearch : Wu_2017_J.Biol.Chem_292_10014
PubMedID: 28450392
Gene_locus related to this paper: human-KANSL3

Title : Melt With This Kiss: Paralyzing and Liquefying Venom of The Assassin Bug Pristhesancus plagipennis (Hemiptera: Reduviidae) - Walker_2017_Mol.Cell.Proteomics_16_552
Author(s) : Walker AA , Madio B , Jin J , Undheim EA , Fry BG , King GF
Ref : Mol Cell Proteomics , 16 :552 , 2017
Abstract : Assassin bugs (Hemiptera: Heteroptera: Reduviidae) are venomous insects, most of which prey on invertebrates. Assassin bug venom has features in common with venoms from other animals, such as paralyzing and lethal activity when injected, and a molecular composition that includes disulfide-rich peptide neurotoxins. Uniquely, this venom also has strong liquefying activity that has been hypothesized to facilitate feeding through the narrow channel of the proboscis-a structure inherited from sap- and phloem-feeding phytophagous hemipterans and adapted during the evolution of Heteroptera into a fang and feeding structure. However, further understanding of the function of assassin bug venom is impeded by the lack of proteomic studies detailing its molecular composition.By using a combined transcriptomic/proteomic approach, we show that the venom proteome of the harpactorine assassin bug Pristhesancus plagipennis includes a complex suite of >100 proteins comprising disulfide-rich peptides, CUB domain proteins, cystatins, putative cytolytic toxins, triabin-like protein, odorant-binding protein, S1 proteases, catabolic enzymes, putative nutrient-binding proteins, plus eight families of proteins without homology to characterized proteins. S1 proteases, CUB domain proteins, putative cytolytic toxins, and other novel proteins in the 10-16-kDa mass range, were the most abundant venom components. Thus, in addition to putative neurotoxins, assassin bug venom includes a high proportion of enzymatic and cytolytic venom components likely to be well suited to tissue liquefaction. Our results also provide insight into the trophic switch to blood-feeding by the kissing bugs (Reduviidae: Triatominae). Although some protein families such as triabins occur in the venoms of both predaceous and blood-feeding reduviids, the composition of venoms produced by these two groups is revealed to differ markedly. These results provide insights into the venom evolution in the insect suborder Heteroptera.
ESTHER : Walker_2017_Mol.Cell.Proteomics_16_552
PubMedSearch : Walker_2017_Mol.Cell.Proteomics_16_552
PubMedID: 28130397
Gene_locus related to this paper: 9hemi-a0a1q1np79

Title : Characterization and crystal structure of a novel zearalenone hydrolase from Cladophialophora bantiana - Hui_2017_Acta.Crystallogr.F.Struct.Biol.Commun_73_515
Author(s) : Hui R , Hu X , Liu W , Zheng Y , Chen Y , Guo RT , Jin J , Chen CC
Ref : Acta Crystallographica F Struct Biol Commun , 73 :515 , 2017
Abstract : Zearalenone (ZEN) is a mycotoxin which causes huge economic losses in the food and animal feed industries. The lactonase ZHD101 from Clonostachys rosea, which catalyzes the hydrolytic degradation of ZEN, is the only known ZEN-detoxifying enzyme. Here, a protein homologous to ZHD101, denoted CbZHD, from Cladophialophora batiana was expressed and characterized. Sequence alignment indicates that CbZHD possesses the same catalytic triad and ZEN-interacting residues as found in ZHD101. CbZHD exhibits optimal enzyme activity at 35 degrees C and pH 8, and is sensitive to heat treatment. The crystal structure of apo CbZHD was determined to 1.75 A resolution. The active-site compositions of CbZHD and ZHD101 were analyzed.
ESTHER : Hui_2017_Acta.Crystallogr.F.Struct.Biol.Commun_73_515
PubMedSearch : Hui_2017_Acta.Crystallogr.F.Struct.Biol.Commun_73_515
PubMedID: 28876230
Gene_locus related to this paper: xylba-a0a0d2h023

Title : Graveoline Analogs Exhibiting Selective Acetylcholinesterase Inhibitory Activity as Potential Lead Compounds for the Treatment of Alzheimer's Disease - Li_2016_Molecules_21_132
Author(s) : Li Z , Mu C , Wang B , Jin J
Ref : Molecules , 21 :132 , 2016
Abstract : This study designed and synthesized a series of new graveoline analogs on the basis of the structural characteristics of acetylcholinesterase (AChE) dual-site inhibitors. The activity of these analogs was also evaluated. Results showed that the synthesized graveoline analogs displayed stronger inhibitory activity against AChE and higher selectivity than butyrylcholine esterase (BuChE) (Selectivity Index from 45 to 486). When the two sites in the graveoline parent ring substituting phenyl and amino terminal had six chemical bonds (n = 3) and the terminal amino was piperidine, compound 5c showed the best activity. Furthermore, the mechanism of action and binding mode were explored by enzyme kinetic simulation, molecular docking, and thioflavin T-based fluorometric assay. Cytotoxicity assay showed that the low concentration of the analogs did not affect the viability of the neurocyte SH-SY5Y.
ESTHER : Li_2016_Molecules_21_132
PubMedSearch : Li_2016_Molecules_21_132
PubMedID: 26805806

Title : Associations of MDR1, TBXA2R, PLA2G7, and PEAR1 genetic polymorphisms with the platelet activity in Chinese ischemic stroke patients receiving aspirin therapy - Peng_2016_Acta.Pharmacol.Sin_37_1442
Author(s) : Peng LL , Zhao YQ , Zhou ZY , Jin J , Zhao M , Chen XM , Chen LY , Cai YF , Li JL , Huang M
Ref : Acta Pharmacol Sin , 37 :1442 , 2016
Abstract : AIM: Aspirin resistance has an incidence of 5%-65% in patients with ischemic stroke, who receive the standard dose of aspirin, but the platelet function is inadequately inhibited, thereby leading to thrombotic events. Numerous evidence shows that thromboxane A2 receptor (TXA2 receptor, encoded by TBXA2R), lipoprotein-associated phospholipase A2 (Lp-PLA2, encoded by PLA2G7) and platelet endothelial aggregation receptor-1 (PEAR1, encoded by PEAR1) are crucial in regulating platelet activation, and P-glycoprotein (P-gp, encoded by MDR1) influences the absorption of aspirin in the intestine. In this study we examined the correlation between MDR1, TBXA2R, PLA2G7, PEAR1 genetic polymorphisms and platelet activity in Chinese ischemic stroke patients receiving aspirin therapy.
METHODS: A total of 283 ischemic stroke patients receiving 100 mg aspirin for 7 d were genotyped for polymorphisms in MDR1 C3435T, TBXA2R (rs1131882), PLA2G7 (rs1051931, rs7756935), and PEAR1 (rs12566888, rs12041331). The platelet aggregation response was measured using an automatic platelet aggregation analyzer and a commercially available TXB2 ELISA kit.
RESULTS: Thirty-three patients (11.66%) were insensitive to aspirin treatment. MDR1 3435TT genotype carriers, whose arachidonic acid (AA) or adenosine diphosphate (ADP)-induced platelet aggregation was lower than that of CC+CT genotype carriers, were less likely to suffer from aspirin resistance (odds ratio=0.421, 95% CI: 0.233-0.759). The TBXA2R rs1131882 CC genotype, which was found more frequently in the aspirin-insensitive group (81.8% vs 62.4%) than in the sensitive group, was identified as a risk factor for aspirin resistance (odds ratio=2.712, 95% CI: 1.080-6.810) with a higher level of AA-induced platelet aggregation. Due to the combined effects of PLA2G7 rs1051931 and rs7756935, carriers of the AA-CC haplotype had a higher level of ADP-induced platelet aggregation, and were at considerably higher risk of aspirin resistance than noncarriers (odds ratio=8.233, 95% CI: 1.590-42.638). CONCLUSION: A considerable portion (11.66%) of Chinese ischemic stroke patients are insensitive to aspirin treatment, which may be correlated with the MDR1 C3435T, TBXA2R (rs1131882), and PLA2G7 (rs1051931-rs7756935) polymorphisms.
ESTHER : Peng_2016_Acta.Pharmacol.Sin_37_1442
PubMedSearch : Peng_2016_Acta.Pharmacol.Sin_37_1442
PubMedID: 27641736

Title : Pretreatment serum pseudocholinesterase level as a novel prognostic biomarker for upper tract urothelial carcinoma - Zhang_2016_Int.Urol.Nephrol_48_1993
Author(s) : Zhang B , Shen C , Jin J , Song Y , Zhao Z , Zhang X , Wang G , Fan Y , Mi Y , Hu S , Cui Y , Zhou L , He Z , Yu W , Han W
Ref : International Urology & Nephrology , 48 :1993 , 2016
Abstract : PURPOSE: Pretreatment serum pseudocholinesterase (PChE) has been reported to be a prognostic predictor in several cancers. However, the prognostic significance of serum PChE level in patients with upper tract urothelial carcinoma (UTUC) remains unknown.
METHODS: A total of 180 patients who underwent radical nephroureterectomy (RNU) for UTUC were included in this retrospective analysis. The associations of pretreatment serum PChE levels with clinicopathological characteristics and clinical outcomes were assessed.
RESULTS: The median (IQR) pretreatment serum PChE level was 6385 (5449-7260) IU/L, and an optimal cutoff value of 5336 IU/L was set according to ROC analysis. Decreased pretreatment serum PChE levels were significantly correlated with older patient age, higher preoperative chronic kidney disease (CKD) stage and pT stage (all P < 0.05). On multivariate analysis, adjusting for preoperative variables, decreased pretreatment serum PChE levels independently predicted higher pT stage (P = 0.011). Moreover, Kaplan-Meier curves suggested that patients with PChE levels <5336 IU/L were predicted to have a shorter overall survival (OS) and cancer-specific survival (CSS) than those with PChE levels >/=5336 IU/L (both P < 0.001). On multivariate analysis, decreased pretreatment serum PChE levels were significantly associated with shorter OS (HR 0.553; 95 %CI 0.322-0.951; P = 0.032) and CSS (HR 0.484; 95 %CI 0.269-0.870; P = 0.015).
CONCLUSIONS: Decreased pretreatment serum PChE level is an independent predictor for higher pT stage, shorter OS and CSS in patients with UTUC. Pretreatment serum PChE levels may act as a simple and effective parameter to predict prognosis for UTUC patients after RNU.
ESTHER : Zhang_2016_Int.Urol.Nephrol_48_1993
PubMedSearch : Zhang_2016_Int.Urol.Nephrol_48_1993
PubMedID: 27554671

Title : Enhanced alpha-Zearalenol Hydrolyzing Activity of a Mycoestrogen-Detoxifying Lactonase by Structure-Based Engineering - Xu_2016_ACS.Catal_6_7657
Author(s) : Xu Z , Liu W , Chen CC , Li Q , Huang JW , Ko TP , Liu G , Peng W , Cheng YS , Chen Y , Jin J , Li H , Zheng Y , Guo RT
Ref : ACS Catal , 6 :7657 , 2016
Abstract : The enzyme ZHD101 from Clonostachys rosea hydrolyzes and deactivates the mycotoxin zearalenone (ZEN) and its zearalenol (ZOL) derivatives. ZHD101 prefers ZEN to ZOL as its substrate, but ZOL, especially the -form, shows higher estrogenic toxicity than ZEN. To enhance alpha-ZOL selectivity, we solved the complex structures of ZHD101 with both ZOLs and modified several lactone-surrounding residues. Among the mutants, V153H maintained activity for ZEN but showed a 3.7-fold increase in specific activity against alpha-ZOL, with an 2.7-fold reduction in substrate affinity but a 5.2-fold higher turnover rate. We then determined two V153H/ZOL complex structures. Here, the alpha-ZOL lactone ring is hydrogen-bonded to the H153 side chain, yielding a larger space for H242 to reconstitute the catalytic triad. In conclusion, structure-based engineering was successfully employed to improve the ZHD101 activity toward the more toxic alpha-ZOL, with great potential in further industrial applications.
ESTHER : Xu_2016_ACS.Catal_6_7657
PubMedSearch : Xu_2016_ACS.Catal_6_7657
Gene_locus related to this paper: biooc-ZHD101

Title : Hopeahainol A attenuates memory deficits by targeting beta-amyloid in APP\/PS1 transgenic mice - Zhu_2013_Aging.Cell_12_85
Author(s) : Zhu X , Ye L , Ge H , Chen L , Jiang N , Qian L , Li L , Liu R , Ji S , Zhang S , Jin J , Guan D , Fang W , Tan R , Xu Y
Ref : Aging Cell , 12 :85 , 2013
Abstract : Increasing evidence demonstrates that amyloid beta (Abeta) elicits mitochondrial dysfunction and oxidative stress, which contributes to the pathogenesis of Alzheimer's disease (AD). Identification of the molecules targeting Abeta is thus of particular significance in the treatment of AD. Hopeahainol A (HopA), a polyphenol with a novel skeleton obtained from Hopea hainanensis, is potentially acetylcholinesterase-inhibitory and anti-oxidative in H(2) O(2) -treated PC12 cells. In this study, we reported that HopA might bind to Abeta(1-42) directly and inhibit the Abeta(1-42) aggregation using a combination of molecular dynamics simulation, binding assay, transmission electron microscopic analysis and staining technique. We also demonstrated that HopA decreased the interaction between Abeta(1-42) and Abeta-binding alcohol dehydrogenase, which in turn reduced mitochondrial dysfunction and oxidative stress in vivo and in vitro. In addition, HopA was able to rescue the long-term potentiation induction by protecting synaptic function and attenuate memory deficits in APP/PS1 mice. Our data suggest that HopA might be a promising drug for therapeutic intervention in AD.
ESTHER : Zhu_2013_Aging.Cell_12_85
PubMedSearch : Zhu_2013_Aging.Cell_12_85
PubMedID: 23107435

Title : Study on the dynamic compound structure composed of mast cells, blood vessels, and nerves in rat acupoint - Mingfu_2013_Evid.Based.Complement.Alternat.Med_2013_160651
Author(s) : Mingfu L , Xiaotong D , Xiaojing S , Jin J , Jinling Z , Ying H
Ref : Evid Based Complement Alternat Med , 2013 :160651 , 2013
Abstract : Background. Circulation system, immunity system, and nervous system have a close relationship with meridian phenomen. However, there is still lack of the results of dynamic changes of these structures in acupoint. The aim of this study is to explore the interrelationship by composite staining techniques. Methodology/Principal Findings. Twenty rats were separated into electroacupuncture group (EA) and control group (Con) randomly. In EA group, the Zusanli and Weishu were stimulated with the 0.1 mA for 25 min. The tissue of these acupoints was double-stained with acetylcholinesterase and Toluidine blue. The compound structure of mast cells, nervous fibers, and mast cells in the acupoint was observed. Conclusions/Significance. The blood vessels, mast cells and acetylcholinesterase responded nerves were clearly observed in acupoint tissues. EA can result in the mast cell recruitment and migration along the blood vessels and nervous bundle, which conformed the dynamic compound structure and played important roles in acupuncture.
ESTHER : Mingfu_2013_Evid.Based.Complement.Alternat.Med_2013_160651
PubMedSearch : Mingfu_2013_Evid.Based.Complement.Alternat.Med_2013_160651
PubMedID: 23878591

Title : Production of diacylglycerols from glycerol monooleate and ethyl oleate through free and immobilized lipase-catalyzed consecutive reactions - Jin_2011_N.Biotechnol_28_190
Author(s) : Jin J , Li D , Zhu XM , Adhikari P , Lee KT , Lee JH
Ref : N Biotechnol , 28 :190 , 2011
Abstract : The ability of free and immobilized lipase on the production of diacylglycerols (DAG) by transesterification of glycerol monooleate (GMO) and ethyl oleate was investigated. Among three free lipases such as lipase G (Penicillium cyclopium), lipase AK (Pseudomonas fluorescens) and lipase PS (Pseudomonas cepacia), lipase PS exhibited the highest DAG productivity, and the DAG content gradually increased up to 24 hours reaction and then remained steady. The comparative result for DAG productivity between free lipase PS and immobilized lipases (lipase PS-D and Lipozyme RM IM) during nine times of 24 hours reaction indicated that total DAG production was higher in immobilized lipase PS-D (183.5mM) and Lipozyme RM IM (309.5mM) than free lipase PS (122.0mM) at the first reaction, and that the DAG production rate was reduced by consecutive reactions, in which more sn-1,3-DAG was synthesized than sn-1,2-DAG. During the consecutive reactions, the activity of lipase PS was relatively steady by showing similar DAG content, whereas DAG production of lipase PS-D and Lipozyme RM IM was gradually decreased to 69.9 and 167.1mM at 9th reaction, respectively, resulting in 62% and 46% reduced production when compared with 1st reaction. Interestingly, from 7th reaction lipase PS produced more DAG than immobilized lipase PS-D, and exhibited a stable activity for DAG production. Therefore, the present study suggested that DAG productivity between GMO and ethyl oleate was higher in immobilized lipases than free lipases, but the activity was reduced with repeated uses.
ESTHER : Jin_2011_N.Biotechnol_28_190
PubMedSearch : Jin_2011_N.Biotechnol_28_190
PubMedID: 20951847

Title : Subunit composition and substrate specificity of a MOF-containing histone acetyltransferase distinct from the male-specific lethal (MSL) complex - Cai_2010_J.Biol.Chem_285_4268
Author(s) : Cai Y , Jin J , Swanson SK , Cole MD , Choi SH , Florens L , Washburn MP , Conaway JW , Conaway RC
Ref : Journal of Biological Chemistry , 285 :4268 , 2010
Abstract : Human MOF (MYST1), a member of the MYST (Moz-Ybf2/Sas3-Sas2-Tip60) family of histone acetyltransferases (HATs), is the human ortholog of the Drosophila males absent on the first (MOF) protein. MOF is the catalytic subunit of the male-specific lethal (MSL) HAT complex, which plays a key role in dosage compensation in the fly and is responsible for a large fraction of histone H4 lysine 16 (H4K16) acetylation in vivo. MOF was recently reported to be a component of a second HAT complex, designated the non-specific lethal (NSL) complex (Mendjan, S., Taipale, M., Kind, J., Holz, H., Gebhardt, P., Schelder, M., Vermeulen, M., Buscaino, A., Duncan, K., Mueller, J., Wilm, M., Stunnenberg, H. G., Saumweber, H., and Akhtar, A. (2006) Mol. Cell 21, 811-823). Here we report an analysis of the subunit composition and substrate specificity of the NSL complex. Proteomic analyses of complexes purified through multiple candidate subunits reveal that NSL is composed of nine subunits. Two of its subunits, WD repeat domain 5 (WDR5) and host cell factor 1 (HCF1), are shared with members of the MLL/SET family of histone H3 lysine 4 (H3K4) methyltransferase complexes, and a third subunit, MCRS1, is shared with the human INO80 chromatin-remodeling complex. In addition, we show that assembly of the MOF HAT into MSL or NSL complexes controls its substrate specificity. Although MSL-associated MOF acetylates nucleosomal histone H4 almost exclusively on lysine 16, NSL-associated MOF exhibits a relaxed specificity and also acetylates nucleosomal histone H4 on lysines 5 and 8.
ESTHER : Cai_2010_J.Biol.Chem_285_4268
PubMedSearch : Cai_2010_J.Biol.Chem_285_4268
PubMedID: 20018852
Gene_locus related to this paper: human-KANSL3

Title : Enrichment of pinolenic acid at the sn-2 position of triacylglycerol molecules through lipase-catalyzed reaction - Zhu_2010_Int.J.Food.Sci.Nutr_61_138
Author(s) : Zhu XM , Hu JN , Shin JA , Li D , Jin J , Adhikari P , Akoh CC , Lee JH , Choi SW , Lee KT
Ref : Int J Food Sci Nutr , 61 :138 , 2010
Abstract : Reports have shown that Delta-5 polyunsaturated fatty acids (-5 PUFA) are enriched at sn-1,3 positions of triacylglycerols (TAG) in pine (Pinus koraiensis) nut oil (Pn). As a major Delta-5 PUFA, pinolenic acid (Pi) is about 14.2% in the oil, while the percentage of Pi at the sn-1 and/or sn-3 positions in TAG was found more than 20%. In this current study, the enhancement of Pi at the sn-2 position has been achieved by acyl migration during the lipase-catalyzed inter-esterification between Pn and palm stearin (Ps). After reaction, the proportion of Pi increased at sn-2 positional fatty acid even is similar to that in total fatty acid; for example, in the inter-esterified product of 50:50 (Pn:Ps), the same amount of Pi (7.1%) present was detected both at the sn-2 and sn-1,3 positions. However, the reduction of phytosterols and tocopherols are observed in the inter-esterified products.
ESTHER : Zhu_2010_Int.J.Food.Sci.Nutr_61_138
PubMedSearch : Zhu_2010_Int.J.Food.Sci.Nutr_61_138
PubMedID: 20001760

Title : Draft genome of the filarial nematode parasite Brugia malayi - Ghedin_2007_Science_317_1756
Author(s) : Ghedin E , Wang S , Spiro D , Caler E , Zhao Q , Crabtree J , Allen JE , Delcher AL , Guiliano DB , Miranda-Saavedra D , Angiuoli SV , Creasy T , Amedeo P , Haas B , El-Sayed NM , Wortman JR , Feldblyum T , Tallon L , Schatz M , Shumway M , Koo H , Salzberg SL , Schobel S , Pertea M , Pop M , White O , Barton GJ , Carlow CK , Crawford MJ , Daub J , Dimmic MW , Estes CF , Foster JM , Ganatra M , Gregory WF , Johnson NM , Jin J , Komuniecki R , Korf I , Kumar S , Laney S , Li BW , Li W , Lindblom TH , Lustigman S , Ma D , Maina CV , Martin DM , McCarter JP , McReynolds L , Mitreva M , Nutman TB , Parkinson J , Peregrin-Alvarez JM , Poole C , Ren Q , Saunders L , Sluder AE , Smith K , Stanke M , Unnasch TR , Ware J , Wei AD , Weil G , Williams DJ , Zhang Y , Williams SA , Fraser-Liggett C , Slatko B , Blaxter ML , Scott AL
Ref : Science , 317 :1756 , 2007
Abstract : Parasitic nematodes that cause elephantiasis and river blindness threaten hundreds of millions of people in the developing world. We have sequenced the approximately 90 megabase (Mb) genome of the human filarial parasite Brugia malayi and predict approximately 11,500 protein coding genes in 71 Mb of robustly assembled sequence. Comparative analysis with the free-living, model nematode Caenorhabditis elegans revealed that, despite these genes having maintained little conservation of local synteny during approximately 350 million years of evolution, they largely remain in linkage on chromosomal units. More than 100 conserved operons were identified. Analysis of the predicted proteome provides evidence for adaptations of B. malayi to niches in its human and vector hosts and insights into the molecular basis of a mutualistic relationship with its Wolbachia endosymbiont. These findings offer a foundation for rational drug design.
ESTHER : Ghedin_2007_Science_317_1756
PubMedSearch : Ghedin_2007_Science_317_1756
PubMedID: 17885136
Gene_locus related to this paper: bruma-a8ndk6 , bruma-a8njt8 , bruma-a8nl88 , bruma-a8npi4 , bruma-a8npi6 , bruma-a8p6g9 , bruma-a8pah3 , bruma-a8pc38 , bruma-a8pek5 , bruma-a8piq4 , bruma-a8pnw8 , bruma-a8psu4 , bruma-a8pte1 , bruma-a8q606 , bruma-a8q632 , bruma-a8q937 , bruma-a8qav5 , bruma-a8qbd9 , bruma-a8qgj6 , bruma-a8qh78 , bruma-a8q143 , bruma-a0a024mej5 , bruma-a0a0k0jju9 , bruma-a0a0i9n517

Title : [Significance of the ratio of circulating endothelial cell expressing endothelial lipase and supersensitivity C-reactive protein in prognosis of patients with coronary artery disease] - Fang_2007_Zhongguo.Wei.Zhong.Bing.Ji.Jiu.Yi.Xue_19_644
Author(s) : Fang YQ , Huang L , Li AM , Song YM , Jin J , Geng ZH , Yu XJ , Deng MY
Ref : Zhongguo Wei Zhong Bing Ji Jiu Yi Xue , 19 :644 , 2007
Abstract : OBJECTIVE: To evaluate the significance of the ratio of circulating endothelial cell expressing endothelial lipase (EL(+)/CECs) and supersensitivity C-reactive protein (hsCRP) in prognosis of patients with coronary artery disease (CAD).
METHODS: one hundred and seven patients with acute coronary syndrome (ACS), 69 patients with stable angina pain (SAP), and 82 patients in whom CAD was excluded to serve as control were included for study. Blood samples were collected from ulnar vein, and hsCRP was detected, circulating endothelial cells (CECs) were isolated, and the ratio of CEC (EL(+)/CECs) which expressed endothelial lipase (EL) was determined by immunohistochemistry. Over a follow-up period of 6 months, the incidence of cardiac event of all patients was recorded.
RESULTS: In patients with CAD, the EL(+)/CECs and hsCRP were significantly different among groups (P<0.05 or P<0.01). Among them, hsCRP and EL(+)/CECs were higher in ACS group than SAP group patients, whose hsCRP and EL(+)/CECs higher than the control group. The incidence rate of cardiovascular event was significantly higher (all P<0.01) in those whose hsCRP or EL(+)/CECs was higher than those whose with lower average values of these two parameters. Regression analysis indicated that the EL(+)/CECs and hsCRP could be used as the prognostic factor of CAD. The prognostic value of combined determination of EL(+)/CECs and hsCRP was higher. CONCLUSION: The expression of EL in endothelial cells may play a role in the progression of CAD. The EL(+)/CECs may be a good prognostic factor. EL(+)/CECs together with hsCRP may increase the prognostic value.
ESTHER : Fang_2007_Zhongguo.Wei.Zhong.Bing.Ji.Jiu.Yi.Xue_19_644
PubMedSearch : Fang_2007_Zhongguo.Wei.Zhong.Bing.Ji.Jiu.Yi.Xue_19_644
PubMedID: 17996128

Title : GIP2, a putative transcription factor that regulates the aurofusarin biosynthetic gene cluster in Gibberella zeae - Kim_2006_Appl.Environ.Microbiol_72_1645
Author(s) : Kim JE , Jin J , Kim H , Kim JC , Yun SH , Lee YW
Ref : Applied Environmental Microbiology , 72 :1645 , 2006
Abstract : Gibberella zeae (anamorph: Fusarium graminearum) is an important pathogen of maize, wheat, and rice. Colonies of G. zeae produce yellow-to-tan mycelia with the white-to-carmine red margins. In this study, we focused on nine putative open reading frames (ORFs) closely linked to PKS12 and GIP1, which are required for aurofusarin biosynthesis in G. zeae. Among them is an ORF designated GIP2 (for Gibberella zeae pigment gene 2), which encodes a putative protein of 398 amino acids that carries a Zn(II)2Cys6 binuclear cluster DNA-binding domain commonly found in transcription factors of yeasts and filamentous fungi. Targeted gene deletion and complementation analyses confirmed that GIP2 is required for aurofusarin biosynthesis. Expression of GIP2 in carrot medium correlated with aurofusarin production by G. zeae and was restricted to vegetative mycelia. Inactivation of the 10 contiguous genes in the DeltaGIP2 strain delineates an aurofusarin biosynthetic gene cluster. Overexpression of GIP2 in both the DeltaGIP2 and the wild-type strains increases aurofusarin production and reduces mycelial growth. Thus, GIP2 is a putative positive regulator of the aurofusarin biosynthetic gene cluster, and aurofusarin production is negatively correlated with vegetative growth by G. zeae.
ESTHER : Kim_2006_Appl.Environ.Microbiol_72_1645
PubMedSearch : Kim_2006_Appl.Environ.Microbiol_72_1645
PubMedID: 16461721
Gene_locus related to this paper: gibze-q66sy0

Title : Two different polyketide synthase genes are required for synthesis of zearalenone in Gibberella zeae - Kim_2005_Mol.Microbiol_58_1102
Author(s) : Kim YT , Lee YR , Jin J , Han KH , Kim H , Kim JC , Lee T , Yun SH , Lee YW
Ref : Molecular Microbiology , 58 :1102 , 2005
Abstract : Zearalenone (ZEA) is a polyketide mycotoxin produced by some species of Gibberella/Fusarium and causes hyperestrogenic syndrome in animals. ZEA occurs naturally in cereals infected by Gibberella zeae in temperate regions and threatens animal health. In this study, we report on a set of genes that participate in the biosynthesis of ZEA in G. zeae. Focusing on the non-reducing polyketide synthase (PKS) genes of the G. zeae genome, we demonstrated that PKS13 is required for ZEA production. Subsequent analyses revealed that a continuous, 50 kb segment of DNA carrying PKS13 consisted of three additional open reading frames that were coexpressed as a cluster during the condition for ZEA biosynthesis. These genes, in addition to PKS13, were essential for the ZEA biosynthesis. They include another PKS gene (PKS4) encoding a fungal reducing PKS; zearalenone biosynthesis gene 1 (ZEB1), which shows a high similarity to putative isoamyl alcohol oxidase genes; and ZEB2 whose deduced product carries a conserved, basic-region leucine zipper domain. ZEB1 is responsible for the chemical conversion of beta-zearalenonol (beta-ZOL) to ZEA in the biosynthetic pathway, and ZEB2 controls transcription of the cluster members. Transcription of these genes was strongly influenced by different culture conditions such as nutrient starvations and ambient pH. Furthermore, the same set of genes regulated by ZEB2 was dramatically repressed in the transgenic G. zeae strain with the deletion of PKS13 or PKS4 but not in the ZEB1 deletion strain, suggesting that ZEA or beta-ZOL may be involved in transcriptional activation of the gene cluster required for ZEA biosynthesis in G. zeae. This is the first published report on the molecular characterization of genes required for ZEA biosynthesis.
ESTHER : Kim_2005_Mol.Microbiol_58_1102
PubMedSearch : Kim_2005_Mol.Microbiol_58_1102
PubMedID: 16262793
Gene_locus related to this paper: gibze-q2vlj3

Title : Putative polyketide synthase and laccase genes for biosynthesis of aurofusarin in Gibberella zeae - Kim_2005_Appl.Environ.Microbiol_71_1701
Author(s) : Kim JE , Han KH , Jin J , Kim H , Kim JC , Yun SH , Lee YW
Ref : Applied Environmental Microbiology , 71 :1701 , 2005
Abstract : Mycelia of Gibberella zeae (anamorph, Fusarium graminearum), an important pathogen of cereal crops, are yellow to tan with white to carmine red margins. We isolated genes encoding the following two proteins that are required for aurofusarin biosynthesis from G. zeae: a type I polyketide synthase (PKS) and a putative laccase. Screening of insertional mutants of G. zeae, which were generated by using a restriction enzyme-mediated integration procedure, resulted in the isolation of mutant S4B3076, which is a pigment mutant. In a sexual cross of the mutant with a strain with normal pigmentation, the pigment mutation was linked to the inserted vector. The vector insertion site in S4B3076 was a HindIII site 38 bp upstream from an open reading frame (ORF) on contig 1.116 in the F. graminearum genome database. The ORF, designated Gip1 (for Gibberella zeae pigment mutation 1), encodes a putative laccase. A 30-kb region surrounding the insertion site and Gip1 contains 10 additional ORFs, including a putative ORF identified as PKS12 whose product exhibits about 40% amino acid identity to the products of type I fungal PKS genes, which are involved in pigment biosynthesis. Targeted gene deletion and complementation analyses confirmed that both Gip1 and PKS12 are required for aurofusarin production in G. zeae. This information is the first information concerning the biosynthesis of these pigments by G. zeae and could help in studies of their toxicity in domesticated animals.
ESTHER : Kim_2005_Appl.Environ.Microbiol_71_1701
PubMedSearch : Kim_2005_Appl.Environ.Microbiol_71_1701
PubMedID: 15811992
Gene_locus related to this paper: gibze-q66sy0

Title : The Genomes of Oryza sativa: a history of duplications - Yu_2005_PLoS.Biol_3_e38
Author(s) : Yu J , Wang J , Lin W , Li S , Li H , Zhou J , Ni P , Dong W , Hu S , Zeng C , Zhang J , Zhang Y , Li R , Xu Z , Li X , Zheng H , Cong L , Lin L , Yin J , Geng J , Li G , Shi J , Liu J , Lv H , Li J , Deng Y , Ran L , Shi X , Wang X , Wu Q , Li C , Ren X , Li D , Liu D , Zhang X , Ji Z , Zhao W , Sun Y , Zhang Z , Bao J , Han Y , Dong L , Ji J , Chen P , Wu S , Xiao Y , Bu D , Tan J , Yang L , Ye C , Xu J , Zhou Y , Yu Y , Zhang B , Zhuang S , Wei H , Liu B , Lei M , Yu H , Li Y , Xu H , Wei S , He X , Fang L , Huang X , Su Z , Tong W , Tong Z , Ye J , Wang L , Lei T , Chen C , Chen H , Huang H , Zhang F , Li N , Zhao C , Huang Y , Li L , Xi Y , Qi Q , Li W , Hu W , Tian X , Jiao Y , Liang X , Jin J , Gao L , Zheng W , Hao B , Liu S , Wang W , Yuan L , Cao M , McDermott J , Samudrala R , Wong GK , Yang H
Ref : PLoS Biol , 3 :e38 , 2005
Abstract : We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000-40,000. Only 2%-3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family.
ESTHER : Yu_2005_PLoS.Biol_3_e38
PubMedSearch : Yu_2005_PLoS.Biol_3_e38
PubMedID: 15685292
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Title : Characteristics of memory dysfunction in olfactory bulbectomized rats and the effects of cholinergic drugs - Yamamoto_1997_Behav.Brain.Res_83_57
Author(s) : Yamamoto T , Jin J , Watanabe S
Ref : Behavioural Brain Research , 83 :57 , 1997
Abstract : The memory impairment of olfactory bulbs (OB)-lesioned rats was characterized using 4 different tasks of learning/memory, and the effects of certain cholinergic drugs on such memory impairment were examined. In reference memory and working memory tasks using a 3-panel runway apparatus, OB-lesioned rats showed a marked increase in errors. In the 3-lever operant task using delayed matching to a sample (DMTS) procedure, OB lesions significantly decreased the correct response in choice (test) trials without affecting the in sample (training) trials. An interesting finding is that impairment in the DMTS performance did not appear immediately after the OB lesion, but tended to appear after a delay. Based on this finding, it is unlikely that memory impairment in the OB-lesioned rats is due to the olfactory deficit itself. However, OB lesions significantly reduced the choice accuracy and delayed the choice reaction time during the 3-choice serial time task for assessing attentional function, using a 3-lever operant apparatus. These findings suggest that marked impairment of learning and memory in OB-lesioned rats may be caused by the attention deficit. Furthermore, the memory impairment in OB-lesioned rats was reduced by cholinesterase inhibitors, physostigmine and NIK-247. These finding suggest that dysfunction of the cholinergic system is involved, at least in part, in the memory impairment of OB-lesioned rats.
ESTHER : Yamamoto_1997_Behav.Brain.Res_83_57
PubMedSearch : Yamamoto_1997_Behav.Brain.Res_83_57
PubMedID: 9062661