Tang H


Full name : Tang Hui

First name : Hui

Mail : Dept. of Ph anna co logy, Mayo Clinic, 200 First Street SW, Rochester, MN 55905

Zip Code :

City :

Country : USA

Email : tang.hui@mayo.edu

Phone : 507-284-3109

Fax : 507-284-9111

Website :

Directory :

References (55)

Title : A novel pomegranate-inspired bifunctional electrode materials design for acetylcholinesterase biosensor and methanol oxidation reaction - Wei_2022_Bioelectrochemistry_145_108094
Author(s) : Wei W , Tang H , Dong S , Fu Y , Huang T
Ref : Bioelectrochemistry , 145 :108094 , 2022
Abstract : A pomegranate-inspired bifunctional electrode material based on Ni/NiO nanoparticle embedded in nitrogen-doped, partially graphitized carbon framework (Ni/NiO@NPGC) was designed and prepared for the construction of novel electrochemical biosensor and methanol oxidation reaction (MOR). Profiting from itsspecialstructureandfunction, Ni/NiO@NPGC was employed as a matrix immobilizing acetylcholinesterase (AChE) for methyl parathion (MP) sensor. The developed biosensor was proved to have wide linear range (1.0 x 10(-14)-1.0 x 10(-8) g mL(-1)), low detection limit (3.5 x 10(-15) g mL(-1)), and good stability for the determination of MP in practical samples. In addition, the Ni/NiO@NPGC electrode exhibited high electrocatalytic activity (specific activity 73.1 mA cm(-2)) and durability for the MOR in alkaline medium. The results were mainly attributed to the pomegranate-like architecture structure with pyridinic N and carbon frame of Ni/NiO@NPGC, which ensured the electrochemical activities of all nanoparticles and immobilization of enzyme. In addition, the metal oxide was well dispersed to prevent from self-agglomeration and kept mass transfer paths. The work provides a reference for the development of high-performance bifunctional electrode material for the biosensor and MOR.
ESTHER : Wei_2022_Bioelectrochemistry_145_108094
PubMedSearch : Wei_2022_Bioelectrochemistry_145_108094
PubMedID: 35299151

Title : The potential of natural sources for pancreatic lipase inhibitors: a solution of the obesity crisis? -
Author(s) : Hou XD , Qin XY , Hou J , Tang H , Ge GB
Ref : Expert Opin Drug Discov , :1 , 2022
PubMedID: 36508256

Title : Discovery and Characterization of the Naturally Occurring Inhibitors Against Human Pancreatic Lipase in Ampelopsis grossedentata - Qin_2022_Front.Nutr_9_844195
Author(s) : Qin XY , Hou XD , Zhu GH , Xiong Y , Song YQ , Zhu L , Zhao DF , Jia SN , Hou J , Tang H , Ge GB
Ref : Front Nutr , 9 :844195 , 2022
Abstract : Pancreatic lipase (PL) inhibitor therapy has been validated as an efficacious way for preventing and treating obesity and overweight. In the past few decades, porcine PL (pPL) is widely used as the enzyme source for screening the PL inhibitors, which generates a wide range of pPL inhibitors. By contrast, the efficacious inhibitors against human PL (hPL) are rarely reported. This study aims to discover the naturally occurring hPL inhibitors from edible herbal medicines (HMs) and to characterize the inhibitory mechanisms of the newly identified hPL inhibitors. Following the screening of the inhibition potentials of more than 100 HMs against hPL, Ampelopsis grossedentata extract (AGE) displayed the most potent hPL inhibition activity. After that, the major constituents in AGE were identified and purified, while their anti-hPL effects were assayed in vitro. The results clearly showed that two abundant constituents in AGE (dihydromyricetin and iso-dihydromyricetin) were moderate hPL inhibitors, while myricetin and quercetin were strong hPL inhibitors [half-maximal inhibitory concentration (IC (50)) values were around 1.5 microM]. Inhibition kinetic analyses demonstrated that myricetin and quercetin potently inhibited hPL-catalyzed near-infrared fluorogenic substrate of human pancreatic lipase (DDAO-ol) hydrolysis in a non-competitive inhibition manner, with K (i) values of 2.04 and 2.33 microM, respectively. Molecular dynamics simulations indicated that myricetin and quercetin could stably bind on an allosteric site of hPL. Collectively, this study reveals the key anti-obesity constituents in AGE and elucidates their inhibitory mechanisms against hPL, which offers convincing evidence to support the anti-obesity and lipid-lowering effects of this edible herb.
ESTHER : Qin_2022_Front.Nutr_9_844195
PubMedSearch : Qin_2022_Front.Nutr_9_844195
PubMedID: 35284458

Title : Novel sampangine derivatives as potent inhibitors of Cu(2+)-mediated amyloid-beta protein aggregation, oxidative stress and inflammation - Zou_2021_Int.J.Biol.Macromol__
Author(s) : Zou XY , Xie RR , Li W , Su CL , Chen YS , Tang H
Ref : Int J Biol Macromol , : , 2021
Abstract : A series of 11-substituted sampangine derivatives have been designed, synthesized, and tested for their ability to inhibit cholinesterase. Their chelating ability and selectivity for Cu(2+) over other biologically relevant metal ions were demonstrated by isothermal titration calorimetry. Their blood-brain barrier permeability was also tested by parallel artificial membrane permeation assay. Among the synthesized derivatives, compound 11 with the strong anti-acetylcholinesterase activity, high blood-brain barrier penetration ability and high binding affinity to Cu(2+) was selected for further research. Western blotting analysis, transmission electron microscopy, DCFH-DA assay and paralysis experiment indicated that compound 11 suppressed the formation of Cu(2+)-Abeta complexes, alleviated the Cu(2+) induced neurotoxicity and inhibited the production of ROS catalyzed by Cu(2+) in Abeta42 transgenic C. elegans. Moreover, compound 11 also inhibited the expressions of proinflammatory cytokines, such as NO, TNF-alpha, IL-6 and IL-1beta, induced by Cu(2+) + Abeta(1-42) in BV2 microglial cells. In general, this work provided new insights into the design and development of potent metal-chelating agents for AD treatment.
ESTHER : Zou_2021_Int.J.Biol.Macromol__
PubMedSearch : Zou_2021_Int.J.Biol.Macromol__
PubMedID: 33476619

Title : Triphenyl phosphate disturbs the lipidome and induces endoplasmic reticulum stress and apoptosis in JEG-3 cells - Wang_2021_Chemosphere_275_129978
Author(s) : Wang Y , Hong J , Shi M , Guo L , Liu L , Tang H , Liu X
Ref : Chemosphere , 275 :129978 , 2021
Abstract : Triphenyl phosphate (TPP) is a frequently used aryl organophosphate flame retardant. Epidemiological studies have shown that TPP and its metabolite diphenyl phosphate (DPP) can accumulate in the placenta, and positively correlated with abnormal birth outcomes. TPP can disturb placental hormone secretion through the peroxisome proliferator-activated receptor gamma (PPARgamma) pathway. However, the extent and mechanism of placental toxicity mediation by TPP remains unknown. In this study, we used JEG-3 cells to investigate the role of PPARgamma-regulated lipid metabolism in TPP-mediated placental toxicity. The results of lipidomic analysis showed that TPP increased the production of triglycerides (TG), fatty acids (FAs), and phosphatidic acid (PA), but decreased the levels of phosphatidylethanol (PE), phosphatidylserine (PS), and sphingomyelin (SM). TG accumulation was accompanied by increased levels of sterol regulatory element binding transcription factor 1 (SREBP1), acetyl-coA carboxylase (ACC), and fatty acid transport protein (CD36). Although PPARgamma and its target CCAAT/enhancer binding proteins (C/EBPalpha) was decreased, the TG content and gene expression of SREBP1, ACC, and CD36 decreased when TPP was co-exposed to the PPARgamma antagonist GW9662. TPP also induced inflammatory responses, endoplasmic reticulum stress (ERS), and cell apoptosis. Expression of genes related to ERS and apoptosis were attenuated by GW9662. Together, these results show that TPP can disturb lipid metabolism and cause lipid accumulation through PPARgamma, induce ERS, and cell apoptosis. Our findings reveal that the developmental toxicity of TPP through placental toxicity should not be ignored.
ESTHER : Wang_2021_Chemosphere_275_129978
PubMedSearch : Wang_2021_Chemosphere_275_129978
PubMedID: 33662732

Title : Synthesis and biological evaluation of novel 8- substituted sampangine derivatives as potent inhibitor of Zn(2+)-Abeta complex mediated toxicity, oxidative stress and inflammation - Xie_2021_Bioorg.Chem_109_104710
Author(s) : Xie RR , Su CL , Li W , Zou XY , Chen YS , Tang H
Ref : Bioorg Chem , 109 :104710 , 2021
Abstract : A series of 8-substituted sampangine derivatives have been designed, synthesized and tested for their ability to inhibit cholinesterase and penetrate the blood-brain barrier. Their chelating ability toward Zn(2+) and other biologically relevant metal ions was also demonstrated by isothermal titration calorimetry. The new derivatives exhibited high acetylcholinesterase inhibitory activity, high blood-brain barrier penetration ability and high chelating selectivity for Zn(2+). Moreover, compound 10 with the strongest binding affinity to Zn(2+) was selected for further research. Western blotting analysis, transmission electron microscopy, DCFH-DA assay and paralysis experiment indicated that compound 10 suppressed the formation of Zn(2+)-Abeta complexes, alleviated the Zn(2+) induced neurotoxicity and inhibited the production of ROS catalyzed by Zn(2+) in Abeta42 transgenic C. elegans. Furthermore, compound 10 also inhibited the expressions of pro-inflammatory cytokines, such as NO, TNF-alpha, IL-6 and IL-1beta, induced by Zn(2+) + Abeta(1-42) in BV2 microglial cells. In general, this work provided new insights into the design and development of potent metal-chelating agents for Alzheimer's disease treatment.
ESTHER : Xie_2021_Bioorg.Chem_109_104710
PubMedSearch : Xie_2021_Bioorg.Chem_109_104710
PubMedID: 33611137

Title : Pentacyclic triterpenoid acids in Styrax as potent and highly specific inhibitors against human carboxylesterase 1A - Wang_2020_Food.Funct_11_8680
Author(s) : Wang L , Guan XQ , He RJ , Qin WW , Xiong Y , Zhang F , Song YQ , Huo PC , Song PF , Tang H , Ge GB
Ref : Food Funct , 11 :8680 , 2020
Abstract : Human carboxylesterase 1A1 (hCES1A) is a promising target for the treatment of hyperlipidemia and obesity-associated metabolic diseases. To date, the highly specific and efficacious hCES1A inhibitors are rarely reported. This study aims to find potent and highly specific hCES1A inhibitors from herbs, and to investigate their inhibitory mechanisms. Following large-scale screening of herbal products, Styrax was found to have the most potent hCES1A inhibition activity. After that, a practical bioactivity-guided fractionation coupling with a chemical profiling strategy was used to identify the fractions from Styrax with strong hCES1A inhibition activity and the major constituents in these bioactive fractions were characterized by LC-TOF-MS/MS. The results demonstrated that seven pentacyclic triterpenoid acids (PTAs) in two bioactive fractions from Styrax potently inhibit hCES1A, with IC50 values ranging from 41 nM to 478 nM. Among all the identified PTAs, epibetulinic acid showed the most potent inhibition activity and excellent specificity towards hCES1A. Both inhibition kinetic analyses and in silico analysis suggested that epibetulinic acid potently inhibited hCES1A in a mixed inhibition manner. Collectively, our findings demonstrate that some PTAs in Styrax are potent and highly specific inhibitors of hCES1A and these constituents can be used as promising lead compounds for the development of more efficacious hCES1A inhibitors.
ESTHER : Wang_2020_Food.Funct_11_8680
PubMedSearch : Wang_2020_Food.Funct_11_8680
PubMedID: 32940318

Title : Rationally design and chemical modification: Getting a new and efficient biocatalyst for Henry reaction - Yu_2020_Enzyme.Microb.Technol_142_109695
Author(s) : Yu Z , Zhang Q , Tang H , Xu G
Ref : Enzyme Microb Technol , 142 :109695 , 2020
Abstract : A robust biocatalyst for green Henry reaction was achieved. Based on the fact that Henry reaction requires a base for proton transfer, we firstly proposed that the catalytic triad of lipase could play this role. The distance between the substrate and the catalytic center and the surrounding amino acid interaction network were used as the criterion. Benzaldehyde and nitromethane were used as the model reaction, RNL (Lipase from Rhizopus niveus) was considered to be the best Henry reaction catalyst via a molecular dynamics simulation. Then experiments demonstrated that RNL has a yield of 48 % using model substrate in water. Further, in order to increase product yield, the chemical modifier 1, 2-cyclohexanedione (CHD) was used to modify Arg on RNL. As a result, RNL (CHD) increased the activity of catalyzing Henry reaction and had a broad spectrum of substrates, the yield of the product was as high as 67-99 %.
ESTHER : Yu_2020_Enzyme.Microb.Technol_142_109695
PubMedSearch : Yu_2020_Enzyme.Microb.Technol_142_109695
PubMedID: 33220873
Gene_locus related to this paper: rhidl-lipas

Title : Inhibitory Potency of 4- Substituted Sampangine Derivatives toward Cu(2+) mediated aggregation of amyloid beta-peptide, Oxidative Stress, and Inflammation in Alzheimer's Disease - Su_2020_Neurochem.Int__104794
Author(s) : Su C , Chen Y , Chen K , Li W , Tang H
Ref : Neurochem Int , :104794 , 2020
Abstract : Cu(2+) plays a key role in the pathogenesis of Alzheimer's disease (AD). The dysregulation of Cu(2+) can cause neuronal damage and aggravate development of AD. Moreover, a series of 4-substituted sampangine derivatives have been investigated as inhibitors of acetylcholinesterase and beta-amyloid (Abeta) aggregation for the treatment of AD in our previous studies. In the present study, we reported that one of these derivatives SD-1 was able to modulate Cu(2+)-mediated multiple pathological elements in AD. The high selectivity of SD-1 for Cu(2+) over other biologically relevant metal ions was demonstrated by ITC. Western blotting analysis, light-scattering study, DCF-DA assay and paralysis experiment indicated that SD-1 suppressed the formation of Cu(2+)-Abeta species, alleviated the Cu(2+)-Abeta species induced neurotoxicity and inhibited the production of ROS catalyzed by Cu(2+)-Abeta species in SH-SY5Y cells over-expressing the Swedish mutant form of human APP (APPsw SH-SY5Y) and Abeta42 transgenic C elegans (CL2020). Furthermore, SD-1 inhibited the expressions of NO, iNOS, TNF-alpha, IL-1beta and IL-6 induced by Cu(2+) in BV2 microglial cells. Collectively, these findings provided valuable insights into the design and development of potent metal-chelating agents for AD treatment.
ESTHER : Su_2020_Neurochem.Int__104794
PubMedSearch : Su_2020_Neurochem.Int__104794
PubMedID: 32650027

Title : Triphenyl phosphate permeates the blood brain barrier and induces neurotoxicity in mouse brain - Liu_2020_Chemosphere_252_126470
Author(s) : Liu X , Zhao X , Wang Y , Hong J , Shi M , Pfaff D , Guo L , Tang H
Ref : Chemosphere , 252 :126470 , 2020
Abstract : Concerns have been raised over the neurotoxicity of triphenyl phosphate (TPP), but there have been few studies of the neurotoxic effects of TPP on mammals and the underlying mechanisms. In this study, weaned male mice (C57/BL6) were used and exposed to 0, 50, or 150 mg/kg TPP daily by oral gavage for 30 days. The blood brain barrier (BBB) permeability of TPP and its metabolite diphenyl phosphate (DPP) in the brain, and TPP induced metabolomic and transcriptomic changes of the brain were investigated. The results showed that TPP and DPP can cross the BBB of mice. Histopathological examination of the brain revealed abnormalities in the hippocampus, cortex and thalamus, and mice treated with high doses showed a potential inflammation in the thalamus and hippocampus. Untargeted metabolomic results revealed that the changed level of glutamic acid, N-acetyl CoA metabolites, and organic acid in the brain of treated mice, suggest that amino acid and lipid metabolism was interfered. RNA-seq data indicated that neuronal transcription processes and cell apoptosis pathway (forkhead box (FOXO), and mitogen-activated protein kinase (MAPK) signaling pathways) were significantly affected by TPP exposure. RT-PCR showed proinflammation cytokine tumor necrosis factor alpha (TNF-alpha) and interleukin-6 (IL-6)) levels were increased, while antioxidant genes including nuclear factor-E2-related factor 2 (Nrf2), heme oxygenase1 (HO-1) and superoxide dismutase (SOD1) decreased. These results suggest that TPP could cause a degree of neurotoxicity by inducing neuroinflammation and neuronal apoptosis, which are related to oxidative stress. The potential implications for neurophysiology and behavioral regulation cannot be ignored.
ESTHER : Liu_2020_Chemosphere_252_126470
PubMedSearch : Liu_2020_Chemosphere_252_126470
PubMedID: 32443258

Title : Effect of Salvia miltiorrhiza on acetylcholinesterase: Enzyme kinetics and interaction mechanism merging with molecular docking analysis - Tang_2019_Int.J.Biol.Macromol_135_303
Author(s) : Tang H , Song P , Li J , Zhao D
Ref : Int J Biol Macromol , 135 :303 , 2019
Abstract : Acetylcholinesterase (AchE) serves as an important target for Alzheimer's disease. Salvia miltiorrhiza has been used to treat cardiovascular disease for hundreds of years. However, the interaction between S. miltiorrhiza and AchE is still inadequate. Herein, an integrated method including molecular docking and experimental studies was employed to investigate the interaction. Consequently, some components were screened as potent AchE inhibitors by in silico and in vitro. Among them, miltirone (MT) and salvianolic acid A (SAA) reversibly inhibited AchE in a mixed-competitive manner. Fluorescence data revealed that SAA and salvianolic acid C (SAC) strongly quenched the intrinsic fluorescence of AchE through a static quenching mechanism, and the binding was spontaneous and dominated by hydrophobic interaction inferred by the thermodynamic parameters. The synchronous and ANS-binding fluorescence spectra suggested that SAA and SAC could bind to the enzyme and induce its conformation changes of secondary structures, which was further confirmed by Fourier transform infrared spectra. Meanwhile, molecular docking presented the probable binding modes of inhibitors to AchE and highlighted the key role of hydrophobic interaction and hydrogen bonds for the stability of docking complex. These findings put more insights into understanding the interaction of S. miltiorrhiza chemicals and AchE, as well as Alzheimer's disease.
ESTHER : Tang_2019_Int.J.Biol.Macromol_135_303
PubMedSearch : Tang_2019_Int.J.Biol.Macromol_135_303
PubMedID: 31128195

Title : Interspecies variation of clopidogrel hydrolysis in liver microsomes from various manmmals - Wang_2019_Chem.Biol.Interact__108871
Author(s) : Wang YQ , Shang XF , Wang L , Zhang P , Zou LW , Song YQ , Hao DC , Fang SQ , Ge GB , Tang H
Ref : Chemico-Biological Interactions , :108871 , 2019
Abstract : Clopidogrel, a clinically used antiplatelet agent, can be readily hydrolyzed by human carboxylesterase 1A (CES1A) to release an inactive metabolite clopidogrel carboxylic acid (CCA). In this study, clopidogrel was used as a tool substrate to investigate the interspecies variation of clopidogrel hydrolysis in hepatic microsomes from various mammals including human and six laboratory animals (such as mouse, rat, rabbit, beagle dog, minipig and cynomolgus monkey). The results demonstrated that clopidogrel could be hydrolyzed into CCA by all tested hepatic microsomes from human or other mammals, but the hydrolytic rates greatly varied among species. Inhibition assays demonstrated that BNPP (an inactivator of mammalian CES) strongly inactivated clopidogrel hydrolytic activity in all tested hepatic microsomes, suggested that mammalian CES were major contributor(s) responsible for clopidogrel hydrolysis in hepatic preparations from all above-mentioned species. By contrast, the response of a reversible inhibitor of human CES1A on clopidogrel hydrolysis in these liver preparations varied significantly among different species. Moreover, the enzymatic kinetics and the apparent kinetic parameters of clopidogrel hydrolysis in hepatic microsomes from various animal species were evaluated and compared to each other. These findings provide crucial information for deeply understanding the differences in catalytic behaviors of mammalian CES, which will be very helpful for choosing suitable laboratory animal(s) for whole tests of CES1A substrate-drugs.
ESTHER : Wang_2019_Chem.Biol.Interact__108871
PubMedSearch : Wang_2019_Chem.Biol.Interact__108871
PubMedID: 31669218

Title : A Unique Role of Carboxylesterase 3 (Ces3) in beta-Adrenergic Signaling-Stimulated Thermogenesis - Yang_2019_Diabetes_68_1178
Author(s) : Yang L , Li X , Tang H , Gao Z , Zhang K , Sun K
Ref : Diabetes , 68 :1178 , 2019
Abstract : Carboxylesterase 3 (Ces3) is a hydrolase with a wide range of activities in liver and adipose tissue. In this study, we identified Ces3 as a major lipid droplet surface-targeting protein in adipose tissue upon cold exposure by liquid chromatography-tandem mass spectrometry. To investigate the function of Ces3 in the beta-adrenergic signaling-activated adipocytes, we applied WWL229, a specific Ces3 inhibitor, or genetic inhibition by siRNA to Ces3 on isoproterenol (ISO)-treated 3T3-L1 and brown adipocyte cells. We found that blockage of Ces3 by WWL229 or siRNA dramatically attenuated the ISO-induced lipolytic effect in the cells. Furthermore, Ces3 inhibition led to impaired mitochondrial function measured by Seahorse. Interestingly, Ces3 inhibition attenuated an ISO-induced thermogenic program in adipocytes by downregulating Ucp1 and Pgc1alpha genes via peroxisome proliferator-activated receptor gamma. We further confirmed the effects of Ces3 inhibition in vivo by showing that the thermogenesis in adipose tissues was significantly attenuated in WWL229-treated or adipose tissue-specific Ces3 heterozygous knockout (Adn-Cre-Ces3(flx/wt)) mice. As a result, the mice exhibited dramatically impaired ability to defend their body temperature in coldness. In conclusion, our study highlights a lipolytic signaling induced by Ces3 as a unique process to regulate thermogenesis in adipose tissue.
ESTHER : Yang_2019_Diabetes_68_1178
PubMedSearch : Yang_2019_Diabetes_68_1178
PubMedID: 30862682
Gene_locus related to this paper: human-CES3 , mouse-Ces1d

Title : Hybrids of oxoisoaporphine-tetrahydroisoquinoline: novel multi-target inhibitors of inflammation and amyloid-beta aggregation in Alzheimer's disease - Chen_2019_Mol.Divers_23_709
Author(s) : Chen Y , Su C , Wang L , Qin J , Wei S , Tang H
Ref : Mol Divers , 23 :709 , 2019
Abstract : A series of 8- and 11-substituted hybrids of oxoisoaporphine-tetrahydroisoquinoline have been designed and synthesized. The new derivatives strongly suppressed NO and iNOS production and modulated the production of cytokines by decreasing TNF-alpha and IL-1beta formation in lipopolysaccharide-activated BV-2 microglia and RAW 264.7 macrophages. Meanwhile, incubation of these derivatives with SH-SY5Y cells that were transfected with human APP containing the Swedish mutations significantly decreased the secretion of Abeta42. Moreover, these hybrids could strongly inhibit the activity of acetylcholinesterase and butyrylcholinesterase. Further investigations in vivo indicated that the 8-substituted hybrid 3b significantly delayed paralysis caused by Abeta1-42 toxicity in GMC101. In sum, these new hybrids could target multiple pathogenetic factors in Alzheimer's disease and merit further investigation.
ESTHER : Chen_2019_Mol.Divers_23_709
PubMedSearch : Chen_2019_Mol.Divers_23_709
PubMedID: 30603938

Title : Nevadensin is a naturally occurring selective inhibitor of human carboxylesterase 1 - Wang_2018_Int.J.Biol.Macromol_120_1944
Author(s) : Wang YQ , Weng ZM , Dou TY , Hou J , Wang DD , Ding LL , Zou LW , Yu Y , Chen J , Tang H , Ge GB
Ref : Int J Biol Macromol , 120 :1944 , 2018
Abstract : Human carboxylesterase 1 (hCE1) is a key enzyme responsible for the hydrolysis of a wide range of endogenous and xenobiotic esters, but the highly selective inhibitors against hCE1 are rarely reported. This study aimed to assess the inhibitory effects of natural flavonoids against hCE1 and to find potential specific hCE1 inhibitors. To this end, fifty-eight natural flavonoids were collected and their inhibitory effects against both hCE1 and hCE2 were assayed. Among all tested compounds, nevadensin, an abundant natural constitute from Lysionotus pauciflorus Maxim., displayed the best combination of inhibition potency and selectivity towards hCE1. The inhibition mechanism of nevadensin on hCE1 was further investigated using two site-specific hCE1 substrates including D-luciferin methyl ester (DME) and 2(2benzoyloxy3methoxyphenyl)benzothiazole (BMBT). Furthermore, docking simulations demonstrated that the binding area of nevadensin on hCE1 was highly overlapped with that of DME but was far away from that of BMBT, which was highly consistent with the inhibition modes of nevadensin. These findings found a natural occurring specific inhibitor of hCE1, which could be served as a lead compound for the development of novel hCE1 inhibitor with improved properties, and also hold great promise for investigating hCE1-ligand interactions.
ESTHER : Wang_2018_Int.J.Biol.Macromol_120_1944
PubMedSearch : Wang_2018_Int.J.Biol.Macromol_120_1944
PubMedID: 30268757

Title : Assessment of novel azaanthraquinone derivatives as potent multi-target inhibitors of inflammation and amyloid-beta aggregation in Alzheimer's disease - Wang_2018_Bioorg.Chem_83_477
Author(s) : Wang J , Li W , Qin J , Wang L , Wei S , Tang H
Ref : Bioorg Chem , 83 :477 , 2018
Abstract : A series of 6-substituted azaanthraquinone derivatives have been designed, synthesized, and their anti-inflammatory activities, antiaggregation effects on beta-amyloid proteins, anticholinesterase and neuroprotective activity were tested. The new derivatives strongly suppressed NO and iNOS production and modulate the production of cytokines by decreasing TNF-a, IL-1beta and IL-6 formation in lipopolysaccharide (LPS)-activated RAW 264.7 macrophages. Meanwhile, the derivatives exhibited a significant in vitro inhibitory activity toward the self-induced Abeta aggregation. While, treatment of SH-SY5Y cells overexpressing the Swedish mutant form of human b-amyloid precursor protein (APPsw) with derivatives was associated with significant reduction of Abeta42 secretion levels. Moreover, the derivatives exhibited moderate inhibitory potency toward acetylcholinesterase (AChE) and butyrylcholinesterase (BChE). Further investigations indicated that compound 7b could attenuate H2O2-induced neurotoxicity toward SH-SY5Y neuroblastoma cells and half of the synthetic compounds were predicted to be able to cross the blood-brain barrier (BBB) to reach their targets in the central nervous system (CNS) according to a parallel artificial membrane permeation assay for BBB. Taken together, azaanthraquinone derivatives targeting multiple pathogenetic factors deserves further investigation for prevention and treatment of AD.
ESTHER : Wang_2018_Bioorg.Chem_83_477
PubMedSearch : Wang_2018_Bioorg.Chem_83_477
PubMedID: 30448726

Title : 4- Substituted sampangine derivatives: Novel acetylcholinesterase and beta-myloid aggregation inhibitors - Chen_2018_Int.J.Biol.Macromol_107_2725
Author(s) : Chen KL , Gan L , Wu ZH , Qin JF , Liao WX , Tang H
Ref : Int J Biol Macromol , 107 :2725 , 2018
Abstract : A series of 4- substituted sampangine derivatives (4-aminoalkylaminosampangine Ar-NH(CH2)nNR1R2) has been designed, synthesized, and tested for their ability to inhibit acetylcholinesterase (AChE), butyrylcholinesterase (BChE) and beta-myloid (Abeta) aggregation. The synthetic compounds exhibited high AChE inhibitory activity and a significant in vitro inhibitory potency toward the self-induced Abeta aggregation. While, treatment of SH-SY5Y cells overexpressing the Swedish mutant form of human beta-amyloid precursor protein (APPsw) with derivatives was associated with significant reduction of Abeta42 secretion levels. Moreover, most of the synthetic compounds were predicted to be able to cross the blood-brain barrier (BBB) to reach their targets in the central nervous system (CNS) according to a parallel artificial membrane permeation assay for BBB. The result encourages us to study this class of compounds thoroughly and systematically.
ESTHER : Chen_2018_Int.J.Biol.Macromol_107_2725
PubMedSearch : Chen_2018_Int.J.Biol.Macromol_107_2725
PubMedID: 29111270

Title : Oxoisoaporphine alkaloid derivative 8-1 reduces Abeta1-42 secretion and toxicity in human cell and Caenorhabditis elegans models of Alzheimer's disease - Huang_2017_Neurochem.Int_108_157
Author(s) : Huang L , Luo Y , Pu Z , Kong X , Fu X , Xing H , Wei S , Chen W , Tang H
Ref : Neurochem Int , 108 :157 , 2017
Abstract : Alzheimer's disease (AD) is a multifactorial neurodegenerative disease and a growing health problem worldwide. Because the drugs currently used to treat AD have certain drawbacks such as single targeting, there is a need to develop novel multi-target compounds, among which oxoisoaporphine alkaloid derivatives are promising candidates. In this study, the possible anti-AD activities of 14 novel oxoisoaporphine alkaloid derivatives that we synthesized were screened and evaluated. We found that, in the 14 novel derivatives, compound 8-1 significantly reduced Abeta1-42 secretion in SH-SY5Y cells overexpressing the Swedish mutant form of human beta-amyloid precursor protein (APPsw). Next, we found that compound 8-1 could down-regulate the expression level of beta-amyloid precursor protein (APP) in APPsw cells. Moreover, compound 8-1 significantly delayed paralysis in the Abeta1-42-transgenic Caenorhabditis elegans strain GMC101, which could be explained by the fact that compound 8-1 down-regulated acetylcholinesterase activity, protected against H2O2-induced acute oxidative stress and paraquat-induced chronic oxidative stress, and enhanced autophagy activity. Taken together, our data suggest that compound 8-1 could attenuate the onset and development of AD.
ESTHER : Huang_2017_Neurochem.Int_108_157
PubMedSearch : Huang_2017_Neurochem.Int_108_157
PubMedID: 28286208

Title : The asparagus genome sheds light on the origin and evolution of a young Y chromosome - Harkess_2017_Nat.Commun_8_1279
Author(s) : Harkess A , Zhou J , Xu C , Bowers JE , Van der Hulst R , Ayyampalayam S , Mercati F , Riccardi P , McKain MR , Kakrana A , Tang H , Ray J , Groenendijk J , Arikit S , Mathioni SM , Nakano M , Shan H , Telgmann-Rauber A , Kanno A , Yue Z , Chen H , Li W , Chen Y , Xu X , Zhang Y , Luo S , Gao J , Mao Z , Pires JC , Luo M , Kudrna D , Wing RA , Meyers BC , Yi K , Kong H , Lavrijsen P , Sunseri F , Falavigna A , Ye Y , Leebens-Mack JH , Chen G
Ref : Nat Commun , 8 :1279 , 2017
Abstract : Sex chromosomes evolved from autosomes many times across the eukaryote phylogeny. Several models have been proposed to explain this transition, some involving male and female sterility mutations linked in a region of suppressed recombination between X and Y (or Z/W, U/V) chromosomes. Comparative and experimental analysis of a reference genome assembly for a double haploid YY male garden asparagus (Asparagus officinalis L.) individual implicates separate but linked genes as responsible for sex determination. Dioecy has evolved recently within Asparagus and sex chromosomes are cytogenetically identical with the Y, harboring a megabase segment that is missing from the X. We show that deletion of this entire region results in a male-to-female conversion, whereas loss of a single suppressor of female development drives male-to-hermaphrodite conversion. A single copy anther-specific gene with a male sterile Arabidopsis knockout phenotype is also in the Y-specific region, supporting a two-gene model for sex chromosome evolution.
ESTHER : Harkess_2017_Nat.Commun_8_1279
PubMedSearch : Harkess_2017_Nat.Commun_8_1279
PubMedID: 29093472
Gene_locus related to this paper: aspof-a0a5p1ew48

Title : Synthesis of derivatives of cleistopholine and their anti-acetylcholinesterase and anti-beta-amyloid aggregation activity - Wu_2017_Bioorg.Chem_76_228
Author(s) : Wu Z , Liao W , Chen K , Qin J , Tang H
Ref : Bioorg Chem , 76 :228 , 2017
Abstract : A series of 6- and 9-substituted cleistopholine derivatives has been designed, synthesized and investigated to inhibit the aggregation of acetylcholinesterase (AChE), butyrylcholinesterase (BChE) and beta-myloid (A beta). Results showed that these synthetic compounds had excellent AChE inhibitory activity and a significant in vitro inhibitory potency toward the self-induced A beta aggregation. When SH-SY5Y cells were treated with these substituted cleistopholine derivatives during they overexpressed the Swedish mutant form of human beta -amyloid precursor protein (APPsw), A beta 42 secretion levels were significantly reduced. According to a parallel artificial membrane permeation assay for BBB, seven out of these sixteen synthetic compounds probably could cross the blood-brain barrier (BBB) to reach their targets in the central nervous system (CNS).
ESTHER : Wu_2017_Bioorg.Chem_76_228
PubMedSearch : Wu_2017_Bioorg.Chem_76_228
PubMedID: 29195093

Title : The pomegranate (Punica granatum L.) genome and the genomics of punicalagin biosynthesis - Qin_2017_Plant.J_91_1108
Author(s) : Qin G , Xu C , Ming R , Tang H , Guyot R , Kramer EM , Hu Y , Yi X , Qi Y , Xu X , Gao Z , Pan H , Jian J , Tian Y , Yue Z , Xu Y
Ref : Plant J , 91 :1108 , 2017
Abstract : Pomegranate (Punica granatum L.) is a perennial fruit crop grown since ancient times that has been planted worldwide and is known for its functional metabolites, particularly punicalagins. We have sequenced and assembled the pomegranate genome with 328 Mb anchored into nine pseudo-chromosomes and annotated 29 229 gene models. A Myrtales lineage-specific whole-genome duplication event was detected that occurred in the common ancestor before the divergence of pomegranate and Eucalyptus. Repetitive sequences accounted for 46.1% of the assembled genome. We found that the integument development gene INNER NO OUTER (INO) was under positive selection and potentially contributed to the development of the fleshy outer layer of the seed coat, an edible part of pomegranate fruit. The genes encoding the enzymes for synthesis and degradation of lignin, hemicelluloses and cellulose were also differentially expressed between soft- and hard-seeded varieties, reflecting differences in their accumulation in cultivars differing in seed hardness. Candidate genes for punicalagin biosynthesis were identified and their expression patterns indicated that gallic acid synthesis in tissues could follow different biochemical pathways. The genome sequence of pomegranate provides a valuable resource for the dissection of many biological and biochemical traits and also provides important insights for the acceleration of breeding. Elucidation of the biochemical pathway(s) involved in punicalagin biosynthesis could assist breeding efforts to increase production of this bioactive compound.
ESTHER : Qin_2017_Plant.J_91_1108
PubMedSearch : Qin_2017_Plant.J_91_1108
PubMedID: 28654223
Gene_locus related to this paper: prupe-a0a251r634 , pungr-a0a218xv87 , pungr-a0a218xi98 , pungr-a0a218wma5 , pungr-a0a218w0a8 , pungr-a0a218w138 , pungr-a0a218w7t6 , pungr-a0a218weu3 , pungr-a0a218xzu6

Title : Multitarget-directed oxoisoaporphine derivatives: Anti-acetylcholinesterase, anti-beta-amyloid aggregation and enhanced autophagy activity against Alzheimer's disease - Wei_2016_Bioorg.Med.Chem_24_6031
Author(s) : Wei S , Chen W , Qin J , Huangli Y , Wang L , Shen Y , Tang H
Ref : Bioorganic & Medicinal Chemistry , 24 :6031 , 2016
Abstract : A series of 8- and 11-substituted oxoisoaporphine derivatives have been designed, synthesized, and tested for their ability to inhibit cholinesterase (ChE) in vitro and in vivo, and self-induced beta-amyloid (Abeta) aggregation. Their autophagy activity and blood-brain barrier (BBB) permeability were also assessed. The new derivatives exhibited high AChE inhibitory activity in vivo and in intro. Over half the derivatives exhibited a significant in vitro inhibitory activity toward the self-induced Abeta aggregation. While, treatment of SH-SY5Y cells overexpressing the Swedish mutant form of human beta-amyloid precursor protein (APPsw) with derivatives was associated with significant reduction of Abeta secretion levels. Moreover, one-third of the synthetic compounds were predicted to be able to cross the BBB to reach their targets in the central nervous system (CNS) according to a parallel artificial membrane permeation assay for BBB. Compounds 5b and 6b were chosen for assessing their autophagy activity. The fluorescence intensity of the BC12921 was decreased significantly after treatment with compounds. The result encourages us to study such compounds thoroughly and systematically.
ESTHER : Wei_2016_Bioorg.Med.Chem_24_6031
PubMedSearch : Wei_2016_Bioorg.Med.Chem_24_6031
PubMedID: 27720328

Title : [The value of determination of serum cholinesterase levels in judgment of severity and prognosis in patients with severe pneumonia] - Mo_2016_Zhonghua.Wei.Zhong.Bing.Ji.Jiu.Yi.Xue_28_38
Author(s) : Mo X , Tang H , Zeng L , Lu H , Guo L , Ma Z
Ref : Zhonghua Wei Zhong Bing Ji Jiu Yi Xue , 28 :38 , 2016
Abstract : OBJECTIVE: To investigate the value of serum cholinesterase (S-ChE) levels in judgment of severity and prognosis in patients with severe pneumonia.
METHODS: The clinical data of patients with severe pneumonia, who were admitted to the Department of Internal Medicine in the First Affiliated Hospital of Sun Yat-sen University, or the Department of Neurology in the Third People's Hospital of Foshan from May 2011 to May 2015, whose hospital time was longer than 24 hours, were retrospectively analyzed. They were divided into survival group and death group according to the final outcome. Lab data, acute physiology and chronic health evaluation II (APACHE II) score, multiple organ dysfunction syndrome (MODS) score, the improved pneumonia score of British Thoracic Society (confusion, uremia, respiratory, blood pressure, age 65 years, CURB-65), and S-ChE levels of all patients were collected after they were hospitalized into the intensive care unit (ICU) within 24 hours. Independent risk factors for prognosis were analyzed by binary logistic regression analysis, and receiver operating characteristic curve (ROC) was plotted. Best truncation point analysis was used to compare their estimated value for prognosis of patients with severe pneumonia.
RESULTS: Eighty-six patients with severe pneumonia were studied. Among them 46 patients survived, and 40 patients died. By the single factor analysis, the following lab data in the death group were found significantly lower than those in the survival group: S-ChE levels (kU/L: 2.748+/-0.826 vs. 4.489+/-1.360, t' = 7.274, P = 0.000), arterial partial pressure of oxygen [PaO2 (mmHg, 1 mmHg = 0.133 kPa): 52.55+/-18.29 vs. 60.83+/-16.65, t = 2.196, P = 0.031], oxygenation index (mmHg: 114.20+/-48.01 vs. 167.10+/-69.68, t' = 4.229, P = 0.000), and carbon dioxide combining power [CO2-CP (mmol/L): 22.85+/-5.44 vs. 26.00+/-7.63, t' = 2.225, P = 0.029]. The following clinical data were significantly higher in the death group than those in the survival group, namely body temperature (centigrade: 38.67+/-1.18 vs. 37.74+/-1.18, t = -3.627, P = 0.000), pulse (bpm: 130.65+/-15.72 vs. 107.26+/-19.61, t' = -6.133, P = 0.000), the ratio of concomitant chronic lung disease [45.0% (18/40) vs. 13.0% (6/46), chi(2) = 10.860, P = 0.001], fraction of inspired oxygen [FiO2: 0.495 (0.410, 0.600) vs. 0.380 (0.290, 0.500), Z = -3.265, P = 0.001], APACHE II score (25.80+/-5.07 vs. 16.39+/-5.12, t =-8.540, P = 0.000), CURB-65 score [3 (3, 4) vs. 2 (1, 2), Z = -5.562, P = 0.000], MODS score (8.15+/-2.49 vs. 4.35+/-2.01, t = -7.832, P = 0.000), international normalized ratio [INR: 1.22 (1.08, 1.31) vs. 1.07 (1.00, 1.10), Z = -4.231, P = 0.000], and activated partial thromboplastin time [APTT (s): 33.80 (32.13, 38.75) vs. 28.50 (25.70, 36.00), Z = -3.482, P = 0.000]. Binary logistic regression analysis showed that, S-ChE levels, APACHE II score and MODS score were found to be the independent risk factors for prognosis in the patients with severe pneumonia, respectively [S-ChE: odds ratio (OR) = 0.084, 95% confidence interval (95%CI) = 0.017-0.424, P = 0.003; APACHE II score: OR = 1.675, 95%CI = 1.098-2.556, P = 0.017; MODS score: OR = 2.189, 95%CI = 1.262-3.800, P = 0.005]. The area under ROC (AUC) for S-ChE levels, APACHE II score and MODS score were 0.874+/-0.036, 0.889+/-0.033 and 0.884+/-0.035, respectively (all P > 0.05 as compared between any two means). At the best truncation points of S-ChE levels, APACHE II score and MODS score were 3.372 kU/L, 19.5 score, and 6.5 score respectively. The sensitivity, specificity, positive predictive value and negative predictive value in predicting death risk in patients with severe pneumonia were (80.0%, 78.0%, 76.19% and 81.82%), (95.0%, 70.0%, 73.08% and 94.12%) and (70.0%, 91.0%, 87.50%, 77.78%), respectively. If S-ChE levels was combined with APACHE II score or combined with MODS score, the sensitivity, specificity, positive predictive value and negative predictive value [S-ChE levels combined APACHE II score: 100%, 92.0%, 93.75% and 100%; S-ChE levels combined MODS score: all 100%] were higher than single power of S-ChE levels, APACHE II score or MODS score.
CONCLUSIONS: S-ChE levels can be considered as an effective and practical index to estimate the severity and prognosis in patients with severe pneumonia. The combined application of S-ChE levels and APACHE II score or MODS score can obviously improve the prognostic power in patients with severe pneumonia.
ESTHER : Mo_2016_Zhonghua.Wei.Zhong.Bing.Ji.Jiu.Yi.Xue_28_38
PubMedSearch : Mo_2016_Zhonghua.Wei.Zhong.Bing.Ji.Jiu.Yi.Xue_28_38
PubMedID: 26805533

Title : Molecular mechanism of nicotine degradation by a newly isolated strain, Ochrobactrum sp. strain SJY1 - Yu_2015_Appl.Environ.Microbiol_81_272
Author(s) : Yu H , Tang H , Zhu X , Li Y , Xu P
Ref : Applied Environmental Microbiology , 81 :272 , 2015
Abstract : A newly isolated strain, SJY1, identified as Ochrobactrum sp., utilizes nicotine as a sole source of carbon, nitrogen, and energy. Strain SJY1 could efficiently degrade nicotine via a variant of the pyridine and pyrrolidine pathways (the VPP pathway), which highlights bacterial metabolic diversity in relation to nicotine degradation. A 97-kbp DNA fragment containing six nicotine degradation-related genes was obtained by gap closing from the genome sequence of strain SJY1. Three genes, designated vppB, vppD, and vppE, in the VPP pathway were cloned and heterologously expressed, and the related proteins were characterized. The vppB gene encodes a flavin-containing amine oxidase converting 6-hydroxynicotine to 6-hydroxy-N-methylmyosmine. Although VppB specifically catalyzes the dehydrogenation of 6-hydroxynicotine rather than nicotine, it shares higher amino acid sequence identity with nicotine oxidase (38%) from the pyrrolidine pathway than with its isoenzyme (6-hydroxy-l-nicotine oxidase, 24%) from the pyridine pathway. The vppD gene encodes an NADH-dependent flavin-containing monooxygenase, which catalyzes the hydroxylation of 6-hydroxy-3-succinoylpyridine to 2,5-dihydroxypyridine. VppD shows 62% amino acid sequence identity with the hydroxylase (HspB) from Pseudomonas putida strain S16, whereas the specific activity of VppD is approximately 10-fold higher than that of HspB. VppE is responsible for the transformation of 2,5-dihydroxypyridine. Sequence alignment and phylogenetic analysis suggested that the VPP pathway, which evolved independently from nicotinic acid degradation, might have a closer relationship with the pyrrolidine pathway. The proteins and functional pathway identified here provide a sound basis for future studies aimed at a better understanding of molecular principles of nicotine degradation.
ESTHER : Yu_2015_Appl.Environ.Microbiol_81_272
PubMedSearch : Yu_2015_Appl.Environ.Microbiol_81_272
PubMedID: 25344232
Gene_locus related to this paper: 9rhiz-a0a075xai2

Title : Structural insights into the specific recognition of N-heterocycle biodenitrogenation-derived substrates by microbial amide hydrolases - Wu_2014_Mol.Microbiol_91_1009
Author(s) : Wu G , Chen D , Tang H , Ren Y , Chen Q , Lv Y , Zhang Z , Zhao YL , Yao Y , Xu P
Ref : Molecular Microbiology , 91 :1009 , 2014
Abstract : N-heterocyclic compounds from industrial wastes, including nicotine, are environmental pollutants or toxicants responsible for a variety of health problems. Microbial biodegradation is an attractive strategy for the removal of N-heterocyclic pollutants, during which carbon-nitrogen bonds in N-heterocycles are converted to amide bonds and subsequently severed by amide hydrolases. Previous studies have failed to clarify the molecular mechanism through which amide hydrolases selectively recognize diverse amide substrates and complete the biodenitrogenation process. In this study, structural, computational and enzymatic analyses showed how the N-formylmaleamate deformylase Nfo and the maleamate amidase Ami, two pivotal amide hydrolases in the nicotine catabolic pathway of Pseudomonas putida S16, specifically recognize their respective substrates. In addition, comparison of the alpha-beta-alpha groups of amidases, which include Ami, pinpointed several subgroup-characteristic residues differentiating the two classes of amide substrates as containing either carboxylate groups or aromatic rings. Furthermore, this study reveals the molecular mechanism through which the specially tailored active sites of deformylases and amidases selectively recognize their unique substrates. Our work thus provides a thorough elucidation of the molecular mechanism through which amide hydrolases accomplish substrate-specific recognition in the microbial N-heterocycles biodenitrogenation pathway.
ESTHER : Wu_2014_Mol.Microbiol_91_1009
PubMedSearch : Wu_2014_Mol.Microbiol_91_1009
PubMedID: 24397579
Gene_locus related to this paper: psep6-f8g0m2

Title : Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea - Parkin_2014_Genome.Biol_15_R77
Author(s) : Parkin IA , Koh C , Tang H , Robinson SJ , Kagale S , Clarke WE , Town CD , Nixon J , Krishnakumar V , Bidwell SL , Denoeud F , Belcram H , Links MG , Just J , Clarke C , Bender T , Huebert T , Mason AS , Pires JC , Barker G , Moore J , Walley PG , Manoli S , Batley J , Edwards D , Nelson MN , Wang X , Paterson AH , King G , Bancroft I , Chalhoub B , Sharpe AG
Ref : Genome Biol , 15 :R77 , 2014
Abstract : BACKGROUND: Brassica oleracea is a valuable vegetable species that has contributed to human health and nutrition for hundreds of years and comprises multiple distinct cultivar groups with diverse morphological and phytochemical attributes. In addition to this phenotypic wealth, B. oleracea offers unique insights into polyploid evolution, as it results from multiple ancestral polyploidy events and a final Brassiceae-specific triplication event. Further, B. oleracea represents one of the diploid genomes that formed the economically important allopolyploid oilseed, Brassica napus. A deeper understanding of B. oleracea genome architecture provides a foundation for crop improvement strategies throughout the Brassica genus.
RESULTS: We generate an assembly representing 75% of the predicted B. oleracea genome using a hybrid Illumina/Roche 454 approach. Two dense genetic maps are generated to anchor almost 92% of the assembled scaffolds to nine pseudo-chromosomes. Over 50,000 genes are annotated and 40% of the genome predicted to be repetitive, thus contributing to the increased genome size of B. oleracea compared to its close relative B. rapa. A snapshot of both the leaf transcriptome and methylome allows comparisons to be made across the triplicated sub-genomes, which resulted from the most recent Brassiceae-specific polyploidy event.
CONCLUSIONS: Differential expression of the triplicated syntelogs and cytosine methylation levels across the sub-genomes suggest residual marks of the genome dominance that led to the current genome architecture. Although cytosine methylation does not correlate with individual gene dominance, the independent methylation patterns of triplicated copies suggest epigenetic mechanisms play a role in the functional diversification of duplicate genes.
ESTHER : Parkin_2014_Genome.Biol_15_R77
PubMedSearch : Parkin_2014_Genome.Biol_15_R77
PubMedID: 24916971
Gene_locus related to this paper: braol-a0a0d3dpb2 , braol-a0a0d3dx76 , brana-a0a078jxa8 , brana-a0a078i2k3 , braol-a0a0d3ef55 , braol-a0a0d3bur9 , braol-a0a0d3ck99 , braol-a0a0d3cns1 , braol-a0a0d3e654 , brana-a0a078i6d2 , braol-a0a0d3a922

Title : An improved genome release (version Mt4.0) for the model legume Medicago truncatula - Tang_2014_BMC.Genomics_15_312
Author(s) : Tang H , Krishnakumar V , Bidwell S , Rosen B , Chan A , Zhou S , Gentzbittel L , Childs KL , Yandell M , Gundlach H , Mayer KF , Schwartz DC , Town CD
Ref : BMC Genomics , 15 :312 , 2014
Abstract : BACKGROUND: Medicago truncatula, a close relative of alfalfa, is a preeminent model for studying nitrogen fixation, symbiosis, and legume genomics. The Medicago sequencing project began in 2003 with the goal to decipher sequences originated from the euchromatic portion of the genome. The initial sequencing approach was based on a BAC tiling path, culminating in a BAC-based assembly (Mt3.5) as well as an in-depth analysis of the genome published in 2011.
RESULTS: Here we describe a further improved and refined version of the M. truncatula genome (Mt4.0) based on de novo whole genome shotgun assembly of a majority of Illumina and 454 reads using ALLPATHS-LG. The ALLPATHS-LG scaffolds were anchored onto the pseudomolecules on the basis of alignments to both the optical map and the genotyping-by-sequencing (GBS) map. The Mt4.0 pseudomolecules encompass ~360 Mb of actual sequences spanning 390 Mb of which ~330 Mb align perfectly with the optical map, presenting a drastic improvement over the BAC-based Mt3.5 which only contained 70% sequences (~250 Mb) of the current version. Most of the sequences and genes that previously resided on the unanchored portion of Mt3.5 have now been incorporated into the Mt4.0 pseudomolecules, with the exception of ~28 Mb of unplaced sequences. With regard to gene annotation, the genome has been re-annotated through our gene prediction pipeline, which integrates EST, RNA-seq, protein and gene prediction evidences. A total of 50,894 genes (31,661 high confidence and 19,233 low confidence) are included in Mt4.0 which overlapped with ~82% of the gene loci annotated in Mt3.5. Of the remaining genes, 14% of the Mt3.5 genes have been deprecated to an "unsupported" status and 4% are absent from the Mt4.0 predictions.
CONCLUSIONS: Mt4.0 and its associated resources, such as genome browsers, BLAST-able datasets and gene information pages, can be found on the JCVI Medicago web site (http://www.jcvi.org/medicago). The assembly and annotation has been deposited in GenBank (BioProject: PRJNA10791). The heavily curated chromosomal sequences and associated gene models of Medicago will serve as a better reference for legume biology and comparative genomics.
ESTHER : Tang_2014_BMC.Genomics_15_312
PubMedSearch : Tang_2014_BMC.Genomics_15_312
PubMedID: 24767513
Gene_locus related to this paper: medtr-q1s5d8 , medtr-q1s9m3 , medtr-q1t171 , medtr-g7iam1 , medtr-g7iam3 , medtr-a0a072vrv9 , medtr-g7kmk5 , medtr-a0a072uuf6 , medtr-a0a072urp3 , medtr-g7zzc3 , medtr-g7ie19 , medtr-g7kst7 , medtr-a0a072u5k5 , medtr-a0a072v056 , medtr-scp1 , medtr-g7kyn0 , medtr-g7inw6 , medtr-g7j3q3

Title : Anti-neurotoxicity effects of oxoisoaporphine-lipoic acid hybrids - Chen_2014_Chem.Biol.Interact_223C_45
Author(s) : Chen W , Wu Y , Zhong S , Cheng L , Li Q , Tang H
Ref : Chemico-Biological Interactions , 223C :45 , 2014
Abstract : Four oxoisoaporphine-lipoic acid hybrids were designed, synthesized, and investigated in this study. To develop the hybrids, the oxoisoaporphine fragment was used for its inhibition of cholinesterases and beta-amyloid (Abeta) aggregation, while the unit of lipoic acid was used for its radical-capturing and neuroprotective effects. The hybrids exhibited moderate inhibitory effects on the activity of acetylcholinesterase (AChE), with IC50 values in the micromolar range and low toxicity in SH-SY5Y cells. Moreover, the learning and memory abilities, climbing capability, and average life expectancy of the Abeta42 transgenic Drosophila were all significantly improved by the hybrids. They also enhanced the intracephalic antioxidant activity, the metabolism, and the activity cholinesterase in the flies. More strikingly, Abeta42 aggregation in the hybrids-treated Drosophila was attenuated with effective neuroprotection. Our results indicate the potential of using these oxoisoaporphine-lipoic acid hybrids in AD treatments.
ESTHER : Chen_2014_Chem.Biol.Interact_223C_45
PubMedSearch : Chen_2014_Chem.Biol.Interact_223C_45
PubMedID: 25234849

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 : Systematic unraveling of the unsolved pathway of nicotine degradation in Pseudomonas - Tang_2013_PLoS.Genet_9_e1003923
Author(s) : Tang H , Wang L , Wang W , Yu H , Zhang K , Yao Y , Xu P
Ref : PLoS Genet , 9 :e1003923 , 2013
Abstract : Microorganisms such as Pseudomonas putida play important roles in the mineralization of organic wastes and toxic compounds. To comprehensively and accurately elucidate key processes of nicotine degradation in Pseudomonas putida, we measured differential protein abundance levels with MS-based spectral counting in P. putida S16 grown on nicotine or glycerol, a non-repressive carbon source. In silico analyses highlighted significant clustering of proteins involved in a functional pathway in nicotine degradation. The transcriptional regulation of differentially expressed genes was analyzed by using quantitative reverse transcription-PCR. We observed the following key results: (i) The proteomes, containing 1,292 observed proteins, provide a detailed view of enzymes involved in nicotine metabolism. These proteins could be assigned to the functional groups of transport, detoxification, and amino acid metabolism. There were significant differences in the cytosolic protein patterns of cells growing in a nicotine medium and those in a glycerol medium. (ii) The key step in the conversion of 3-succinoylpyridine to 6-hydroxy-3-succinoylpyridine was catalyzed by a multi-enzyme reaction consisting of a molybdopeterin binding oxidase (spmA), molybdopterin dehydrogenase (spmB), and a (2Fe-2S)-binding ferredoxin (spmC) with molybdenum molybdopterin cytosine dinucleotide as a cofactor. (iii) The gene of a novel nicotine oxidoreductase (nicA2) was cloned, and the recombinant protein was characterized. The proteins and functional pathway identified in the current study represent attractive targets for degradation of environmental toxic compounds.
ESTHER : Tang_2013_PLoS.Genet_9_e1003923
PubMedSearch : Tang_2013_PLoS.Genet_9_e1003923
PubMedID: 24204321

Title : Iron(II)-dependent dioxygenase and N-formylamide deformylase catalyze the reactions from 5-hydroxy-2-pyridone to maleamate - Yao_2013_Sci.Rep_3_3235
Author(s) : Yao Y , Tang H , Ren H , Yu H , Wang L , Zhang W , Behrman EJ , Xu P
Ref : Sci Rep , 3 :3235 , 2013
Abstract : 5-Hydroxy-2-pyridone (2,5-DHP) is a central metabolic intermediate in catabolism of many pyridine derivatives, and has been suggested as a potential carcinogen. 2,5-DHP is frequently transformed to N-formylmaleamic acid (NFM) by a 2,5-DHP dioxygenase. Three hypotheses were formerly discussed for conversion of 2,5-DHP to maleamate. Based on enzymatic reactions of dioxygenase (Hpo) and N-formylamide deformylase (Nfo), we demonstrated that the dioxygenase does not catalyze the hydrolysis of NFM but rather that this activity is brought about by a separate deformylase. We report that the deformylase acts both on NFM and its trans-isomer, N-formylfumaramic acid (NFF), but the catalytic efficiency of Nfo for NFM is about 1,400 times greater than that for NFF. In addition, we uncover catalytic and structural characteristics of the new family that the Hpo belongs to, and support a potential 2-His-1-carboxylate motif (HX52HXD) by three-dimensional modeling and site-directed mutagenesis. This study provides a better understanding of 2,5-DHP catabolism.
ESTHER : Yao_2013_Sci.Rep_3_3235
PubMedSearch : Yao_2013_Sci.Rep_3_3235
PubMedID: 24241081

Title : Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.) - Ming_2013_Genome.Biol_14_R41
Author(s) : Ming R , VanBuren R , Liu Y , Yang M , Han Y , Li LT , Zhang Q , Kim MJ , Schatz MC , Campbell M , Li J , Bowers JE , Tang H , Lyons E , Ferguson AA , Narzisi G , Nelson DR , Blaby-Haas CE , Gschwend AR , Jiao Y , Der JP , Zeng F , Han J , Min XJ , Hudson KA , Singh R , Grennan AK , Karpowicz SJ , Watling JR , Ito K , Robinson SA , Hudson ME , Yu Q , Mockler TC , Carroll A , Zheng Y , Sunkar R , Jia R , Chen N , Arro J , Wai CM , Wafula E , Spence A , Xu L , Zhang J , Peery R , Haus MJ , Xiong W , Walsh JA , Wu J , Wang ML , Zhu YJ , Paull RE , Britt AB , Du C , Downie SR , Schuler MA , Michael TP , Long SP , Ort DR , Schopf JW , Gang DR , Jiang N , Yandell M , dePamphilis CW , Merchant SS , Paterson AH , Buchanan BB , Li S , Shen-Miller J
Ref : Genome Biol , 14 :R41 , 2013
Abstract : BACKGROUND: Sacred lotus is a basal eudicot with agricultural, medicinal, cultural and religious importance. It was domesticated in Asia about 7,000 years ago, and cultivated for its rhizomes and seeds as a food crop. It is particularly noted for its 1,300-year seed longevity and exceptional water repellency, known as the lotus effect. The latter property is due to the nanoscopic closely packed protuberances of its self-cleaning leaf surface, which have been adapted for the manufacture of a self-cleaning industrial paint, Lotusan. RESULTS: The genome of the China Antique variety of the sacred lotus was sequenced with Illumina and 454 technologies, at respective depths of 101x and 5.2x. The final assembly has a contig N50 of 38.8 kbp and a scaffold N50 of 3.4 Mbp, and covers 86.5% of the estimated 929 Mbp total genome size. The genome notably lacks the paleo-triplication observed in other eudicots, but reveals a lineage-specific duplication. The genome has evidence of slow evolution, with a 30% slower nucleotide mutation rate than observed in grape. Comparisons of the available sequenced genomes suggest a minimum gene set for vascular plants of 4,223 genes. Strikingly, the sacred lotus has 16 COG2132 multi-copper oxidase family proteins with root-specific expression; these are involved in root meristem phosphate starvation, reflecting adaptation to limited nutrient availability in an aquatic environment. CONCLUSIONS: The slow nucleotide substitution rate makes the sacred lotus a better resource than the current standard, grape, for reconstructing the pan-eudicot genome, and should therefore accelerate comparative analysis between eudicots and monocots.
ESTHER : Ming_2013_Genome.Biol_14_R41
PubMedSearch : Ming_2013_Genome.Biol_14_R41
PubMedID: 23663246
Gene_locus related to this paper: nelnu-a0a1u8aj84 , nelnu-a0a1u8bpe4 , nelnu-a0a1u7z9m9 , nelnu-a0a1u7ywy5 , nelnu-a0a1u8aik2 , nelnu-a0a1u7zmb5 , nelnu-a0a1u8a7m7 , nelnu-a0a1u8b0n9 , nelnu-a0a1u8b461 , nelnu-a0a1u7zzj3 , nelnu-a0a1u8ave7 , nelnu-a0a1u7yn26

Title : Genomic analysis of Pseudomonas putida: genes in a genome island are crucial for nicotine degradation - Tang_2012_Sci.Rep_2_377
Author(s) : Tang H , Yao Y , Wang L , Yu H , Ren Y , Wu G , Xu P
Ref : Sci Rep , 2 :377 , 2012
Abstract : Nicotine is an important chemical compound in nature that has been regarded as an environmental toxicant causing various preventable diseases. Several bacterial species are adapted to decompose this heterocyclic compound, including Pseudomonas and Arthrobacter. Pseudomonas putida S16 is a bacterium that degrades nicotine through the pyrrolidine pathway, similar to that present in animals. The corresponding late steps of the nicotine degradation pathway in P. putida S16 was first proposed and demonstrated to be from 2,5-dihydroxy-pyridine through the intermediates N-formylmaleamic acid, maleamic acid, maleic acid, and fumaric acid. Genomics of strain S16 revealed that genes located in the largest genome island play a major role in nicotine degradation and may originate from other strains, as suggested by the constructed phylogenetic tree and the results of comparative genomic analysis. The deletion of gene hpo showed that this gene is essential for nicotine degradation. This study defines the mechanism of nicotine degradation.
ESTHER : Tang_2012_Sci.Rep_2_377
PubMedSearch : Tang_2012_Sci.Rep_2_377
PubMedID: 22530095

Title : Genome sequence of a novel nicotine-degrading strain, Pseudomonas geniculata N1 - Tang_2012_J.Bacteriol_194_3553
Author(s) : Tang H , Yu H , Tai C , Huang K , Liu Y , Wang L , Yao Y , Wu G , Xu P
Ref : Journal of Bacteriology , 194 :3553 , 2012
Abstract : A newly isolated bacterium, Pseudomonas geniculata N1, can efficiently degrade nicotine. Here we present a 4.51-Mb assembly of its genome, which is the first sequence of the P. geniculata group. The sequence contains the genes related to nicotine catabolism and may provide insights into its molecular mechanism for N-heterocyclic degradation.
ESTHER : Tang_2012_J.Bacteriol_194_3553
PubMedSearch : Tang_2012_J.Bacteriol_194_3553
PubMedID: 22689240
Gene_locus related to this paper: 9gamm-a0a0l8ag98

Title : Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres - Paterson_2012_Nature_492_423
Author(s) : Paterson AH , Wendel JF , Gundlach H , Guo H , Jenkins J , Jin D , Llewellyn D , Showmaker KC , Shu S , Udall J , Yoo MJ , Byers R , Chen W , Doron-Faigenboim A , Duke MV , Gong L , Grimwood J , Grover C , Grupp K , Hu G , Lee TH , Li J , Lin L , Liu T , Marler BS , Page JT , Roberts AW , Romanel E , Sanders WS , Szadkowski E , Tan X , Tang H , Xu C , Wang J , Wang Z , Zhang D , Zhang L , Ashrafi H , Bedon F , Bowers JE , Brubaker CL , Chee PW , Das S , Gingle AR , Haigler CH , Harker D , Hoffmann LV , Hovav R , Jones DC , Lemke C , Mansoor S , ur Rahman M , Rainville LN , Rambani A , Reddy UK , Rong JK , Saranga Y , Scheffler BE , Scheffler JA , Stelly DM , Triplett BA , Van Deynze A , Vaslin MF , Waghmare VN , Walford SA , Wright RJ , Zaki EA , Zhang T , Dennis ES , Mayer KF , Peterson DG , Rokhsar DS , Wang X , Schmutz J
Ref : Nature , 492 :423 , 2012
Abstract : Polyploidy often confers emergent properties, such as the higher fibre productivity and quality of tetraploid cottons than diploid cottons bred for the same environments. Here we show that an abrupt five- to sixfold ploidy increase approximately 60 million years (Myr) ago, and allopolyploidy reuniting divergent Gossypium genomes approximately 1-2 Myr ago, conferred about 30-36-fold duplication of ancestral angiosperm (flowering plant) genes in elite cottons (Gossypium hirsutum and Gossypium barbadense), genetic complexity equalled only by Brassica among sequenced angiosperms. Nascent fibre evolution, before allopolyploidy, is elucidated by comparison of spinnable-fibred Gossypium herbaceum A and non-spinnable Gossypium longicalyx F genomes to one another and the outgroup D genome of non-spinnable Gossypium raimondii. The sequence of a G. hirsutum A(t)D(t) (in which 't' indicates tetraploid) cultivar reveals many non-reciprocal DNA exchanges between subgenomes that may have contributed to phenotypic innovation and/or other emergent properties such as ecological adaptation by polyploids. Most DNA-level novelty in G. hirsutum recombines alleles from the D-genome progenitor native to its New World habitat and the Old World A-genome progenitor in which spinnable fibre evolved. Coordinated expression changes in proximal groups of functionally distinct genes, including a nuclear mitochondrial DNA block, may account for clusters of cotton-fibre quantitative trait loci affecting diverse traits. Opportunities abound for dissecting emergent properties of other polyploids, particularly angiosperms, by comparison to diploid progenitors and outgroups.
ESTHER : Paterson_2012_Nature_492_423
PubMedSearch : Paterson_2012_Nature_492_423
PubMedID: 23257886
Gene_locus related to this paper: gosra-a0a0d2qg22 , gosra-a0a0d2w3z1 , gosra-a0a0d2uuz7 , gosra-a0a0d2rxs2 , gosra-a0a0d2sdk0 , gosra-a0a0d2tng2 , gosra-a0a0d2twz7 , gosra-a0a0d2vdc5 , gosra-a0a0d2vj24 , gosra-a0a0d2sr31 , goshi-a0a1u8knd1 , goshi-a0a1u8nhw9 , goshi-a0a1u8kis4 , gosra-a0a0d2pul0 , gosra-a0a0d2p3f2 , gosra-a0a0d2ril5 , gosra-a0a0d2s7d5 , gosra-a0a0d2t9b3 , gosra-a0a0d2tw88 , gosra-a0a0d2umz5 , gosra-a0a0d2pzd7 , gosra-a0a0d2scu7 , gosra-a0a0d2vcx6

Title : Novel oxoisoaporphine-based inhibitors of acetyl- and butyrylcholinesterase and acetylcholinesterase-induced beta-amyloid aggregation - Tang_2012_Bioorg.Med.Chem.Lett_22_2257
Author(s) : Tang H , Zhao HT , Zhong SM , Wang ZY , Chen ZF , Liang H
Ref : Bioorganic & Medicinal Chemistry Lett , 22 :2257 , 2012
Abstract : A series of novel oxoisoaporphine-based inhibitors (10-aminoalkylamino-1-azabenzanthrone Ar-NH(CH(2))(n)NR(1)R(2)) of acetylcholinesterase (AChE) has been designed, synthesized, and tested for their ability to inhibit AChE, butyrylcholinesterase (BChE) and AChE-induced beta-amyloid (Abeta) aggregation. The synthetic compounds exhibited high AChE inhibitory activity with IC(50) values in the submicromolar range in most cases. Non-competitive binding mode was found for these derivatives by the graphical analysis of steady-state inhibition data. Moreover, all compounds exhibit significant inhibitory activity on AChE-induced Abeta aggregation with inhibitory potency from 54.5% to 93.5%. Finally, six out of twelve synthetic compounds were predicted to be able to cross the blood-brain barrier (BBB) to reach their targets in the central nervous system (CNS) according to a parallel artificial membrane permeation assay for BBB. The result encourages us to study this class of compounds thoroughly and systematically.
ESTHER : Tang_2012_Bioorg.Med.Chem.Lett_22_2257
PubMedSearch : Tang_2012_Bioorg.Med.Chem.Lett_22_2257
PubMedID: 22341944

Title : Genome sequence of Enterobacter cloacae subsp. dissolvens SDM, an efficient biomass-utilizing producer of platform chemical 2,3-butanediol - Xu_2012_J.Bacteriol_194_897
Author(s) : Xu Y , Wang A , Tao F , Su F , Tang H , Ma C , Xu P
Ref : Journal of Bacteriology , 194 :897 , 2012
Abstract : Enterobacter cloacae subsp. dissolvens SDM has an extraordinary characteristic of biomass utilization for 2,3-butanediol production. Here we present a 4.9-Mb assembly of its genome. The key genes for regulation and metabolism of 2,3-butanediol production were annotated, which could provide further insights into the molecular mechanism of high-yield production of 2,3-butanediol.
ESTHER : Xu_2012_J.Bacteriol_194_897
PubMedSearch : Xu_2012_J.Bacteriol_194_897
PubMedID: 22275097
Gene_locus related to this paper: entcl-i6s5g2 , entcl-y1bd05 , entcl-g8lek8

Title : Complete genome sequence of the nicotine-degrading Pseudomonas putida strain S16 - Yu_2011_J.Bacteriol_193_5541
Author(s) : Yu H , Tang H , Wang L , Yao Y , Wu G , Xu P
Ref : Journal of Bacteriology , 193 :5541 , 2011
Abstract : Pseudomonas putida S16 is an efficient degrader of nicotine. The complete genome of strain S16 (5,984,790 bp in length) includes genes related to catabolism of aromatic and heterocyclic compounds. The genes of enzymes in the core genome and a genomic island encode the proteins responsible for nicotine catabolism.
ESTHER : Yu_2011_J.Bacteriol_193_5541
PubMedSearch : Yu_2011_J.Bacteriol_193_5541
PubMedID: 21914868
Gene_locus related to this paper: psep6-f8g0m2 , psepu-PIP , psepu-PP4249 , psepu-PP4916 , psepu-q9wwz4

Title : A novel NADH-dependent and FAD-containing hydroxylase is crucial for nicotine degradation by Pseudomonas putida - Tang_2011_J.Biol.Chem_286_39179
Author(s) : Tang H , Yao Y , Zhang D , Meng X , Wang L , Yu H , Ma L , Xu P
Ref : Journal of Biological Chemistry , 286 :39179 , 2011
Abstract : Nicotine, the main alkaloid produced by Nicotiana tabacum and other Solanaceae, is very toxic and may be a leading toxicant causing preventable disease and death, with the rise in global tobacco consumption. Several different microbial pathways of nicotine metabolism have been reported: Arthrobacter uses the pyridine pathway, and Pseudomonas, like mammals, uses the pyrrolidine pathway. We identified and characterized a novel 6-hydroxy-3-succinoyl-pyridine (HSP) hydroxylase (HspB) using enzyme purification, peptide sequencing, and sequencing of the Pseudomonas putida S16 genome. The HSP hydroxylase has no known orthologs and converts HSP to 2,5-dihydroxy-pyridine and succinic semialdehyde, using NADH. (18)O(2) labeling experiments provided direct evidence for the incorporation of oxygen from O(2) into 2,5-dihydroxy-pyridine. The hspB gene deletion showed that this enzyme is essential for nicotine degradation, and site-directed mutagenesis identified an FAD-binding domain. This study demonstrates the importance of the newly discovered enzyme HspB, which is crucial for nicotine degradation by the Pseudomonas strain.
ESTHER : Tang_2011_J.Biol.Chem_286_39179
PubMedSearch : Tang_2011_J.Biol.Chem_286_39179
PubMedID: 21949128
Gene_locus related to this paper: psep6-f8g0m2

Title : Genome sequence of the thermophilic strain Bacillus coagulans 2-6, an efficient producer of high-optical-purity L-lactic acid - Su_2011_J.Bacteriol_193_4563
Author(s) : Su F , Yu B , Sun J , Ou HY , Zhao B , Wang L , Qin J , Tang H , Tao F , Jarek M , Scharfe M , Ma C , Ma Y , Xu P
Ref : Journal of Bacteriology , 193 :4563 , 2011
Abstract : Bacillus coagulans 2-6 is an efficient producer of lactic acid. The genome of B. coagulans 2-6 has the smallest genome among the members of the genus Bacillus known to date. The frameshift mutation at the start of the d-lactate dehydrogenase sequence might be responsible for the production of high-optical-purity l-lactic acid.
ESTHER : Su_2011_J.Bacteriol_193_4563
PubMedSearch : Su_2011_J.Bacteriol_193_4563
PubMedID: 21705584
Gene_locus related to this paper: bacc6-f7z0w1 , bacco-c1p801 , bacco-g2tqg6

Title : The Medicago genome provides insight into the evolution of rhizobial symbioses - Young_2011_Nature_480_520
Author(s) : Young ND , Debelle F , Oldroyd GE , Geurts R , Cannon SB , Udvardi MK , Benedito VA , Mayer KF , Gouzy J , Schoof H , Van de Peer Y , Proost S , Cook DR , Meyers BC , Spannagl M , Cheung F , De Mita S , Krishnakumar V , Gundlach H , Zhou S , Mudge J , Bharti AK , Murray JD , Naoumkina MA , Rosen B , Silverstein KA , Tang H , Rombauts S , Zhao PX , Zhou P , Barbe V , Bardou P , Bechner M , Bellec A , Berger A , Berges H , Bidwell S , Bisseling T , Choisne N , Couloux A , Denny R , Deshpande S , Dai X , Doyle JJ , Dudez AM , Farmer AD , Fouteau S , Franken C , Gibelin C , Gish J , Goldstein S , Gonzalez AJ , Green PJ , Hallab A , Hartog M , Hua A , Humphray SJ , Jeong DH , Jing Y , Jocker A , Kenton SM , Kim DJ , Klee K , Lai H , Lang C , Lin S , Macmil SL , Magdelenat G , Matthews L , McCorrison J , Monaghan EL , Mun JH , Najar FZ , Nicholson C , Noirot C , O'Bleness M , Paule CR , Poulain J , Prion F , Qin B , Qu C , Retzel EF , Riddle C , Sallet E , Samain S , Samson N , Sanders I , Saurat O , Scarpelli C , Schiex T , Segurens B , Severin AJ , Sherrier DJ , Shi R , Sims S , Singer SR , Sinharoy S , Sterck L , Viollet A , Wang BB , Wang K , Wang M , Wang X , Warfsmann J , Weissenbach J , White DD , White JD , Wiley GB , Wincker P , Xing Y , Yang L , Yao Z , Ying F , Zhai J , Zhou L , Zuber A , Denarie J , Dixon RA , May GD , Schwartz DC , Rogers J , Quetier F , Town CD , Roe BA
Ref : Nature , 480 :520 , 2011
Abstract : Legumes (Fabaceae or Leguminosae) are unique among cultivated plants for their ability to carry out endosymbiotic nitrogen fixation with rhizobial bacteria, a process that takes place in a specialized structure known as the nodule. Legumes belong to one of the two main groups of eurosids, the Fabidae, which includes most species capable of endosymbiotic nitrogen fixation. Legumes comprise several evolutionary lineages derived from a common ancestor 60 million years ago (Myr ago). Papilionoids are the largest clade, dating nearly to the origin of legumes and containing most cultivated species. Medicago truncatula is a long-established model for the study of legume biology. Here we describe the draft sequence of the M. truncatula euchromatin based on a recently completed BAC assembly supplemented with Illumina shotgun sequence, together capturing approximately 94% of all M. truncatula genes. A whole-genome duplication (WGD) approximately 58 Myr ago had a major role in shaping the M. truncatula genome and thereby contributed to the evolution of endosymbiotic nitrogen fixation. Subsequent to the WGD, the M. truncatula genome experienced higher levels of rearrangement than two other sequenced legumes, Glycine max and Lotus japonicus. M. truncatula is a close relative of alfalfa (Medicago sativa), a widely cultivated crop with limited genomics tools and complex autotetraploid genetics. As such, the M. truncatula genome sequence provides significant opportunities to expand alfalfa's genomic toolbox.
ESTHER : Young_2011_Nature_480_520
PubMedSearch : Young_2011_Nature_480_520
PubMedID: 22089132
Gene_locus related to this paper: medtr-b7fki4 , medtr-b7fmi1 , medtr-g7itl1 , medtr-g7iu67 , medtr-g7izm0 , medtr-g7j641 , medtr-g7jtf8 , medtr-g7jtg2 , medtr-g7jtg4 , medtr-g7kem3 , medtr-g7kml3 , medtr-g7ksx5 , medtr-g7leb3 , medtr-q1s5d8 , medtr-q1s9m3 , medtr-q1t171 , medtr-g7k9e1 , medtr-g7k9e3 , medtr-g7k9e5 , medtr-g7k9e8 , medtr-g7k9e9 , medtr-g7lbp2 , medtr-g7lch3 , medtr-g7ib94 , medtr-g7ljk8 , medtr-g7i6w5 , medtr-g7kvg4 , medtr-g7iam1 , medtr-g7iam3 , medtr-g7l754 , medtr-g7jr41 , medtr-g7l4f5 , medtr-g7l755 , medtr-a0a072vyl4 , medtr-g7jwk8 , medtr-a0a072vhg0 , medtr-a0a072vrv9 , medtr-g7kmk5 , medtr-a0a072uuf6 , medtr-a0a072urp3 , medtr-g7zzc3 , medtr-g7ie19 , medtr-g7kst7 , medtr-a0a072u5k5 , medtr-a0a072v056 , medtr-scp1 , medtr-g7kyn0 , medtr-g7inw6 , medtr-g7j3q3

Title : The ecoresponsive genome of Daphnia pulex - Colbourne_2011_Science_331_555
Author(s) : Colbourne JK , Pfrender ME , Gilbert D , Thomas WK , Tucker A , Oakley TH , Tokishita S , Aerts A , Arnold GJ , Basu MK , Bauer DJ , Caceres CE , Carmel L , Casola C , Choi JH , Detter JC , Dong Q , Dusheyko S , Eads BD , Frohlich T , Geiler-Samerotte KA , Gerlach D , Hatcher P , Jogdeo S , Krijgsveld J , Kriventseva EV , Kultz D , Laforsch C , Lindquist E , Lopez J , Manak JR , Muller J , Pangilinan J , Patwardhan RP , Pitluck S , Pritham EJ , Rechtsteiner A , Rho M , Rogozin IB , Sakarya O , Salamov A , Schaack S , Shapiro H , Shiga Y , Skalitzky C , Smith Z , Souvorov A , Sung W , Tang Z , Tsuchiya D , Tu H , Vos H , Wang M , Wolf YI , Yamagata H , Yamada T , Ye Y , Shaw JR , Andrews J , Crease TJ , Tang H , Lucas SM , Robertson HM , Bork P , Koonin EV , Zdobnov EM , Grigoriev IV , Lynch M , Boore JL
Ref : Science , 331 :555 , 2011
Abstract : We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than a third of Daphnia's genes have no detectable homologs in any other available proteome, and the most amplified gene families are specific to the Daphnia lineage. The coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random, and the analysis of gene expression under different environmental conditions reveals that numerous paralogs acquire divergent expression patterns soon after duplication. Daphnia-specific genes, including many additional loci within sequenced regions that are otherwise devoid of annotations, are the most responsive genes to ecological challenges.
ESTHER : Colbourne_2011_Science_331_555
PubMedSearch : Colbourne_2011_Science_331_555
PubMedID: 21292972
Gene_locus related to this paper: dappu-e9fut0 , dappu-e9fut9 , dappu-e9fvw6 , dappu-e9fxt4 , dappu-e9fyr6 , dappu-e9fzg6 , dappu-e9g1e2 , dappu-e9g1e6 , dappu-e9g1e7 , dappu-e9g1e8 , dappu-e9g1v3 , dappu-e9g1z2 , dappu-e9gb99 , dappu-e9gba0 , dappu-e9gcb4 , dappu-e9gdv5 , dappu-e9gdv7 , dappu-e9gi24 , dappu-e9gj77 , dappu-e9gja7 , dappu-e9gmp5 , dappu-e9gmr0 , dappu-e9gn32 , dappu-e9gp76 , dappu-e9gp82 , dappu-e9gp98 , dappu-e9gp99 , dappu-e9gvl2 , dappu-e9gzn7 , dappu-e9h1p4 , dappu-e9h2c8 , dappu-e9h2c9 , dappu-e9h6x9 , dappu-e9h6y4 , dappu-e9h7w9 , dappu-e9h8r4 , dappu-e9hd06 , dappu-e9hh56 , dappu-e9hh57 , dappu-e9hh59 , dappu-e9hmp4 , dappu-e9hp64 , dappu-e9hp65 , dappu-e9hpy8 , dappu-e9htg8 , dapul-ACHE1 , dapul-ACHE2 , dappu-e9gnj1 , dappu-e9gu36 , dappu-e9hpc4 , dappu-e9gb07 , dappu-e9glp6 , dappu-e9glp5 , dappu-e9gjv2 , dappu-e9h0c7 , dappu-e9g4g2 , dappu-e9gw69 , dappu-e9h3h9 , dappu-e9g545 , dappu-e9gw71 , dappu-e9gw68 , dappu-e9h3e7 , dappu-e9gfg9 , dappu-e9fvy6 , dappu-e9hgt2

Title : The genome of the mesopolyploid crop species Brassica rapa - Wang_2011_Nat.Genet_43_1035
Author(s) : Wang X , Wang H , Wang J , Sun R , Wu J , Liu S , Bai Y , Mun JH , Bancroft I , Cheng F , Huang S , Li X , Hua W , Freeling M , Pires JC , Paterson AH , Chalhoub B , Wang B , Hayward A , Sharpe AG , Park BS , Weisshaar B , Liu B , Li B , Tong C , Song C , Duran C , Peng C , Geng C , Koh C , Lin C , Edwards D , Mu D , Shen D , Soumpourou E , Li F , Fraser F , Conant G , Lassalle G , King GJ , Bonnema G , Tang H , Belcram H , Zhou H , Hirakawa H , Abe H , Guo H , Jin H , Parkin IA , Batley J , Kim JS , Just J , Li J , Xu J , Deng J , Kim JA , Yu J , Meng J , Min J , Poulain J , Hatakeyama K , Wu K , Wang L , Fang L , Trick M , Links MG , Zhao M , Jin M , Ramchiary N , Drou N , Berkman PJ , Cai Q , Huang Q , Li R , Tabata S , Cheng S , Zhang S , Sato S , Sun S , Kwon SJ , Choi SR , Lee TH , Fan W , Zhao X , Tan X , Xu X , Wang Y , Qiu Y , Yin Y , Li Y , Du Y , Liao Y , Lim Y , Narusaka Y , Wang Z , Li Z , Xiong Z , Zhang Z
Ref : Nat Genet , 43 :1035 , 2011
Abstract : We report the annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage. We modeled 41,174 protein coding genes in the B. rapa genome, which has undergone genome triplication. We used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution. The extent of gene loss (fractionation) among triplicated genome segments varies, with one of the three copies consistently retaining a disproportionately large fraction of the genes expected to have been present in its ancestor. Variation in the number of members of gene families present in the genome may contribute to the remarkable morphological plasticity of Brassica species. The B. rapa genome sequence provides an important resource for studying the evolution of polyploid genomes and underpins the genetic improvement of Brassica oil and vegetable crops.
ESTHER : Wang_2011_Nat.Genet_43_1035
PubMedSearch : Wang_2011_Nat.Genet_43_1035
PubMedID: 21873998
Gene_locus related to this paper: braol-Q8GTM3 , braol-Q8GTM4 , brarp-m4ei94 , brarp-m4c988 , brana-a0a078j4a9 , brana-a0a078e1m0 , brana-a0a078cd75 , brarp-m4dwa6 , brana-a0a078j4f0 , brana-a0a078cus4 , brana-a0a078f8c2 , brana-a0a078jql1 , brana-a0a078dgj3 , brana-a0a078hw50 , brana-a0a078cuu0 , brana-a0a078dfa9 , brana-a0a078ic91 , brarp-m4ctw3 , brana-a0a078ca65 , brana-a0a078ctc8 , brana-a0a078h021 , brana-a0a078jx23 , brarp-m4da84 , brarp-m4dwr7 , brana-a0a078dh94 , brana-a0a078h612 , brana-a0a078j2t3 , braol-a0a0d3dpb2 , braol-a0a0d3dx76 , brana-a0a078jxa8 , brana-a0a078i2k3 , brarp-m4cwq4 , brarp-m4dcj8 , brarp-m4eh17 , brarp-m4eey4 , brarp-m4dnj8 , brarp-m4ey83 , brarp-m4ey84

Title : Hybrids of oxoisoaporphine-tacrine congeners: novel acetylcholinesterase and acetylcholinesterase-induced beta-amyloid aggregation inhibitors - Tang_2011_Eur.J.Med.Chem_46_4970
Author(s) : Tang H , Zhao LZ , Zhao HT , Huang SL , Zhong SM , Qin JK , Chen ZF , Huang ZS , Liang H
Ref : Eur Journal of Medicinal Chemistry , 46 :4970 , 2011
Abstract : A series of dual binding site acetylcholinesterase (AChE) inhibitors have been designed, synthesized, and tested for their ability to inhibit AChE, butyrylcholinesterase (BChE), AChE-induced and self-induced beta-amyloid (Abeta) aggregation. The new hybrids consist of a unit of 1-azabenzanthrone and a tacrine or its congener, connected through an oligomethylene linker containing an amine group at variable position. These hybrids exhibit high AChE inhibitory activity with IC(50) values in the nanomolar range in most cases. Moreover, five out of the 12 hybrids of this series, particularly those bearing a tetrahydroacridine moiety, exhibit a significant in vitro inhibitory activity toward the AChE-induced and self-induced Abeta aggregation, which makes them promising anti-Alzheimer drug candidates.
ESTHER : Tang_2011_Eur.J.Med.Chem_46_4970
PubMedSearch : Tang_2011_Eur.J.Med.Chem_46_4970
PubMedID: 21871694

Title : The genes coding for the conversion of carbazole to catechol are flanked by IS6100 elements in Sphingomonas sp. strain XLDN2-5 - Gai_2010_PLoS.One_5_e10018
Author(s) : Gai Z , Wang X , Liu X , Tai C , Tang H , He X , Wu G , Deng Z , Xu P
Ref : PLoS ONE , 5 :e10018 , 2010
Abstract : BACKGROUND: Carbazole is a recalcitrant compound with a dioxin-like structure and possesses mutagenic and toxic activities. Bacteria respond to a xenobiotic by recruiting exogenous genes to establish a pathway to degrade the xenobiotic, which is necessary for their adaptation and survival. Usually, this process is mediated by mobile genetic elements such as plasmids, transposons, and insertion sequences. FINDINGS: The genes encoding the enzymes responsible for the degradation of carbazole to catechol via anthranilate were cloned, sequenced, and characterized from a carbazole-degrading Sphingomonas sp. strain XLDN2-5. The car gene cluster (carRAaBaBbCAc) and fdr gene were accompanied on both sides by two copies of IS6100 elements, and organized as IS6100::ISSsp1-ORF1-carRAaBaBbCAc-ORF8-IS6100-fdr-IS6100. Carbazole was converted by carbazole 1,9a-dioxygenase (CARDO, CarAaAcFdr), meta-cleavage enzyme (CarBaBb), and hydrolase (CarC) to anthranilate and 2-hydroxypenta-2,4-dienoate. The fdr gene encoded a novel ferredoxin reductase whose absence resulted in lower transformation activity of carbazole by CarAa and CarAc. The ant gene cluster (antRAcAdAbAa) which was involved in the conversion of anthranilate to catechol was also sandwiched between two IS6100 elements as IS6100-antRAcAdAbAa-IS6100. Anthranilate 1,2-dioxygenase (ANTDO) was composed of a reductase (AntAa), a ferredoxin (AntAb), and a two-subunit terminal oxygenase (AntAcAd). Reverse transcription-PCR results suggested that carAaBaBbCAc gene cluster, fdr, and antRAcAdAbAa gene cluster were induced when strain XLDN2-5 was exposed to carbazole. Expression of both CARDO and ANTDO in Escherichia coli required the presence of the natural reductases for full enzymatic activity. CONCLUSIONS/SIGNIFICANCE: We predict that IS6100 might play an important role in the establishment of carbazole-degrading pathway, which endows the host to adapt to novel compounds in the environment. The organization of the car and ant genes in strain XLDN2-5 was unique, which showed strong evolutionary trail of gene recruitment mediated by IS6100 and presented a remarkable example of rearrangements and pathway establishments.
ESTHER : Gai_2010_PLoS.One_5_e10018
PubMedSearch : Gai_2010_PLoS.One_5_e10018
PubMedID: 20368802

Title : [Effects of lipoprotein lipase gene Ser447stop polymorphism on changes of serum lipid ratios induced by high-carbohydrate\/low-fat diet in healthy youth] - Huang_2010_Sichuan.Da.Xue.Xue.Bao.Yi.Xue.Ban_41_243
Author(s) : Huang X , Fang DZ , Du J , Tang H , Li RH
Ref : Sichuan Da Xue Xue Bao Yi Xue Ban , 41 :243 , 2010
Abstract : OBJECTIVE To investigate the effects of lipoprotein lipase gene (LPL) Ser447stop polymorphism on serum lipid ratios and their responses to high-carbohydrate/low-fat (HC/LF) diet in healthy youth. METHODS: Fifty-six healthy subjects [(22.89 +/- 1.80) years) were given control diets of 31% fat and 54% carbohydrate for 7 days, followed by HC diets of 15% fat and 70% carbohydrate for 6 days, without total energy restriction. Serum lipid profiles at baseline, before and after HC diets, as well as LPL Ser447stop polymorphisms were analyzed. TG/ HDL-C, log (TG/HDL-C), TC/HDL-C, and LDL-C/HDL-C were calculated. RESULTS: No significant differences were found of the lipid ratios at baseline and before and after HC/LF diet between subjects of wild type (S447S) and mutation carriers (447XC) in the whole study population or males and females separately. When compared with those before HC/LF diet, significantly decreased LDL-C/HDL-C and TC/HDL-C were found regardless of LPL Ser447stop genotype (P < 0.05) and increased log (TG/HDL-C) in subjects with S447S (P < 0.05) in the whole study population. After gender was taken into account, LDL-C/HDL-C and TC/HDL-C were significantly decreased in males (P < 0.001) regardless of LPL Ser447stop polymorphism. TG/HDL-C and log (TG/HDL-C) were significantly increased (P < 0.05), and LDL-C/HDL-C and TC/HDL-C were significantly decreased (P < 0.05) in females with S447S. No significant differences were found in females with 447XC. CONCLUSION: The functional C to G mutation of LPL Ser447Stop could attenuate the elevated log (TG/HDL-C) induced by HC/LF diet. Interactions of LPL Ser447Stop polymorphism with HC/LF diet on the lipid ratios were gender-specific and effective only in females.
ESTHER : Huang_2010_Sichuan.Da.Xue.Xue.Bao.Yi.Xue.Ban_41_243
PubMedSearch : Huang_2010_Sichuan.Da.Xue.Xue.Bao.Yi.Xue.Ban_41_243
PubMedID: 20506644

Title : Synthesis, biological evaluation and molecular modeling of oxoisoaporphine and oxoaporphine derivatives as new dual inhibitors of acetylcholinesterase\/butyrylcholinesterase - Tang_2009_Eur.J.Med.Chem_44_2523
Author(s) : Tang H , Wei YB , Zhang C , Ning FX , Qiao W , Huang SL , Ma L , Huang ZS , Gu LQ
Ref : Eur Journal of Medicinal Chemistry , 44 :2523 , 2009
Abstract : Aporphine alkaloids, isolated from Chinese medicinal herb, are important natural products. We recently reported that synthetic derivatives of oxoisoaporphine alkaloids exhibited high acetylcholinesterase inhibitory activity and high selectivity for AChE over BuChE (Bioorg. Med. Chem. Lett. 2007, 17, 3765-3768). In this paper, further research results were presented. A series of novel derivatives of oxoaporphine alkaloids (5a-j, 4-carboxylic amide-7-oxo-7H-dibenzo[de,g]quinoline, Ar-CONH(CH(2))(n)NR) and their quaternary methiodide salts (6a-h, Ar-CONH(CH(2))(n)N(+)(CH(3))RI(-)) were designed and synthesized as acetylcholinesterase (AChE) and/or butyrylcholinesterase (BuChE) inhibitors. The AChE inhibition potency of synthetic oxoaporphine derivatives was decreased about 2-3 orders of magnitude as compared with that of oxoisoaporphine derivatives. Non-competitive binding mode was found for both kinds of derivatives. Molecular docking simulations on the oxoisoaporphine derivatives 7 series and oxoaporphine derivatives 6 series with AChE from Torpedo californica have demonstrated that the ligands bound to the dual-site of the enzyme.
ESTHER : Tang_2009_Eur.J.Med.Chem_44_2523
PubMedSearch : Tang_2009_Eur.J.Med.Chem_44_2523
PubMedID: 19243862

Title : The Sorghum bicolor genome and the diversification of grasses - Paterson_2009_Nature_457_551
Author(s) : Paterson AH , Bowers JE , Bruggmann R , Dubchak I , Grimwood J , Gundlach H , Haberer G , Hellsten U , Mitros T , Poliakov A , Schmutz J , Spannagl M , Tang H , Wang X , Wicker T , Bharti AK , Chapman J , Feltus FA , Gowik U , Grigoriev IV , Lyons E , Maher CA , Martis M , Narechania A , Otillar RP , Penning BW , Salamov AA , Wang Y , Zhang L , Carpita NC , Freeling M , Gingle AR , Hash CT , Keller B , Klein P , Kresovich S , McCann MC , Ming R , Peterson DG , Mehboob ur R , Ware D , Westhoff P , Mayer KF , Messing J , Rokhsar DS
Ref : Nature , 457 :551 , 2009
Abstract : Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel. We present an initial analysis of the approximately 730-megabase Sorghum bicolor (L.) Moench genome, placing approximately 98% of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information. Genetic recombination is largely confined to about one-third of the sorghum genome with gene order and density similar to those of rice. Retrotransposon accumulation in recombinationally recalcitrant heterochromatin explains the approximately 75% larger genome size of sorghum compared with rice. Although gene and repetitive DNA distributions have been preserved since palaeopolyploidization approximately 70 million years ago, most duplicated gene sets lost one member before the sorghum-rice divergence. Concerted evolution makes one duplicated chromosomal segment appear to be only a few million years old. About 24% of genes are grass-specific and 7% are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum's drought tolerance.
ESTHER : Paterson_2009_Nature_457_551
PubMedSearch : Paterson_2009_Nature_457_551
PubMedID: 19189423
Gene_locus related to this paper: sorbi-b3vtb2 , sorbi-c5wp75 , sorbi-c5wts6 , sorbi-c5wu07 , sorbi-c5wvl7 , sorbi-c5ww85 , sorbi-c5ww86 , sorbi-c5wxa4 , sorbi-c5x1f6 , sorbi-c5x2x9 , sorbi-c5x5z9 , sorbi-c5x6q0 , sorbi-c5x230 , sorbi-c5x290 , sorbi-c5x345 , sorbi-c5x399 , sorbi-c5x610 , sorbi-c5xbm4 , sorbi-c5xct0 , sorbi-c5xdv0 , sorbi-c5xe87 , sorbi-c5xf40 , sorbi-c5xfu9 , sorbi-c5xh40 , sorbi-c5xh41 , sorbi-c5xh42 , sorbi-c5xh43 , sorbi-c5xh44 , sorbi-c5xh46 , sorbi-c5xhr2 , sorbi-c5xiw7 , sorbi-c5xjf0 , sorbi-c5xky2 , sorbi-c5xm54 , sorbi-c5xmb9 , sorbi-c5xmz5 , sorbi-c5xp10 , sorbi-c5xpm6 , sorbi-c5xr91 , sorbi-c5xr92 , sorbi-c5xs33 , sorbi-c5xtz0 , sorbi-c5xwd3 , sorbi-c5y0d2 , sorbi-c5y0h4 , sorbi-c5y3i5 , sorbi-c5y7x0 , sorbi-c5y517 , sorbi-c5y545 , sorbi-c5ydr3 , sorbi-c5yec0 , sorbi-c5yf71 , sorbi-c5yi32 , sorbi-c5yih2 , sorbi-c5ylw6 , sorbi-c5yn66 , sorbi-c5ynp8 , sorbi-c5yt11 , sorbi-c5yur5 , sorbi-c5ywz3 , sorbi-c5ywz4 , sorbi-c5yx73 , sorbi-c5yyn0 , sorbi-c5z2m6 , sorbi-c5z6a9 , sorbi-c5z6j1 , sorbi-c5z6s5 , sorbi-c5z177 , sorbi-Q9XE80 , sorbi-c5xyg4 , sorbi-c5z4q0 , sorbi-c5xly4 , sorbi-c5z4u8 , sorbi-c5xxg5 , sorbi-c5z9b9 , sorbi-a0a1z5r970 , sorbi-c5xhf9 , sorbi-c5yxt7 , sorbi-c5yxt6 , sorbi-c5y1m2 , sorbi-c5xdy6 , sorbi-a0a194ysf6 , sorbi-a0a1b6pnr2 , sorbi-a0a1b6qcb9 , sorbi-c5xx30 , sorbi-a0a1b6psg4 , sorbi-a0a1z5rj80 , sorbi-a0a1b6qfm2 , sorbi-a0a1b6qmu5 , sorbi-c6jru0

Title : Derivatives of oxoisoaporphine alkaloids: a novel class of selective acetylcholinesterase inhibitors - Tang_2007_Bioorg.Med.Chem.Lett_17_3765
Author(s) : Tang H , Ning FX , Wei YB , Huang SL , Huang ZS , Chan AS , Gu LQ
Ref : Bioorganic & Medicinal Chemistry Lett , 17 :3765 , 2007
Abstract : A series of 9-aminoalkanamido-1-azabenzanthrones derviatives (3a-i Ar-NHCO(CH(2))(n)NR(1)R(2)) and their quaternary methiodide salts (4a-g Ar-NHCO(CH(2))(n)N(+)(CH(3))R(1)R(2)I(-)) were designed and synthesized as acetylcholinesterase (AChE) or butyrylcholinesterase (BuChE) inhibitors. The synthetic compounds exhibited high AChE inhibitory activity with IC(50) values in the nanomolar range and high selectivity for AChE over BuChE (45- to 1980-fold). The structure-activity relationships (SARs) were discussed.
ESTHER : Tang_2007_Bioorg.Med.Chem.Lett_17_3765
PubMedSearch : Tang_2007_Bioorg.Med.Chem.Lett_17_3765
PubMedID: 17451950

Title : Comparative and functional genomic analyses of the pathogenicity of phytopathogen Xanthomonas campestris pv. campestris - Qian_2005_Genome.Res_15_757
Author(s) : Qian W , Jia Y , Ren SX , He YQ , Feng JX , Lu LF , Sun Q , Ying G , Tang DJ , Tang H , Wu W , Hao P , Wang L , Jiang BL , Zeng S , Gu WY , Lu G , Rong L , Tian Y , Yao Z , Fu G , Chen B , Fang R , Qiang B , Chen Z , Zhao GP , Tang JL , He C
Ref : Genome Res , 15 :757 , 2005
Abstract : Xanthomonas campestris pathovar campestris (Xcc) is the causative agent of crucifer black rot disease, which causes severe losses in agricultural yield world-wide. This bacterium is a model organism for studying plant-bacteria interactions. We sequenced the complete genome of Xcc 8004 (5,148,708 bp), which is highly conserved relative to that of Xcc ATCC 33913. Comparative genomics analysis indicated that, in addition to a significant genomic-scale rearrangement cross the replication axis between two IS1478 elements, loss and acquisition of blocks of genes, rather than point mutations, constitute the main genetic variation between the two Xcc strains. Screening of a high-density transposon insertional mutant library (16,512 clones) of Xcc 8004 against a host plant (Brassica oleraceae) identified 75 nonredundant, single-copy insertions in protein-coding sequences (CDSs) and intergenic regions. In addition to known virulence factors, full virulence was found to require several additional metabolic pathways and regulatory systems, such as fatty acid degradation, type IV secretion system, cell signaling, and amino acids and nucleotide metabolism. Among the identified pathogenicity-related genes, three of unknown function were found in Xcc 8004-specific chromosomal segments, revealing a direct correlation between genomic dynamics and Xcc virulence. The present combination of comparative and functional genomic analyses provides valuable information about the genetic basis of Xcc pathogenicity, which may offer novel insight toward the development of efficient methods for prevention of this important plant disease.
ESTHER : Qian_2005_Genome.Res_15_757
PubMedSearch : Qian_2005_Genome.Res_15_757
PubMedID: 15899963
Gene_locus related to this paper: xanax-DHAA , xanax-ENTF2 , xanax-GAA , xanax-PTRB , xanax-XAC0515 , xanax-XAC0628 , xanax-XAC0736 , xanax-XAC0753 , xanax-XAC1713 , xanca-acvB , xanca-BIOH , xanca-CATD , xanca-CPO , xanca-estA1 , xanca-impep , xanca-META , xanca-METX , xanca-PCAD , xanca-PHBC , xanca-Q8PB04 , xanca-W78 , xanca-XCC0080 , xanca-XCC0180 , xanca-XCC0243 , xanca-XCC0266 , xanca-XCC0372 , xanca-XCC0375 , xanca-XCC0753 , xanca-XCC0800 , xanca-XCC0843 , xanca-XCC1105 , xanca-XCC1734 , xanca-XCC2285 , xanca-XCC2374 , xanca-XCC2397 , xanca-XCC2405 , xanca-XCC2566 , xanca-XCC2722 , xanca-XCC2737 , xanca-XCC2811 , xanca-XCC2817 , xanca-XCC2854 , xanca-XCC2869 , xanca-XCC3028 , xanca-XCC3164 , xanca-XCC3219 , xanca-XCC3296 , xanca-XCC3320 , xanca-XCC3514 , xanca-XCC3548 , xanca-XCC3555 , xanca-XCC3623 , xanca-XCC3915 , xanca-XCC3961 , xanca-XCC3970 , xanca-XCC4016 , xanca-XCC4096 , xanca-XCC4180 , xanca-XYNB , xanca-XYNB2 , xancb-b0rq23 , xancp-q8pax3 , xancp-y2094

Title : Death of preganglionic sympathetic neurons after surgical or immunologic lesion of peripheral processes - Tang_2002_Exp.Neurol_177_105
Author(s) : Tang H , Brimijoin S
Ref : Experimental Neurology , 177 :105 , 2002
Abstract : Three months after systemic injection of antibody to acetylcholinesterase (AChE), there is a 60% decrease in the population of preganglionic sympathetic neurons expressing choline acetyltransferase (ChAT) in the intermediolateral (IML) nucleus of the rat spinal cord. In principle, the disappearance of identifiable cholinergic neurons might reflect either outright cell death or severe atrophy with downregulation of cholinergic markers. To distinguish between these possibilities, preganglionic neurons were labeled with the retrograde tracer dye, Fast Blue, 1 week before antibody injection or surgical transection of the cervical sympathetic trunk. Three months after either treatment, the thoracic IML contained 40-60% fewer Fast Blue-labeled neurons than in controls. Therefore, preganglionic sympathetic neurons do degenerate after antibody injection or axotomy. To clarify the role of axonal damage in this process, the effects of three different mechanical lesions were examined. A lumbar ganglionectomy designed to interrupt most sympathetic axons emanating from L2 IML caused 92% loss of ChAT-positive cells observed 10 weeks later at that site. In comparison, transection of the cervical sympathetic trunk, which spared some distally directed axonal branches from the thoracic IML, caused only a 46% loss of ChAT-positive neurons at T1. Still smaller effects were seen after the same nerve was crushed, a lesion that is less destructive. Thus, the ability of central sympathetic neurons to survive a peripheral lesion may be related to the degree of axonal damage and to the opportunity for axonal regrowth.
ESTHER : Tang_2002_Exp.Neurol_177_105
PubMedSearch : Tang_2002_Exp.Neurol_177_105
PubMedID: 12429215

Title : Complement regulatory proteins and selective vulnerability of neurons to lysis on exposure to acetylcholinesterase antibody - Tang_2001_J.Neuroimmunol_115_53
Author(s) : Tang H , Brimijoin S
Ref : Journal of Neuroimmunology , 115 :53 , 2001
Abstract : Systemic injection of antibodies against acetylcholinesterase (AChE) induces complement-mediated destruction of preganglionic nerve terminals in paravertebral sympathetic ganglia, but spares other AChE-rich structures, such as nerve terminals in prevertebral sympathetic ganglia, parasympathetic ganglia, and the neuromuscular junction. This pattern of differing sensitivity to "AChE immunolesion" might be explained by a differing expression of proteins that serve to protect host cells from complement activation. Two major complement regulatory proteins in rats are Crry, which interferes with the assembly of C3 convertase, and CD59, which blocks formation of the terminal cytolytic membrane attack complex. The present study used immunohistochemistry to demonstrate an inverse relation between levels of CD59 and Crry expression and sensitivity to AChE immunolesion in several AChE-rich targets. Thus, the most sensitive structures, i.e., preganglionic nerve terminals in the adrenal gland and superior cervical ganglion (SCG), expressed undetectable levels of CD59 and Crry immunoreactivities. By contrast, AChE-rich, but antibody-resistant, cholinergic nerve terminals in the inferior mesenteric ganglia (IMG) and diaphragm muscle expressed significant amounts of CD59 and Crry. Such expression was functionally important because, after membrane-anchored CD59 was removed from explanted IMG with phosphatidylinositol phospholipase C, exposure to AChE antibody and complement caused greater immunolesion. It was concluded that differential expression of regulatory proteins in different parts of the nervous system influences regional vulnerability to complement mediated damage.
ESTHER : Tang_2001_J.Neuroimmunol_115_53
PubMedSearch : Tang_2001_J.Neuroimmunol_115_53
PubMedID: 11282154

Title : Complement-mediated lesion of sympathetic ganglia in vitro with acetylcholinesterase antibodies - Tang_1999_J.Neuroimmunol_97_86
Author(s) : Tang H , Miller SM , Ermilov LG , Lennon VA , Brimijoin S
Ref : Journal of Neuroimmunology , 97 :86 , 1999
Abstract : When administered to rats, antibodies against acetylcholinesterase (AChE) selectively destroy presynaptic inputs to sympathetic ganglia. To investigate the mechanism of this immunolesion, we created an in vitro system in which relevant components could be manipulated. Freshly dissected rat superior cervical ganglia (SCG) were incubated 15-20 h at 37 degrees C in fresh human serum (a potent source of complement) with continuous oxygenation. More than 96% of neurons in six control ganglia retained synaptic inputs, as defined by action potentials or excitatory postsynaptic potentials (EPSP) upon stimulation of the preganglionic trunk. However, when anti-AChE antibodies were present (0.16 mg/ml), none of 61 neurons from six incubated ganglia showed synaptic responses although membrane potential and input resistance remained normal. Staining for AChE and synaptophysin (a synaptic vesicle marker) was also disrupted in ganglia exposed to AChE antibodies in complement-sufficient serum. When complement was eliminated by substituting serum that was heat-inactivated or deficient in C3, synaptic input was retained in 60-90% of neurons incubated with AChE antibodies. Choline acetyltransferase activity (ChAT), an enzymatic marker of cholinergic cytoplasm in sympathetic ganglia, was largely lost after incubation with AChE antibodies and serum. However, incubation with AChE antibodies in heat-inactivated serum, or serum that was deficient in C3 or C8, caused no measurable loss of ganglionic ChAT activity. These findings strongly implicate the complement cascade in the destruction of preganglionic sympathetic terminals that follows binding of AChE antibodies.
ESTHER : Tang_1999_J.Neuroimmunol_97_86
PubMedSearch : Tang_1999_J.Neuroimmunol_97_86
PubMedID: 10408983

Title : Acetylcholinesterase Autoimmunity In Vitro -
Author(s) : Tang H , Hammond P , Ermilov L , Miller S , Brimijoin S
Ref : In: Structure and Function of Cholinesterases and Related Proteins - Proceedings of Sixth International Meeting on Cholinesterases , (Doctor, B.P., Taylor, P., Quinn, D.M., Rotundo, R.L., Gentry, M.K. Eds) Plenum Publishing Corp. :149 , 1998

Title : Acetylcholinesterase immunolesioning: regional vulnerability of preganglionic sympathetic neurons in rat spinal cord - Tang_1998_Exp.Neurol_152_167
Author(s) : Tang H , Hammond P , Brimijoin S
Ref : Experimental Neurology , 152 :167 , 1998
Abstract : Rats given antibodies against acetylcholinesterase (AChE) develop sympathetic dysfunction stemming from losses of preganglionic neurons in spinal cord. Central effects of AChE antibodies are surprising since IgG does not readily cross the blood-brain barrier, and lesions of peripheral terminals should not cause cell death. This study was designed to explore the distribution of central neural damage and to investigate features that might account for vulnerability. Rat spinal cord and brainstem were stained for choline acetyltransferase (ChAT) and nitric oxide synthase (NOS) immunoreactivity. Four months after administration of AChE antibodies, ChAT-positive neurons in the intermediolateral nucleus (IML) were 61-66% fewer throughout the thoracolumbar cord (T1, T2, T8, T12, L1). NOS-positive neurons in these loci were affected to the same extent by antibody-treatment, although they were only two-thirds as numerous. By contrast, neurons in the central autonomic nucleus of the thoracolumbar cord were scarcely affected. These results point to immunochemical differences in the central autonomic outflow, which may partially explain the puzzling selectivity of neural damage in AChE immunolesioning. Different results were obtained after guanethidine sympathectomy, which ablated nearly all neurons in the superior cervical ganglion without any effect on preganglionic neurons in the IML. Therefore, if the central effects of antibodies are indirectly mediated by loss of trophic support from the periphery, this support cannot arise from adrenergic neurons but must come from other ganglionic cells.
ESTHER : Tang_1998_Exp.Neurol_152_167
PubMedSearch : Tang_1998_Exp.Neurol_152_167
PubMedID: 9710515