Sun F

References (28)

Title : Axially Coordinated Gold Nanoclusters Tailoring Fe-N-C Nanozymes for Enhanced Oxidase-Like Specificity and Activity - Xie_2024_Adv.Sci.(Weinh)__e2306911
Author(s) : Xie Y , Sun F , Chang K , Li G , Song Z , Huang J , Cheng X , Zhuang G , Kuang Q
Ref : Adv Sci (Weinh) , :e2306911 , 2024
Abstract : Metal-organic frameworks (MOF) derived nitrogen-doped carbon-supported monodisperse Fe (Fe-N-C) catalysts are intensively studied, but great challenges remain in understanding the relationship between the coordination structure and the performance of Fe-N-C nanozymes. Herein, a novel nanocluster ligand-bridging strategy is proposed for constructing Fe-S(1) N(4) structures with axially coordinated S and Au nanoclusters on ZIF-8 derived Fe-N-C (labeled Au(x) /Fe-S(1) N(4) -C). The axial Au nanoclusters facilitate electron transfer to Fe active sites, utilizing the bridging ligand S as a medium, thereby enhancing the oxygen adsorption capacity of composite nanozymes. Compared to Fe-N-C, Au(x) /Fe-S(1) N(4) -C exhibits high oxidase-like specificity and activity, and holds great potential for detecting acetylcholinesterase activity with a detection limit of 5.1 microU mL(-1) , surpassing most reported nanozymes.
ESTHER : Xie_2024_Adv.Sci.(Weinh)__e2306911
PubMedSearch : Xie_2024_Adv.Sci.(Weinh)__e2306911
PubMedID: 38196300

Title : ANGPTL3 accelerates atherosclerotic progression via direct regulation of M1 macrophage activation in plaque - Zhang_2024_J.Adv.Res__
Author(s) : Zhang Y , Yan C , Dong Y , Zhao J , Yang X , Deng Y , Su L , Yin J , Sun F , Feng Y
Ref : J Adv Res , : , 2024
Abstract : INTRODUCTION: The N-terminal domain of angiopoietin-like protein 3 (ANGPTL3) inhibits lipoprotein lipase activity. Its C-terminal fibrinogen-like (FBN) domain is a ligand of macrophage integrin alphavbeta3. OBJECTIVES: ANGPTL3 might home to plaque where it directly regulates macrophage function via integrin alphavbeta3 for atherosclerosis progression. METHODS: Ldlr(-/-) mice on a high-fat diet and ApoE(-/-) mice on a chow diet were received adeno-associated virus (AAV)-mediated Angptl3 gene transfer and followed up for 12 weeks. ApoE(-/-) mice were injected AAV containing FLAG-tagged Angptl3 cDNA for tracing. Atherosclerotic features were compared between Angptl3(-/-)ApoE(-/-) mice and ApoE(-/-) littermates. THP-1 cells were exposed to 0 or 50 microg/ml ANGPTL3 FBN domain for 24 h to evaluate Toll-like receptor (TLR)4 expression using western blot analysis and circulating cytokine and chemokine profiles by the MILLIPLEX MAP assay. Phospho-proteomic profile was established in ANGPTL3-treated macrophages. Integrin beta3 deficient THP-1 cells were obtained by sgRNAs targeting RGD sequence using Lentivirus-Cas9 system. RESULTS: Angptl3 overexpression increased atherosclerotic progression and CD68(+) macrophages in plaque (p < 0.05 for all). By immunostaining, FLAG(+) cells were identified in plaque of gene transferred ApoE(-/-) mice. Fluorescent immunostaining detected co-localisation of Angptl3 and CD68 in plaque macrophages. Phospho-proteomic analysis revealed that Angptl3 induced phosphorylation of proteins that were involved in the IL-17 signalling pathway in THP-1 cells. In vitro, ANGPTL3 treatment increased the production of interleukin (IL)-1beta and tumour necrosis factor-alpha in THP-1 cells (p < 0.05 for both). Exposure of ANGPTL3 to THP-1 cells induced Akt phosphorylation which was weakened in integrin beta3 deficient ones. ANGPTL3 elevated TLR4 expression via Akt phosphorylation. In response to lipopolysaccharide, nuclear factor-kappaB activity was 2.2-fold higher in THP-1 cells pre-treated with ANGPTL3 than in untreated cells (p < 0.05). CONCLUSIONS: Targeting ANGPTL3 could yield a dual benefit of lowering lipid levels in the blood and suppressing macrophage activation in plaque.
ESTHER : Zhang_2024_J.Adv.Res__
PubMedSearch : Zhang_2024_J.Adv.Res__
PubMedID: 38740260

Title : Pseudo toxicity abatement effect of norfloxacin and copper combined exposure on Caenorhabditis elegans - Liu_2022_Chemosphere_287_132019
Author(s) : Liu L , He S , Tang M , Zhang M , Wang C , Wang Z , Sun F , Yan Y , Li H , Lin K
Ref : Chemosphere , 287 :132019 , 2022
Abstract : The coexistence of antibiotics and heavy metals may result in complex ecotoxicological effects on living organisms. In this work, the combined toxic effects of norfloxacin (NOR) and copper (Cu) on Caenorhabditis elegans (C. elegans) were investigated due to the highly possible co-pollution tendency. The results indicated that locomotion behaviors (frequency of head thrash and body bend) of C. elegans were more sensitive as the exposure time of NOR or Cu prolonged. Meanwhile, the physiological indexes (locomotion behaviors, body length) of C. elegans were more sensitive to the combined pollution that with lower Cu dosage (0.0125 microM), in prolonged exposure experiments. In addition, the toxic effects of NOR-Cu on physiological indexes of C. elegans seemed to be alleviated during prolonged exposure when Cu was 1.25 microM. Similarly, the ROS production and apoptosis level almost unchanged with the addition of NOR compared with Cu (1.25 microM) exposure groups, but both significantly higher than the control groups. Furthermore, compared with Cu (0.0125 microM and 1.25 microM) exposure experiments, the addition of NOR had resulted in the genetic expression decrease of hsp-16.1, hsp-16.2, hsp-16.48, and the oxidative stress in C. elegans seems to be alleviated. However, the significantly decreased of ape-1 and sod-3 expression indicated the disruption of ROS defense mechanism. The irregular change in ace-1 and ace-2 gene expressions in NOR-Cu (0.0125 microM) would result in the locomotion behaviors disorders of C. elegans, and this also explains why C. elegans are more sensitive to the combination of NOR and lower concentration of Cu.
ESTHER : Liu_2022_Chemosphere_287_132019
PubMedSearch : Liu_2022_Chemosphere_287_132019
PubMedID: 34450372

Title : Retrospective detection for V-type OPNAs exposure via phosphonylation and disulfide adducts in albumin - Wang_2022_Sci.Rep_12_10979
Author(s) : Wang J , Sun F , Lu X , Gao R , Pei C , Wang H
Ref : Sci Rep , 12 :10979 , 2022
Abstract : Organophosphorus nerve agents (OPNAs) that damage the central nervous system by inhibiting acetylcholinesterase activity, pose severe threats to human health and life security. Reliable biomarkers that quickly and accurately detect OPNAs exposure are urgently needed to help diagnose quickly and treat in time. Albumins that covalently bind to OPNAs could serve as important targets for retrospective verification of OPNAs exposure. The goal of this study is to explore the potential biomarkers in albumins with high reactivity and good stability and expand the group of potential biomarkers in different species for detecting the exposure of V-type OPNAs including O-ethyl S-(2-(diisopropylamino)ethyl) methylphosphonothioate (VX), O-isobutyl S-(2(diethylamino)ethyl) methylphosphonothioate (VR), and O-butyl S-(2-(diethylamino)ethyl) methylphosphonothioate (Vs). Taking human serum albumin (HSA), bovine serum albumin (BSA) and rabbit serum albumin (RSA) as the research objectives, multiple active sites including phosphonylation and disulfide adduct sites were observed in albumins from different species. Numerous phosphonylation sites labeled by all agents in one type of albumin were found. Among the different species, four shared phosphonylation sites with high reactivity include K499, K549, K249, and Y108. In addition, Y108 on ETY*GEMADCCAK, Y287 on Y*ICENQDSISSK, Y377 on TY*ETTLEK and Y164 on YLY*EIAR in HSA were stably phosphonylated by all agents in gradient concentration, making them stable and suitable potential biomarkers for V-type OPNAs exposure. Notably, Y108 on ETY*GEMADCCAK in HSA, on DTY*GDVADCCEK in RSA, and on ETY*GDMADCCEK in BSA were highly reactive to all V-type agents, regardless of species. It was also successfully labeled in HSA exposed to class V agents in gradient concentration. Y108 is expected to be used to screen and identify the exposure of V-type agents in the retrospective research. Disulfide adducts sites, consisted of four sites in HSA and two sites in BSA were also successfully labeled by V-type agents, and characteristic ion fragments from these disulfide adducts were also identified by secondary mass spectrometry. Molecular simulation of the stably modified sites were conducted to discover the promoting factors of covalent adduct formation, which help further clarify formation mechanism of albumin adducts at active sites.
ESTHER : Wang_2022_Sci.Rep_12_10979
PubMedSearch : Wang_2022_Sci.Rep_12_10979
PubMedID: 35768567

Title : Study on pathological and clinical characteristics of chronic HBV infected patients with HBsAg positive, HBV DNA negative, HBeAg negative - Zeng_2022_Front.Immunol_13_1113070
Author(s) : Zeng Z , Liu R , Cao W , Yang L , Lin Y , Bi X , Jiang T , Deng W , Wang S , Lu H , Sun F , Shen G , Chang M , Lu Y , Wu S , Hao H , Xu M , Chen X , Hu L , Zhang L , Wan G , Xie Y , Li M
Ref : Front Immunol , 13 :1113070 , 2022
Abstract : AIMS: Study of clinical characteristics of hepatitis B virus deoxyribonucleic acid (HBV DNA)-negative, hepatitis B surface antigen (HBsAg)-positive, hepatitis B e antigen (HBeAg)-negative patients based on liver histopathology. METHODS: We retrospectively enrolled patients with chronic HBV infection diagnosis at Beijing Ditan Hospital from May 2008 to November 2020. To study the differences between patients with significant hepatic histopathology and those without significant hepatic histopathology. And to study the independent factors of significant hepatic histopathology. RESULTS: 85 HBV DNA-negative and HBeAg-negative patients were 37.90 +/- 10.30 years old, 23.50% of patients with grade of inflammation (G) >1, 35.30% of patients with liver fibrosis stage (S) >1, 44.70% patients were diagnosed with significant hepatic histopathology. Compared to the no significant hepatic histopathology group, another group had older age (41.70 +/- 10.70 vs 34.80 +/- 8.87 years, t=-3.28, P=0.002), higher total bilirubin (TBIL) [14.9(10.3, 22.4) vs 11(8.9, 14.4) micromol/L, z=-2.26, P=0.024], lower cholinesterase (CHE) (t=-2.86, P=0.005, 7388.00 +/- 2156.00 vs 8988.00 +/- 2823.00 U/L) and lower platelet (PLT) (t=2.75, P=0.007, 157.00 +/- 61.40 vs 194.00 +/- 61.00 10^9/L). Abnormal ALT patients are more likely to have significant hepatic histopathology (z=5.44, P=0.020, 66.70% vs 337.50%). G had significant correlation with CHE (P=0.008, r=-0.23), alanine aminotransferase (ALT) (P=0.041, r=0.18), aspartate aminotransferase (AST) (P=0.001, r=0.29). S had significant correlation with TBIL (P = 0.008, r = 0.23), age (P < 0.001, r = 0.32), international normalized ratio (INR) (P = 0.04, r = 0.23), CHE (P < 0.001, r = -0.30), PLT (P < 0.001, r = -0.40) and prothrombin time activity (PTA) (P = 0.046, r = -0.22). Multivariate logistic analysis indicated only age (95%CI=1.014~1.130, OR=1.069, P=0.013) was an impact factor for significant hepatic histopathology. The cutoff point of age was 34.30 years. CONCLUSIONS: A large proportion of chronic HBV infection patients with HBeAg-negative and HBV DNA-negative still have chronic hepatitis. Age is an independent factor for significant hepatic histopathology.
ESTHER : Zeng_2022_Front.Immunol_13_1113070
PubMedSearch : Zeng_2022_Front.Immunol_13_1113070
PubMedID: 36685494

Title : Medial septum tau accumulation induces spatial memory deficit via disrupting medial septum-hippocampus cholinergic pathway - Wu_2021_Clin.Transl.Med_11_e428
Author(s) : Wu D , Gao D , Yu H , Pi G , Xiong R , Lei H , Wang X , Liu E , Ye J , Gao Y , He T , Jiang T , Sun F , Su J , Song G , Peng W , Yang Y , Wang JZ
Ref : Clin Transl Med , 11 :e428 , 2021
Abstract : Tau accumulation and cholinergic impairment are characteristic pathologies in Alzheimer's disease (AD). However, the causal role of tau accumulation in cholinergic lesion is elusive. Here, we observed an aberrant tau accumulation in the medial septum (MS) of 3xTg and 5xFAD mice, especially in their cholinergic neurons. Overexpressing hTau in mouse MS (MS(hTau) ) for 6 months but not 3 months induced spatial memory impairment without changing object recognition and anxiety-like behavior, indicating a specific and time-dependent effect of MS-hTau accumulation on spatial cognitive functions. With increasing hTau accumulation, the MS(hTau) mice showed a time-dependent cholinergic neuron loss with reduced cholinergic projections to the hippocampus. Intraperitoneal administration of donepezil, a cholinesterase inhibitor, for 1 month ameliorated the MS-hTau-induced spatial memory deficits with preservation of MS-hippocampal cholinergic pathway and removal of tau load; and the beneficial effects of donepezil was more prominent at low dose. Proteomics revealed that MS-hTau accumulation deregulated multiple signaling pathways with numerous differentially expressed proteins (DEPs). Among them, the vacuolar protein sorting-associated protein 37D (VP37D), an autophagy-related protein, was significantly reduced in MS(hTau) mice; the reduction of VP37D was restored by donepezil, and the effect was more significant at low dose than high dose. These novel evidences reveal a causal role of tau accumulation in linking MS cholinergic lesion to hippocampus-dependent spatial cognitive damages as seen in the AD patients, and the new tau-removal and autophagy-promoting effects of donepezil may extend its application beyond simple symptom amelioration to potential disease modification.
ESTHER : Wu_2021_Clin.Transl.Med_11_e428
PubMedSearch : Wu_2021_Clin.Transl.Med_11_e428
PubMedID: 34185417

Title : Diosgenin alleviates hypercholesterolemia via SRB1\/CES-1\/CYP7A1\/FXR pathway in high-fat diet-fed rats - Yu_2020_Toxicol.Appl.Pharmacol__115388
Author(s) : Yu L , Lu H , Yang X , Li R , Shi J , Yu Y , Ma C , Sun F , Zhang S , Zhang F
Ref : Toxicol Appl Pharmacol , :115388 , 2020
Abstract : Phytosterol diosgenin (DG) exhibits cholesterol-lowering properties. Few studies focused on the underlying mechanism of DG attenuation of hypercholesterolemia by promoting cholesterol metabolism. To investigate the roles of SRB1/CES-1/CYP7A1/FXR pathways in accelerating cholesterol elimination and alleviating hypercholesterolemia, a rat model of hypercholesterolemia was induced by providing a high-fat diet (HFD). Experimental rat models were randomly divided into a normal control (Con) group, HFD group, low-dose DG (LDG) group (150mg/kg/d), high-dose DG (HDG) group (300mg/kg) and Simvastatin (Sim) group (4mg/kg/d). Body weights, serum and hepatic lipid parameters of rats were tested. The expression levels of scavenger receptor class B type I (SRB1), carboxylesterase-1 (CES-1), cholesterol7alpha- hydroxylase (CYP7A1), and farnesoid X receptor (FXR) were determined. The results showed that DG reduced weight and lowered lipid levels in HFD-fed rats. Pathological morphology analyses revealed that DG notably improved hepatic steatosis and intestinal structure. Further studies showed the increased hepatic SRB1, CES-1, CYP7A1 and inhibited FXR-mediated signaling in DG-fed rats, which contributing to the decrease of hepatic cholesterol. DG also increased intestinal SRB1 and CES-1, inhibiting cholesterol absorption and promoting RCT. The expression levels of these receptors in the HDG group were higher than LDG and Sim groups. These data suggested that DG accelerated reverse cholesterol transport (RCT) and enhanced cholesterol elimination via SRB1/CES-1/CYP7A1/FXR pathway, and DG might be a new candidate for the alleviation of hypercholesterolemia.
ESTHER : Yu_2020_Toxicol.Appl.Pharmacol__115388
PubMedSearch : Yu_2020_Toxicol.Appl.Pharmacol__115388
PubMedID: 33383043

Title : Evaluation of toxicological responses and promising biomarkers of topmouth gudgeon (Pseudorasbora parva) exposed to fipronil at environmentally relevant levels - Li_2020_Environ.Sci.Pollut.Res.Int__
Author(s) : Li H , Zhang R , Sun F , Zhang Y
Ref : Environ Sci Pollut Res Int , : , 2020
Abstract : Fipronil is an insecticide commonly used in agriculture. We report here on the sublethal and sub-chronic effects of fipronil on non-target topmouth gudgeon (Pseudorasbora parva) at environmentally relevant levels. The results showed that fipronil did not cause significant changes in brain acetylcholinesterase activities, glutathione S-transferase (GST) activities in the intestine, and GST, glutamic pyruvic transaminase (GPT), and glutamic oxaloacetic transaminase (GOT) activities in the liver tissues at environmentally relevant levels for 96-h exposure. In the further test for a 12-day exposure, dose-dependent responses of the serum GPT and GOT activities were observed in all treated groups with sublethal concentrations of fipronil. Furthermore, fipronil could reduce the liver mitochondrial membrane fluidity of P. parva, especially with high concentration of fipronil at high temperature. The results suggest that serum GPT and GOT in P. parva might be useful biomarkers for effects of fipronil exposure at environmentally relevant level, and reducing fluidity of liver mitochondrial membrane may be one toxic mechanism of fipronil.
ESTHER : Li_2020_Environ.Sci.Pollut.Res.Int__
PubMedSearch : Li_2020_Environ.Sci.Pollut.Res.Int__
PubMedID: 32304060

Title : Transcriptomic analysis of Chlorimuron-ethyl degrading bacterial strain Klebsiella jilinsis 2N3 - Zhang_2019_Ecotoxicol.Environ.Saf_183_109581
Author(s) : Zhang C , Hao Q , Zhang S , Zhang Z , Zhang X , Sun P , Pan H , Zhang H , Sun F
Ref : Ecotoxicology & Environmental Safety , 183 :109581 , 2019
Abstract : Chlorimuron-ethyl is a sulfonylurea herbicide with a long residual period in the field and is toxic to rotational crops. Klebsiella jilinsis 2N3 is a gram-negative bacterium that can rapidly degrade Chlorimuron-ethyl. In this study, the gene expression changes in strain 2N3 during degradation of Chlorimuron-ethyl was analyzed by RNA-Seq. Results showed that 386 genes were up-regulated and 453 genes were down-regulated. KEGG pathway enrichment analysis revealed the highest enrichment ratio in the pathway of sulfur metabolism. On the basis of the functional annotation and gene expression, we predicted that carboxylesterase, monooxygenase, glycosyltransferase, and cytochrome P450 were involved in the metabolism of Chlorimuron-ethyl biodegradation. Results of qRT-PCR showed that the relative mRNA expression levels of these genes were higher in treatment group than those in control group. The cytochrome P450 encoded by Kj-CysJ and the alkanesulfonate monooxygenase encoded by Kj-SsuD were predicted and further experimentally confirmed by gene knockout as the key enzymes in the biodegradation process. Cultured in basal medium containing Chlorimuron-ethyl (5mgL(-1)) in 36h, the strains of DeltaKj-CysJ, DeltaKj-SsuD, and WT reached the highest OD600 values of 0.308, 0.873, and 1.085, and the highest degradation rates of Chlorimuron-ethyl of 11.83%, 96.21%, and 95.62%, respectively.
ESTHER : Zhang_2019_Ecotoxicol.Environ.Saf_183_109581
PubMedSearch : Zhang_2019_Ecotoxicol.Environ.Saf_183_109581
PubMedID: 31446172

Title : Whole Genome Sequencing and Analysis of Chlorimuron-Ethyl Degrading Bacteria Klebsiella pneumoniae 2N3 - Zhang_2019_Int.J.Mol.Sci_20_
Author(s) : Zhang C , Hao Q , Zhang Z , Zhang X , Pan H , Zhang J , Zhang H , Sun F
Ref : Int J Mol Sci , 20 : , 2019
Abstract : Klebsiella pneumoniae 2N3 is a strain of gram-negative bacteria that can degrade chlorimuron-ethyl and grow with chlorimuron-ethyl as the sole nitrogen source. The complete genome of Klebsiella pneumoniae 2N3 was sequenced using third generation high-throughput DNA sequencing technology. The genomic size of strain 2N3 was 5.32 Mb with a GC content of 57.33% and a total of 5156 coding genes and 112 non-coding RNAs predicted. Two hydrolases expressed by open reading frames (ORFs) 0934 and 0492 were predicted and experimentally confirmed by gene knockout to be involved in the degradation of chlorimuron-ethyl. Strains of DeltaORF 0934, DeltaORF 0492, and wild type (WT) reached their highest growth rates after 8-10 hours in incubation. The degradation rates of chlorimuron-ethyl by both DeltaORF 0934 and DeltaORF 0492 decreased in comparison to the WT during the first 8 hours in culture by 25.60% and 24.74%, respectively, while strains DeltaORF 0934, DeltaORF 0492, and the WT reached the highest degradation rates of chlorimuron-ethyl in 36 hours of 74.56%, 90.53%, and 95.06%, respectively. This study provides scientific evidence to support the application of Klebsiella pneumoniae 2N3 in bioremediation to control environmental pollution.
ESTHER : Zhang_2019_Int.J.Mol.Sci_20_
PubMedSearch : Zhang_2019_Int.J.Mol.Sci_20_
PubMedID: 31234527
Gene_locus related to this paper: klep7-a6tb98 , klep7-mhpc

Title : Alterations of drug-metabolizing enzymes and transporters under diabetic conditions: what is the potential clinical significance? - Chen_2018_Drug.Metab.Rev__1
Author(s) : Chen F , Li DY , Zhang B , Sun JY , Sun F , Ji X , Qiu JC , Parker RB , Laizure SC , Xu J
Ref : Drug Metabolism Reviews , :1 , 2018
Abstract : There will be 642 million people worldwide by 2040 suffering from diabetes mellitus. Long-term multidrug therapy aims to achieve normal glycemia and minimize complications, and avoid severe hypoglycemic events. The appreciation of the drug-metabolizing enzymes and drug transporters as critical players in the treatment of diabetes has attracted much attention regarding their potential alterations in the pathogenesis of the disease. This review discusses pharmacokinetics-based alterations of cytochrome P450 enzymes, phase-II metabolizing enzymes, and membrane transporter proteins, as well as the potential mechanisms underlying these alterations. We also discuss the potential influences of altered enzymes and transporters on the disposition of commonly prescribed glucose-lowering medicines. Future studies should delve into the impact of altered drug-metabolizing enzymes and transporters on the progression toward abnormal glucose homeostasis.
ESTHER : Chen_2018_Drug.Metab.Rev__1
PubMedSearch : Chen_2018_Drug.Metab.Rev__1
PubMedID: 30221555

Title : Deglucosylation of zearalenone-14-glucoside in animals and human liver leads to underestimation of exposure to zearalenone in humans - Yang_2018_Arch.Toxicol_92_2779
Author(s) : Yang S , Zhang H , Zhang J , Li Y , Jin Y , Zhang S , De Saeger S , Zhou J , Sun F , De Boevre M
Ref : Archives of Toxicology , 92 :2779 , 2018
Abstract : Zearalenone-14-glucoside (ZEN-14G), the modified mycotoxin of zearalenone (ZEN), has attracted considerable attention due to its high potential to be hydrolyzed into ZEN, which would exert toxicity. It has been confirmed that the microflora could metabolize ZEN-14G to ZEN. However, the metabolic profile of ZEN-14G and whether it could be deglucosidated in the liver are unknown. To thoroughly investigate the metabolism of ZEN-14G, in vitro metabolism including phase I and phase II metabolism was studied using liquid chromatography coupled to high-resolution mass spectrometry. Additionally, in vivo metabolism of ZEN-14G was conducted in model animals, rats, by oral administration. As a result, 29 phase I metabolites and 6 phase II metabolites were identified and significant inter-species metabolic differences were observed as well. What is more, ZEN-14G could be considerably deglucosidated into its free form of ZEN after the incubation with animals and human liver microsomes in the absence of NADPH, which was mainly metabolized by human carboxylesterase CES-I and II. Furthermore, results showed that the major metabolic pathways of ZEN-14G were deglucosylation, hydroxylation, hydrogenation and glucuronidation. Although interspecies differences in the biotransformation of ZEN-14G were observed, ZEN, alpha-ZEL-14G, beta-ZEL-14G, alpha-ZEL, ZEN-14G-16GlcA and ZEN-14GlcA were the major metabolites of ZEN-14G. Additionally, a larger yield of 6-OH-ZEN-14G and 8-OH-ZEN-14G was also observed in human liver microsomes. The obtained data would be of great importance for the safety assessment of modified mycotoxin, ZEN-14G, and provide another perspective for risk assessment of mycotoxin.
ESTHER : Yang_2018_Arch.Toxicol_92_2779
PubMedSearch : Yang_2018_Arch.Toxicol_92_2779
PubMedID: 30019167

Title : Butyrylcholinesterase nanocapsule as a long circulating bioscavenger with reduced immune response - Zhang_2016_J.Control.Release_230_73
Author(s) : Zhang P , Jain P , Tsao C , Sinclair A , Sun F , Hung HC , Bai T , Wu K , Jiang S
Ref : J Control Release , 230 :73 , 2016
Abstract : Butyrylcholinesterase (BChE) is the most promising bioscavenger candidate to treat or prevent organophosphate (OP) poisoning. However, the clinical application of BChE is limited by two obstacles: an inadequate circulation half-life and limited sources for production. Although several modification technologies including glycosylation and PEGylation have been developed to improve its pharmacokinetics, none of them have been able to outperform blood-derived native BChE. In this work, we designed a long-circulating bioscavenger nanogel by coating equine serum-derived BChE with a zwitterionic polymer gel layer. This zwitterionic gel coating protected BChE from denaturation and degradation under harsh conditions. Notably, the nanocapsule exhibited a long circulation half-life of ~45h, a three-fold increase from the unmodified native version, enabling both therapeutic and prophylactic applications. In addition, the gel coating reduced the immunogenicity of equine BChE, unlocking the possibility to use non-human derived BChE as an OP bioscavenger in humans.
ESTHER : Zhang_2016_J.Control.Release_230_73
PubMedSearch : Zhang_2016_J.Control.Release_230_73
PubMedID: 27063423

Title : Identification of new binding sites of human transferrin incubated with organophosphorus agents via Q Exactive LC-MS\/MS - Sun_2016_J.Chromatogr.B.Analyt.Technol.Biomed.Life.Sci_1022_256
Author(s) : Sun F , Ding J , Yu H , Gao R , Wang H , Pei C
Ref : Journal of Chromatography B Analyt Technol Biomed Life Sciences , 1022 :256 , 2016
Abstract : Organophosphorus agents (OPs) like sarin, VX, or soman could inhibit acetylcholinesterase activity and cause poisoning. OPs could bind many proteins, such as butyrylcholinesterase and albumin, and the adducts formed could identify the exposure. In this paper, we studied human transferrin, which was one of the proteins that could be labeled by OPs. Pure human transferrin was incubated with an overdose of organophosphorus agents, including sarin, soman, VX, tabun, cyclosarin, ethyl tabun, and propyl tabun, and then additional OPs was removed through dialysis. Trypsin was used to cleave the OP-treated proteins and Q Exactive liquid chromatography tandem mass spectrometry (Q Exactive LC-MS/MS) was used to identify them. The present study set out to accomplish two goals. The first goal was to find a good method for identifying multiple binding sites on a given protein through Q Exactive LC-MS/MS. The second goal was to investigate the labeled peptides when transferrin was incubated with a numerous molar excess of OPs. Results showed that tyrosine, lysine, and serine formed covalent bonds with OPs. Twenty OP-labeled sites were found: ten tyrosine sites (including two reported sites), seven lysine sites, and three serine sites. Characteristic fragments for labeled-tyrosine and labeled-lysine adducts were summarized in detail. In conclusion, the method by Q Exactive LC-MS/MS using in this present work is a good way to diagnose exposure to OPs accurately when the binding sites of OPs are uncertain. Novel modified peptides and the characteristic ions found in this work could help investigators assess exposure to OPs.
ESTHER : Sun_2016_J.Chromatogr.B.Analyt.Technol.Biomed.Life.Sci_1022_256
PubMedSearch : Sun_2016_J.Chromatogr.B.Analyt.Technol.Biomed.Life.Sci_1022_256
PubMedID: 27128859

Title : Aestuariivita atlantica sp. nov., isolated from deep-sea sediment - Li_2015_Int.J.Syst.Evol.Microbiol_65_3281
Author(s) : Li G , Lai Q , Du Y , Liu X , Sun F , Shao Z
Ref : Int J Syst Evol Microbiol , 65 :3281 , 2015
Abstract : A novel strain, 22II-S11-z3T, was isolated from the deep-sea sediment of the Atlantic Ocean. The bacterium was aerobic, Gram-staining-negative, oxidase-positive and catalase-negative, oval- to rod-shaped, and non-motile. Growth was observed at salinities of 1-9 % NaCl and temperatures of 10-45 degrees C. The isolate could hydrolyse aesculin and Tweens 20, 40 and 80, but not gelatin. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 22II-S11-z3T belonged to the genus Aestuariivita, with highest sequence similarity to Aestuariivita boseongensis KCTC 42052T (97.5 %). The average nucleotide identity and digital DNA-DNA hybridization values between strain 22II-S11-z3T and A. boseongensis KCTC 42052T were 71.5 % and 20.0 +/- 2.3 %, respectively. The G+C content of the chromosomal DNA was 65.5 mol%. The principal fatty acids (>5 %) were summed feature 8 (C18 : 1omega7c/omega6c) (35.2 %), C19 : 0 cyclo omega8c (20.9 %), C16 : 0 (11.8 %), 11-methyl C18 : 1omega7c (11.4 %) and C12 : 1 3-OH (9.4 %). The respiratory quinone was determined to be Q-10. Diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, nine unidentified phospholipids, one unidentified aminolipid and two unidentified lipids were present. The combined genotypic and phenotypic data show that strain 22II-S11-z3T represents a novel species of the genus Aestuariivita, for which the name Aestuariivita atlantica sp. nov. is proposed, with the type strain 22II-S11-z3T ( = KCTC 42276T = MCCC 1A09432T).
ESTHER : Li_2015_Int.J.Syst.Evol.Microbiol_65_3281
PubMedSearch : Li_2015_Int.J.Syst.Evol.Microbiol_65_3281
PubMedID: 26297013
Gene_locus related to this paper: 9rhob-a0a0l1ju54

Title : Pseudooceanicola atlanticus gen. nov. sp. nov., isolated from surface seawater of the Atlantic Ocean and reclassification of Oceanicola batsensis, Oceanicola marinus, Oceanicola nitratireducens, Oceanicola nanhaiensis, Oceanicola antarcticus and Oceanicola flagellatus, as Pseudooceanicola batsensis comb. nov., Pseudooceanicola marinus comb. nov., Pseudooceanicola nitratireducens comb. nov., Pseudooceanicola nanhaiensis comb. nov., Pseudooceanicola antarcticus comb. nov., and Pseudooceanicola flagellatus comb. nov - Lai_2015_Antonie.Van.Leeuwenhoek_107_1065
Author(s) : Lai Q , Li G , Liu X , Du Y , Sun F , Shao Z
Ref : Antonie Van Leeuwenhoek , 107 :1065 , 2015
Abstract : A taxonomic study was carried out on strain 22II-S11g(T), which was isolated from the surface seawater of the Atlantic Ocean. The bacterium was found to be Gram-negative, rod shaped without flagellum, oxidase positive and weakly catalase positive. Growth was observed at NaCl concentrations of 0.5-9 % and at temperatures of 10-41 degrees C. The isolate was incapable of gelatin hydrolysis and unable to reduce nitrate to nitrite, degrade aesculin and Tween 80. On the basis of 16S rRNA gene sequence similarity, strain 22II-S11g(T) was found to be most closely related to Oceanicola batsensis HTCC2597(T) (97.26 %), followed by Oceanicola nitratireducens JLT1210(T) (96.39 %), whilst other species of genus Oceanicola shared 94.00-96.34 % sequence similarity. However, it showed low similarity to Oceanicola granulosus HTCC2516(T) (94.79 %), the type species of the genus Oceanicola. Phylogenetic analysis showed that strain 22II-S11g(T) formed a clade with six species currently classified in the genus Oceanicola, but strain O. granulosus HTCC2516(T) and strain O. litoreus M-M22(T) clustered with two other genera respectively. The ANI values between strain 22II-S11g(T) and two type strains (O. batsensis HTCC2597(T) and O. granulosus HTCC2516(T)) are 91.86 and 91.81 % respectively. The digital DNA-DNA hybridization estimate values between strain 22II-S11g(T) and two type strains (O. batsensis HTCC2597(T) and O. granulosus HTCC2516(T)) are 23.4 +/- 2.4 and 20.0 +/- 2.3 %, respectively. The principal fatty acids were identified as summed feature 8 (C18:1 omega7c/omega6c), C16:0, C18:1 omega7c11-methyl and C12:0 3OH. The G+C content determined from the draft genome sequence is 64.1 mol%. The respiratory quinone was determined to be Q-10 (100 %). Phosphatidylethanolamine, phosphatidylglycerol, an aminolipid, phosphatidylcholine, a phospholipid and three lipids were identified in the polar lipids. The combined genotypic and phenotypic data also show that strain 22II-S11g(T) should not be assigned to the genus Oceanicola; consequently strain 22II-S11g(T) is concluded to represent a novel species of a novel genus in the family Rhodobacteraceae, for which the name Pseudooceanicola atlanticus gen. nov., sp. nov. is proposed (type strain 22II-S11g(T) = KCTC 42004(T) = LMG 27424(T) = MCCC 1A09160(T)). Six misclassified species should be transferred to the novel genus Pseudooceanicola as follows: O. batsensis should be transferred to the genus Pseudooceanicola as Pseudooceanicola batsensis comb. nov. (type strain HTCC2597(T) = ATCC BAA-863(T) = DSM 15984(T) = KCTC 12145(T)); Oceanicola marinus should be transferred to the genus Pseudooceanicola as Pseudooceanicola marinus comb. nov. (type strain AZO-C(T) = LMG 23705(T) = BCRC 17591(T)); O. nitratireducens should be transferred to the genus Pseudooceanicola as Pseudooceanicola nitratireducens comb. nov. (type strain JLT1210(T) = LMG 24663(T) = CGMCC 1.7292(T)); Oceanicola nanhaiensis should be transferred to the genus Pseudooceanicola as Pseudooceanicola nanhaiensis comb. nov. (type strain SS011B1-20(T) = LMG 23508(T) = CGMCC 1.6293(T)); Oceanicola antarcticus should be transferred to the genus Pseudooceanicola as Pseudooceanicola antarcticus comb. nov. (type strain Ar-45(T) = CGMCC 1.12662(T) = LMG 27868(T)); and Oceanicola flagellatus should be transferred to the genus Pseudooceanicola as Pseudooceanicola flagellatus comb. nov. (type strain DY470(T) = CGMCC 1.12664(T) = LMG 27871(T)).
ESTHER : Lai_2015_Antonie.Van.Leeuwenhoek_107_1065
PubMedSearch : Lai_2015_Antonie.Van.Leeuwenhoek_107_1065
PubMedID: 25663028
Gene_locus related to this paper: 9rhob-a0a0a0eep0

Title : Selective blockade of the hydrolysis of the endocannabinoid 2-arachidonoylglycerol impairs learning and memory performance while producing antinociceptive activity in rodents - Griebel_2015_Sci.Rep_5_7642
Author(s) : Griebel G , Pichat P , Beeske S , Leroy T , Redon N , Jacquet A , Francon D , Bert L , Even L , Lopez-Grancha M , Tolstykh T , Sun F , Yu Q , Brittain S , Arlt H , He T , Zhang B , Wiederschain D , Bertrand T , Houtmann J , Rak A , Vallee F , Michot N , Auge F , Menet V , Bergis OE , George P , Avenet P , Mikol V , Didier M , Escoubet J
Ref : Sci Rep , 5 :7642 , 2015
Abstract : Monoacylglycerol lipase (MAGL) represents a primary degradation enzyme of the endogenous cannabinoid (eCB), 2-arachidonoyglycerol (2-AG). This study reports a potent covalent MAGL inhibitor, SAR127303. The compound behaves as a selective and competitive inhibitor of mouse and human MAGL, which potently elevates hippocampal levels of 2-AG in mice. In vivo, SAR127303 produces antinociceptive effects in assays of inflammatory and visceral pain. In addition, the drug alters learning performance in several assays related to episodic, working and spatial memory. Moreover, long term potentiation (LTP) of CA1 synaptic transmission and acetylcholine release in the hippocampus, two hallmarks of memory function, are both decreased by SAR127303. Although inactive in acute seizure tests, repeated administration of SAR127303 delays the acquisition and decreases kindled seizures in mice, indicating that the drug slows down epileptogenesis, a finding deserving further investigation to evaluate the potential of MAGL inhibitors as antiepileptics. However, the observation that 2-AG hydrolysis blockade alters learning and memory performance, suggests that such drugs may have limited value as therapeutic agents.
ESTHER : Griebel_2015_Sci.Rep_5_7642
PubMedSearch : Griebel_2015_Sci.Rep_5_7642
PubMedID: 25560837
Gene_locus related to this paper: mouse-ABHD6

Title : Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution - Li_2015_Nat.Biotechnol_33_524
Author(s) : Li F , Fan G , Lu C , Xiao G , Zou C , Kohel RJ , Ma Z , Shang H , Ma X , Wu J , Liang X , Huang G , Percy RG , Liu K , Yang W , Chen W , Du X , Shi C , Yuan Y , Ye W , Liu X , Zhang X , Liu W , Wei H , Wei S , Zhu S , Zhang H , Sun F , Wang X , Liang J , Wang J , He Q , Huang L , Cui J , Song G , Wang K , Xu X , Yu JZ , Zhu Y , Yu S
Ref : Nat Biotechnol , 33 :524 , 2015
Abstract : Gossypium hirsutum has proven difficult to sequence owing to its complex allotetraploid (AtDt) genome. Here we produce a draft genome using 181-fold paired-end sequences assisted by fivefold BAC-to-BAC sequences and a high-resolution genetic map. In our assembly 88.5% of the 2,173-Mb scaffolds, which cover 89.6% approximately 96.7% of the AtDt genome, are anchored and oriented to 26 pseudochromosomes. Comparison of this G. hirsutum AtDt genome with the already sequenced diploid Gossypium arboreum (AA) and Gossypium raimondii (DD) genomes revealed conserved gene order. Repeated sequences account for 67.2% of the AtDt genome, and transposable elements (TEs) originating from Dt seem more active than from At. Reduction in the AtDt genome size occurred after allopolyploidization. The A or At genome may have undergone positive selection for fiber traits. Concerted evolution of different regulatory mechanisms for Cellulose synthase (CesA) and 1-Aminocyclopropane-1-carboxylic acid oxidase1 and 3 (ACO1,3) may be important for enhanced fiber production in G. hirsutum.
ESTHER : Li_2015_Nat.Biotechnol_33_524
PubMedSearch : Li_2015_Nat.Biotechnol_33_524
PubMedID: 25893780
Gene_locus related to this paper: gosra-a0a0d2rxs2 , gosra-a0a0d2tng2 , gosra-a0a0d2twz7 , goshi-a0a1u8hr03 , gosra-a0a0d2vdc5 , goshi-a0a1u8ljh5 , gosra-a0a0d2vj24 , goshi-a0a1u8pxd3 , gosra-a0a0d2sr31 , goshi-a0a1u8knd1 , goshi-a0a1u8nhw9 , goshi-a0a1u8mt09 , goshi-a0a1u8kis4 , goshi-a0a1u8ibk3 , goshi-a0a1u8ieg2 , goshi-a0a1u8iki6 , goshi-a0a1u8jvp4 , goshi-a0a1u8jw35 , gosra-a0a0d2pzd7 , goshi-a0a1u8ied7

Title : Tamlana nanhaiensis sp. nov., isolated from surface seawater collected from the South China Sea - Liu_2015_Antonie.Van.Leeuwenhoek_107_1189
Author(s) : Liu X , Lai Q , Du Y , Li G , Sun F , Shao Z
Ref : Antonie Van Leeuwenhoek , 107 :1189 , 2015
Abstract : A polyphasic taxonomic study was performed on a strain, designated FHC16(T), which was isolated from surface seawater collected from the South China Sea. Cells of strain FHC16(T) are Gram stain-negative, oxidase- and catalase-positive and non-motile rods. Growth was observed at 15-37 degreesC (optimum, 25-30 degreesC), at pH 6.0-9.0 (optimum, pH 7.0) and in the presence of 0-5 % (w/v) NaCl (optimum, 3%). 16S rRNA gene sequence analysis showed that strain FHC16(T) is most closely related to Tamlana sedimentorum JCM 19808(T) (98.2% sequence similarity). The ANI value between strain FHC16(T) and T. sedimentorum JCM 19808(T) was found to be 81.82-81.81%. The DNA-DNA hybridization estimated value between strain FHC16(T) and T. sedimentorum JCM 19808(T) was determined to be 25.8 +/- 2.41%. The principal fatty acids (>5% of the total) were found to be iso-C(15:0), iso G-C(15:1), iso-C(17:0) 3-OH, iso-C(15:0) 3-OH and summed feature 3 (comprising C(16:1)omega7c/C(16:1)omega6c). The strain was found to have MK-6 as the major respiratory menaquinone, which is consistent with the other three recognized Tamlana species, T. sedimentorum, Tamlana crocina and Tamlana agarivorans. The polar lipids were found to comprise phosphatidylethanolamine, one unidentified aminophospholipid, two unidentified aminolipids and seven unidentified lipids. The G+C content of the chromosomal DNA was determined to be 34.2 mol%. On the basis of phenotypic, chemotaxonomic and molecular data, strain FHC16(T) is considered to represent a novel species of the genus Tamlana, for which the name Tamlana nanhaiensis sp. nov. is proposed. The type strain is FHC16(T) (.LMG 27420(T) = CGMCC 1.12469(T) = MCCC 1A06648(T)).
ESTHER : Liu_2015_Antonie.Van.Leeuwenhoek_107_1189
PubMedSearch : Liu_2015_Antonie.Van.Leeuwenhoek_107_1189
PubMedID: 25735434
Gene_locus related to this paper: 9flao-a0a0d7w993

Title : Molecular traces of alternative social organization in a termite genome - Terrapon_2014_Nat.Commun_5_3636
Author(s) : Terrapon N , Li C , Robertson HM , Ji L , Meng X , Booth W , Chen Z , Childers CP , Glastad KM , Gokhale K , Gowin J , Gronenberg W , Hermansen RA , Hu H , Hunt BG , Huylmans AK , Khalil SM , Mitchell RD , Munoz-Torres MC , Mustard JA , Pan H , Reese JT , Scharf ME , Sun F , Vogel H , Xiao J , Yang W , Yang Z , Zhou J , Zhu J , Brent CS , Elsik CG , Goodisman MA , Liberles DA , Roe RM , Vargo EL , Vilcinskas A , Wang J , Bornberg-Bauer E , Korb J , Zhang G , Liebig J
Ref : Nat Commun , 5 :3636 , 2014
Abstract : Although eusociality evolved independently within several orders of insects, research into the molecular underpinnings of the transition towards social complexity has been confined primarily to Hymenoptera (for example, ants and bees). Here we sequence the genome and stage-specific transcriptomes of the dampwood termite Zootermopsis nevadensis (Blattodea) and compare them with similar data for eusocial Hymenoptera, to better identify commonalities and differences in achieving this significant transition. We show an expansion of genes related to male fertility, with upregulated gene expression in male reproductive individuals reflecting the profound differences in mating biology relative to the Hymenoptera. For several chemoreceptor families, we show divergent numbers of genes, which may correspond to the more claustral lifestyle of these termites. We also show similarities in the number and expression of genes related to caste determination mechanisms. Finally, patterns of DNA methylation and alternative splicing support a hypothesized epigenetic regulation of caste differentiation.
ESTHER : Terrapon_2014_Nat.Commun_5_3636
PubMedSearch : Terrapon_2014_Nat.Commun_5_3636
PubMedID: 24845553
Gene_locus related to this paper: zoone-a0a067r283 , zoone-a0a067qst6 , zoone-a0a067rbc7 , zoone-a0a067qz43 , zoone-a0a067qn94 , zoone-a0a067rbw9 , zoone-a0a067qx93 , zoone-a0a067rcf4 , zoone-a0a067r8q8 , zoone-a0a067rh81 , zoone-a0a067r506 , zoone-a0a067qxd4 , zoone-a0a067qy86 , zoone-a0a067qsw2 , zoone-a0a067qfp9 , zoone-a0a067ru91 , zoone-a0a067rwu7 , zoone-a0a067rmu8 , zoone-a0a067r773 , zoone-a0a067qlt8 , zoone-a0a067qhm6 , zoone-a0a067qjz2 , zoone-a0a067qs20 , zoone-a0a067rmu4 , zoone-a0a067qty7 , zoone-a0a067rk35 , zoone-a0a067rk64 , zoone-a0a067rj74 , zoone-a0a067rp97 , zoone-a0a067rjm1

Title : Roseivivax atlanticus sp. nov., isolated from surface seawater of the Atlantic Ocean - Li_2014_Antonie.Van.Leeuwenhoek_105_863
Author(s) : Li G , Lai Q , Liu X , Sun F , Shao Z
Ref : Antonie Van Leeuwenhoek , 105 :863 , 2014
Abstract : A taxonomic study was carried out on strain 22II-S10s(T), which was isolated from the surface seawater of the Atlantic Ocean. The bacterium was found to be Gram-negative, oxidase and catalase positive, rod shaped and motile by subpolar flagella. The isolate was capable of gelatine hydrolysis but unable to reduce nitrate to nitrite or degrade Tween 80 or aesculin. Growth was observed at salinities of 0.5-18 % (optimum, 2-12 %), at pH of 3-10 (optimum, 7) and at temperatures of 10-41 degrees C (optimum 28 degrees C). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 22II-S10s(T) belongs to the genus Roseivivax, with highest sequence similarity to Roseivivax halodurans JCM 10272(T) (97.2 %), followed by Roseivivax isoporae LMG 25204(T) (97.0 %); other species of genus Roseivivax shared 95.2-96.7 % sequence similarity. The DNA-DNA hybridization estimate values between strain 22II-S10s(T) and the two type strains (R. halodurans JCM 10272(T) and R. isoporae LMG 25204(T)) were 22.00 and 21.40 %. The principal fatty acids were identified as Summed Feature 8 (C18:1 omega7c/omega6c) (67.4 %), C18:0 (7.2 %), C19:0 cyclo omega8c (7.1 %), C18:1 omega7c 11-methyl (6.8 %) and C16:0 (5.9 %). The respiratory quinone was determined to be Q-10 (100 %). Phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an aminolipid, a glycolipid and three phospholipids were present. The G+C content of the chromosomal DNA was determined to be 67.5 mol%. The combined genotypic and phenotypic data show that strain 22II-S10s(T) represents a novel species within the genus Roseivivax, for which the name Roseivivax atlanticus sp. nov. is proposed, with the type strain 22II-S10s(T) (= MCCC 1A09150(T) = LMG 27156(T)).
ESTHER : Li_2014_Antonie.Van.Leeuwenhoek_105_863
PubMedSearch : Li_2014_Antonie.Van.Leeuwenhoek_105_863
PubMedID: 24567080
Gene_locus related to this paper: 9rhob-w4hpi1 , 9rhob-w4hj54 , 9rhob-w4hpb0

Title : Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome - Chalhoub_2014_Science_345_950
Author(s) : Chalhoub B , Denoeud F , Liu S , Parkin IA , Tang H , Wang X , Chiquet J , Belcram H , Tong C , Samans B , Correa M , Da Silva C , Just J , Falentin C , Koh CS , Le Clainche I , Bernard M , Bento P , Noel B , Labadie K , Alberti A , Charles M , Arnaud D , Guo H , Daviaud C , Alamery S , Jabbari K , Zhao M , Edger PP , Chelaifa H , Tack D , Lassalle G , Mestiri I , Schnel N , Le Paslier MC , Fan G , Renault V , Bayer PE , Golicz AA , Manoli S , Lee TH , Thi VH , Chalabi S , Hu Q , Fan C , Tollenaere R , Lu Y , Battail C , Shen J , Sidebottom CH , Canaguier A , Chauveau A , Berard A , Deniot G , Guan M , Liu Z , Sun F , Lim YP , Lyons E , Town CD , Bancroft I , Meng J , Ma J , Pires JC , King GJ , Brunel D , Delourme R , Renard M , Aury JM , Adams KL , Batley J , Snowdon RJ , Tost J , Edwards D , Zhou Y , Hua W , Sharpe AG , Paterson AH , Guan C , Wincker P
Ref : Science , 345 :950 , 2014
Abstract : Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72x genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.
ESTHER : Chalhoub_2014_Science_345_950
PubMedSearch : Chalhoub_2014_Science_345_950
PubMedID: 25146293
Gene_locus related to this paper: braol-Q8GTM3 , braol-Q8GTM4 , brana-a0a078j4a9 , brana-a0a078e1m0 , brana-a0a078cd75 , brana-a0a078evd3 , brana-a0a078j4f0 , brana-a0a078cta5 , brana-a0a078cus4 , brana-a0a078f8c2 , brana-a0a078jql1 , brana-a0a078dgj3 , brana-a0a078hw50 , brana-a0a078cuu0 , brana-a0a078iyl8 , brana-a0a078dfa9 , brana-a0a078ic91 , brana-a0a078cnf7 , brana-a0a078fh41 , brana-a0a078ca65 , brana-a0a078ctc8 , brana-a0a078h021 , brana-a0a078h0h8 , brana-a0a078jx23 , brana-a0a078ci96 , brana-a0a078cqd7 , brana-a0a078dh94 , brana-a0a078h612 , brana-a0a078ild2 , brana-a0a078j2t3 , braol-a0a0d3dpb2 , braol-a0a0d3dx76 , brana-a0a078jxa8 , brana-a0a078i2k3 , braol-a0a0d3ef55 , brarp-m4dcj8 , brana-a0a078fw53 , brana-a0a078itf3 , brana-a0a078jsn1 , brana-a0a078jrt9 , brana-a0a078i6d2 , brana-a0a078jku0 , brana-a0a078fss7 , brana-a0a078i1l0 , brana-a0a078i402

Title : Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing - Qi_2014_Nat.Commun_5_4340
Author(s) : Qi X , Li MW , Xie M , Liu X , Ni M , Shao G , Song C , Kay-Yuen Yim A , Tao Y , Wong FL , Isobe S , Wong CF , Wong KS , Xu C , Li C , Wang Y , Guan R , Sun F , Fan G , Xiao Z , Zhou F , Phang TH , Tong SW , Chan TF , Yiu SM , Tabata S , Wang J , Xu X , Lam HM
Ref : Nat Commun , 5 :4340 , 2014
Abstract : Using a whole-genome-sequencing approach to explore germplasm resources can serve as an important strategy for crop improvement, especially in investigating wild accessions that may contain useful genetic resources that have been lost during the domestication process. Here we sequence and assemble a draft genome of wild soybean and construct a recombinant inbred population for genotyping-by-sequencing and phenotypic analyses to identify multiple QTLs relevant to traits of interest in agriculture. We use a combination of de novo sequencing data from this work and our previous germplasm re-sequencing data to identify a novel ion transporter gene, GmCHX1, and relate its sequence alterations to salt tolerance. Rapid gain-of-function tests show the protective effects of GmCHX1 towards salt stress. This combination of whole-genome de novo sequencing, high-density-marker QTL mapping by re-sequencing and functional analyses can serve as an effective strategy to unveil novel genomic information in wild soybean to facilitate crop improvement.
ESTHER : Qi_2014_Nat.Commun_5_4340
PubMedSearch : Qi_2014_Nat.Commun_5_4340
PubMedID: 25004933
Gene_locus related to this paper: soybn-i1k636 , soybn-i1j4c6 , glyso-a0a0b2sjw6 , soybn-a0a0r0i9y7 , soybn-a0a0r0j241 , soybn-i1kfz9 , glyso-a0a0b2rre9 , soybn-i1jx17

Title : Poster: A Type-II positive allosteric modulator of alpha7 nAChRs significantly reduces brain injury and improves neurological function after focal cerebral ischemia in rats -
Author(s) : Uteshev VV , Jin K , Sun F
Ref : Biochemical Pharmacology , 86 :1233 , 2013
PubMedID:

Title : Efficient assembly and annotation of the transcriptome of catfish by RNA-Seq analysis of a doubled haploid homozygote - Liu_2012_BMC.Genomics_13_595
Author(s) : Liu S , Zhang Y , Zhou Z , Waldbieser G , Sun F , Lu J , Zhang J , Jiang Y , Zhang H , Wang X , Rajendran KV , Khoo L , Kucuktas H , Peatman E , Liu Z
Ref : BMC Genomics , 13 :595 , 2012
Abstract : BACKGROUND: Upon the completion of whole genome sequencing, thorough genome annotation that associates genome sequences with biological meanings is essential. Genome annotation depends on the availability of transcript information as well as orthology information. In teleost fish, genome annotation is seriously hindered by genome duplication. Because of gene duplications, one cannot establish orthologies simply by homology comparisons. Rather intense phylogenetic analysis or structural analysis of orthologies is required for the identification of genes. To conduct phylogenetic analysis and orthology analysis, full-length transcripts are essential. Generation of large numbers of full-length transcripts using traditional transcript sequencing is very difficult and extremely costly.
RESULTS: In this work, we took advantage of a doubled haploid catfish, which has two sets of identical chromosomes and in theory there should be no allelic variations. As such, transcript sequences generated from next-generation sequencing can be favorably assembled into full-length transcripts. Deep sequencing of the doubled haploid channel catfish transcriptome was performed using Illumina HiSeq 2000 platform, yielding over 300 million high-quality trimmed reads totaling 27 Gbp. Assembly of these reads generated 370,798 non-redundant transcript-derived contigs. Functional annotation of the assembly allowed identification of 25,144 unique protein-encoding genes. A total of 2,659 unique genes were identified as putative duplicated genes in the catfish genome because the assembly of the corresponding transcripts harbored PSVs or MSVs (in the form of pseudo-SNPs in the assembly). Of the 25,144 contigs with unique protein hits, around 20,000 contigs matched 50% length of reference proteins, and over 14,000 transcripts were identified as full-length with complete open reading frames. The characterization of consensus sequences surrounding start codon and the stop codon confirmed the correct assembly of the full-length transcripts.
CONCLUSIONS: The large set of transcripts assembled in this study is the most comprehensive set of genome resources ever developed from catfish, which will provide the much needed resources for functional genome research in catfish, serving as a reference transcriptome for genome annotation, analysis of gene duplication, gene family structures, and digital gene expression analysis. The putative set of duplicated genes provide a starting point for genome scale analysis of gene duplication in the catfish genome, and should be a valuable resource for comparative genome analysis, genome evolution, and genome function studies.
ESTHER : Liu_2012_BMC.Genomics_13_595
PubMedSearch : Liu_2012_BMC.Genomics_13_595
PubMedID: 23127152
Gene_locus related to this paper: ictpu-w5u6j2 , ictpu-w5ub99 , ictpu-w5uc03 , ictpu-w5utq3 , ictpu-w5u610 , ictpu-w5ui62 , ictpu-w5uj33 , ictpu-w5u9s1 , ictpu-a0a2d0rtv8 , ictpu-w5uf93 , ictpu-w5u6h4 , ictpu-a0a2d0qam4 , ictpu-w5u7r0 , ictpu-w5ugq3

Title : Crystal structure of a novel esterase Rv0045c from Mycobacterium tuberculosis - Zheng_2011_PLoS.One_6_e20506
Author(s) : Zheng X , Guo J , Xu L , Li H , Zhang D , Zhang K , Sun F , Wen T , Liu S , Pang H
Ref : PLoS ONE , 6 :e20506 , 2011
Abstract : There are at least 250 enzymes in Mycobacterium tuberculosis (M. tuberculosis) involved in lipid metabolism. Some of the enzymes are required for bacterial survival and full virulence. The esterase Rv0045c shares little amino acid sequence similarity with other members of the esterase/lipase family. Here, we report the 3D structure of Rv0045c. Our studies demonstrated that Rv0045c is a novel member of alpha/beta hydrolase fold family. The structure of esterase Rv0045c contains two distinct domains: the alpha/beta fold domain and the cap domain. The active site of esterase Rv0045c is highly conserved and comprised of two residues: Ser154 and His309. We proposed that Rv0045c probably employs two kinds of enzymatic mechanisms when hydrolyzing C-O ester bonds within substrates. The structure provides insight into the hydrolysis mechanism of the C-O ester bond, and will be helpful in understanding the ester/lipid metabolism in M. tuberculosis.
ESTHER : Zheng_2011_PLoS.One_6_e20506
PubMedSearch : Zheng_2011_PLoS.One_6_e20506
PubMedID: 21637775
Gene_locus related to this paper: myctu-RV0045C

Title : Crystallization and preliminary X-ray analysis of a novel esterase Rv0045c from Mycobacterium tuberculosis. - Xu_2010_Acta.Crystallogr.Sect.F.Struct.Biol.Cryst.Commun_66_1579
Author(s) : Xu L , Guo J , Zheng X , Wen T , Sun F , Liu S , Pang H
Ref : Acta Crystallographica Sect F Struct Biol Cryst Commun , 66 :1579 , 2010
Abstract : The Rv0045c protein is predicted to be an esterase that is involved in lipid metabolism in Mycobacterium tuberculosis. The protein was overproduced in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. The Rv0045c protein crystals diffracted to a resolution of 2.7A using a synchrotron-radiation source and belonged to space group P3(1) or P3(2), with unit-cell parameters a=b=73.465, c=48.064A, alpha=beta=90, =120deg. Purified SeMet-labelled Rv0045c protein was also crystallized and formed crystals that diffracted to a resolution of 3.0A using an in-house X-ray radiation source.
ESTHER : Xu_2010_Acta.Crystallogr.Sect.F.Struct.Biol.Cryst.Commun_66_1579
PubMedSearch : Xu_2010_Acta.Crystallogr.Sect.F.Struct.Biol.Cryst.Commun_66_1579
PubMedID: 21139199
Gene_locus related to this paper: myctu-RV0045C

Title : Open-loop and closed-loop optokinetic nystagmus (OKN) in myasthenia gravis and nonmyasthenic subjects - Yang_2000_Exp.Neurol_166_166
Author(s) : Yang Q , Wei M , Sun F , Tian J , Chen X , Lu C
Ref : Experimental Neurology , 166 :166 , 2000
Abstract : Optokinetic nystagmus (OKN) eye movements of myasthenia gravis (MG) and nonmyasthenic ocular palsies, and normal subjects were examined under closed-loop and open-loop conditions. The open-loop OKN condition was achieved by adding the signal of eye-movement velocity of OKN to the computer-generated signal controlling the stimulus grating moving. The OKN was recorded by means of electromagnetic search scleral coil technique. In MG patients, the open-loop gains of OKN increased significantly after the intramuscular injection of an acetylcholinesterase inhibitor, neostigmine, while the closed-loop OKN gains were not significantly changed. Both the closed-loop and open-loop OKN gains of normal subjects and nonmyasthenic patients were not increased for the administration of neostigmine. The experimental results indicated that the open-loop OKN gain could be sensitive to reflect the changes of the function of neuromuscular junction in MG patients.
ESTHER : Yang_2000_Exp.Neurol_166_166
PubMedSearch : Yang_2000_Exp.Neurol_166_166
PubMedID: 11031092