[Objective] The Cu-tolerance and Cu enrichment capacity of TLSB2-K were investigated. [Method] The previously isolated TLSB2-K strain was identified though morphological observation, gram staining and 16S rDNA sequenc...[Objective] The Cu-tolerance and Cu enrichment capacity of TLSB2-K were investigated. [Method] The previously isolated TLSB2-K strain was identified though morphological observation, gram staining and 16S rDNA sequence alignment. In ad- dition, the effects of temperature, pH and osmotic pressure on the growth of strain were also investigated by using shaking culture. The Cu-tolerance and Cu enrich- ment capacity of TLSB2-K strain under Cu stress were also studied. [Result] The results showed TLSB2-K belongs to Bacillus spp., and its optimum growth conditions were as follows： temperature, 27 ~C; pH, 7.0; osmotic pressure, 1.1% NaCI. When the Cu concentration ranged from 100 mg/L to 500 mg/L, the strain grew well; when the Cu concentration ranged from 100 mg/L to 400 mg/L, the Cu content in bacteria was increased with the increase of Cu concentration; when the Cu con- centration was 400 mg/L and the incubation time was 30 h, the Cu content in bac- teria reached the peak （2 250 mg/kg）; the highest tolerant concentration was 700 mg/L. [Conclusion] TLSB2-K strain had relatively high Cu tolerance and Cu enrich- ment capacity. They had important theoretical research and engineering application values.展开更多
In this paper, a feasible scheme is reported for the detection and identification of trace alcohol congeners that have identical elemental composition using laser-induced breakdown spectroscopy （LIBS）. In the scheme...In this paper, a feasible scheme is reported for the detection and identification of trace alcohol congeners that have identical elemental composition using laser-induced breakdown spectroscopy （LIBS）. In the scheme, an intensive pulsed laser is used to break down trace alcohol samples and the optical emission spectra of the induced plasma are collected for the detection and identifq ication of alcohol molecules. In order to prepare trace alcohol samples, pure ethanol or methanol is bubbled by argon carrier gas and then mixed into matrix gases. The key issue for the scheme is to constitute indices from the LIBS data of the alcohol samples. Two indices are found to be suitable for alcohol detection and identification. One is the emission intensity ratio （denoted as H/C） of the hydrogen line （653.3 nm） to the carbon line （247.9 nm） for identification and the other is the ratio of the carbon line （as C/Ar） or the hydrogen line （as H/Ar） to the argon lines （866.7 nm） for quantitative detection. The calibration experiment result shows that the index H/C is specific for alcohol congeners while almost being independent of alcohol concentration. In detail, the H/C keeps a specific constant of 34 and 23 respectively for ethanol and methanol. In the meanwhile, the C/Ar and H/Ar indices respond almost linearly to the alcohol concentration below 1300 ppm, and are therefore competent for concentration measurement. With the indices, trace alcohol concentration measurement achieves a limit of 140 ppm using a laser pulse energy of 300 mJ.展开更多
We studied the activation of β2-adrenergic receptor（β2AR） by norepinephrine, epinephrine and isoprote- renol using docking and molecular dynamics（MD） simulation. The simulation was done on the assumption that β...We studied the activation of β2-adrenergic receptor（β2AR） by norepinephrine, epinephrine and isoprote- renol using docking and molecular dynamics（MD） simulation. The simulation was done on the assumption that β2AR was surrounded with explicit water and infinite lipid bilayer membrane at body temperature. So the result should be close to that under the physiological conditions. We calculated the structure of binding sites in β2AR for the three ac- tivators. We also simulated the change of the conformation ofβ2AR in the transmembrane regions（TMs）, in the mo- lecular switches, and in the conserved DRY（Aspartic acid, Arginine and Tyrosine） motif. This study provides detailed information concerning the structure ofβ2AR during activation process.展开更多
We present a systematic investigation of the impact of changing the geometry structure of the SPC/E water model by performing a series of molecular dynamic simulations at 1 bar （1 bar = 105 Pa） and 298.15 K. The geo...We present a systematic investigation of the impact of changing the geometry structure of the SPC/E water model by performing a series of molecular dynamic simulations at 1 bar （1 bar = 105 Pa） and 298.15 K. The geometric modification includes altering the H-O-H angle range from 90° to 115° and modifying the O-H length range from 0.90 A to 1.10 A in the SPC/E model. The former is achieved by keeping the dipole moment constant by modifying the O-H length, while in the latter only the O-H length is changed. With the larger bond length and angle, we find that the liquid shows a strong quadrupole interaction and high tetrahedral structure order parameter, resulting in the enhancement of the network structure of the liquid. When the bond length or angle is reduced, the hydrogen bond lifetime and self-diffusion constant decrease due to the weakening of the intermolecular interaction. We find that modifying the water molecular bond length leading to the variation of the intermolecular interaction strength is more intensive than changing the bond angle. Through calculating the average reduced density gradient and thermal fluctuation index, it is found that the scope of vdW interaction with neighbouring water molecules is inversely proportional to the change of the bond length and angle. The effect is mainly due to a significant change of the hydrogen bond network. To study the effect of water models as a solvent whose geometry has been modified, the solutions of ions in different solvent environments are examined by introducing NaCI. During the dissolving process, NaCI ions are ideally dissolved in SPC/E water and bond with natural water more easily than with other solvent models.展开更多
Thermodynamic and chemical properties of liquid carbon dioxide and nitrogen（CO_（2~–）N_2） mixture under the conditions of extremely high densities and temperatures are studied by using quantum molecular dynamic（...Thermodynamic and chemical properties of liquid carbon dioxide and nitrogen（CO_（2~–）N_2） mixture under the conditions of extremely high densities and temperatures are studied by using quantum molecular dynamic（QMD） simulations based on density functional theory including dispersion corrections（DFT-D）. We present equilibrium properties of liquid mixture for 112 separate density and temperature points, by selecting densities ranging from ρ = 1.80 g/cm^3 to 3.40 g/cm^3 and temperatures from T = 500 K to 8000 K. In the range of our study, the liquid CO_（2~–）N_2 mixture undergoes a continuous transition from molecular to atomic fluid state and liquid polymerization inferred from pair correlation functions（PCFs）and the distribution of various molecular components. The insulator–metal transition is demonstrated by means of the electronic density of states（DOS）.展开更多
The purpose of this overview is to provide a concise introduction to the methodology and current advances in molecular dynamics(MD) simulations. MD simulations emerged as a powerful and popular tool to study dynamic b...The purpose of this overview is to provide a concise introduction to the methodology and current advances in molecular dynamics(MD) simulations. MD simulations emerged as a powerful and popular tool to study dynamic behavior of proteins and macromolecule complexes at the atomic resolution. This approach can extend static structural data, such as X-ray crystallography, into dynamic domains with realistic timescales(up to millisecond) and high precision, therefore becoming a veritable computational microscope. This perspective covers current advances and methodology in the simulation of protein folding and drug design as illustrated by several important published examples Overall, recent progress in the simulation field points to the direction that MD will have significant impact on molecular biology and pharmaceutical science.展开更多
目的:基于网络药理学方法筛选固本平喘剂(补骨脂、地龙、防风)中的主要活性成分,探讨其治疗支气管哮喘的作用机制。方法:通过中药系统药理学数据库TCMSP数据库、中药与化学成分数据库,筛选固本平喘剂的活性成分及靶标。利用Genecards、O...目的:基于网络药理学方法筛选固本平喘剂(补骨脂、地龙、防风)中的主要活性成分,探讨其治疗支气管哮喘的作用机制。方法:通过中药系统药理学数据库TCMSP数据库、中药与化学成分数据库,筛选固本平喘剂的活性成分及靶标。利用Genecards、OMIM数据库获得支气管哮喘的潜在靶标基因。将两者靶基因进行映射后通过Cytoscape3.6.1软件构建“成分-靶标”网络、结合String数据库构建蛋白质相互作用网络扩充核心靶点。依托功能注释生物信息学分析平台DAVID数据库对固本平喘剂的作用靶点进行基因本体(gene ontology,GO)生物学过程和基因组百科全书(kyoto encyclopedia of genes and genomes,KEGG)通路富集注释分析,通过Autodock vina软件进行分子对接以验证结果。结果:符合筛选条件的共有53个活性成分,补骨脂18个,地龙17个,防风18个,筛选得到固本平喘剂关键成分,包括补骨脂黄酮类、补骨脂查耳酮类、汉黄芩素、补骨脂酚、β-谷甾醇等;通过GenCards、OMIM数据库剔除重复后,共收集支气管哮喘潜在靶点2358个。将固本平喘剂和支气管哮喘靶点进行映射取交集共得到237个交叉靶点,即固本平喘剂治疗支气管哮喘潜在作用靶点。以degree值大于二倍均值的靶点为PTGS2、ESR1、ACHE、ESR2、PTGS1、DPP4、ADORA3,degree值排名前5的靶蛋白为PIK3CA、MAPK3、MAPK1、TP53、AKT1。主要涉及PI3K-Akt信号通路、TNF信号通路、趋化因子信号通路、FoxO信号通路、MAPK信号通路、Toll样受体信号通路、T细胞受体信号通路等。结论:固本平喘剂治疗支气管哮喘潜在作用靶点有PTGS2、ESR1、ACHE、ESR2、PTGS1、DPP4、ADORA3、PIK3CA、MAPK3、MAPK1、TP53、AKT1,可能通过抗感染、调节免疫、抑制气道重塑等发挥作用。展开更多
基金Supported by Hubei Provincial Department of Education Youth Found(Q2014402)Key Project of Natural Science Foundation of Hubei Province(2011CDA037)+2 种基金Special Fund for Agro-scientific Research in the Public Interest of Hubei Province(2012DCA23)Hubei Provincial Key Laboratory of Mining Environmental Pollution Control and Remediation Open Foundation(2012106)Project of Outstanding Yong and Middleaged Scientific and Technological Innovation Team of Colleges and Universities in Hubei Province(T201223)~~
文摘[Objective] The Cu-tolerance and Cu enrichment capacity of TLSB2-K were investigated. [Method] The previously isolated TLSB2-K strain was identified though morphological observation, gram staining and 16S rDNA sequence alignment. In ad- dition, the effects of temperature, pH and osmotic pressure on the growth of strain were also investigated by using shaking culture. The Cu-tolerance and Cu enrich- ment capacity of TLSB2-K strain under Cu stress were also studied. [Result] The results showed TLSB2-K belongs to Bacillus spp., and its optimum growth conditions were as follows： temperature, 27 ~C; pH, 7.0; osmotic pressure, 1.1% NaCI. When the Cu concentration ranged from 100 mg/L to 500 mg/L, the strain grew well; when the Cu concentration ranged from 100 mg/L to 400 mg/L, the Cu content in bacteria was increased with the increase of Cu concentration; when the Cu con- centration was 400 mg/L and the incubation time was 30 h, the Cu content in bac- teria reached the peak （2 250 mg/kg）; the highest tolerant concentration was 700 mg/L. [Conclusion] TLSB2-K strain had relatively high Cu tolerance and Cu enrich- ment capacity. They had important theoretical research and engineering application values.
基金supported by National Natural Science Foundation of China(Nos.11375041,10675028)the Fundamental Research Funds for the Central Universities(No.DUT11ZD(G)06)the Fund of the Key Laboratory of Chemical Laser,CAS(No.20131008)
文摘In this paper, a feasible scheme is reported for the detection and identification of trace alcohol congeners that have identical elemental composition using laser-induced breakdown spectroscopy （LIBS）. In the scheme, an intensive pulsed laser is used to break down trace alcohol samples and the optical emission spectra of the induced plasma are collected for the detection and identifq ication of alcohol molecules. In order to prepare trace alcohol samples, pure ethanol or methanol is bubbled by argon carrier gas and then mixed into matrix gases. The key issue for the scheme is to constitute indices from the LIBS data of the alcohol samples. Two indices are found to be suitable for alcohol detection and identification. One is the emission intensity ratio （denoted as H/C） of the hydrogen line （653.3 nm） to the carbon line （247.9 nm） for identification and the other is the ratio of the carbon line （as C/Ar） or the hydrogen line （as H/Ar） to the argon lines （866.7 nm） for quantitative detection. The calibration experiment result shows that the index H/C is specific for alcohol congeners while almost being independent of alcohol concentration. In detail, the H/C keeps a specific constant of 34 and 23 respectively for ethanol and methanol. In the meanwhile, the C/Ar and H/Ar indices respond almost linearly to the alcohol concentration below 1300 ppm, and are therefore competent for concentration measurement. With the indices, trace alcohol concentration measurement achieves a limit of 140 ppm using a laser pulse energy of 300 mJ.
基金Supported by the Young and Middle-Aged Scientists Research Awards Foundation of Shangdong Province,China(No.BS2011SW002)the Research Foundation for Advanced Talents of Ludong University,China(No.LY2011017)
文摘We studied the activation of β2-adrenergic receptor（β2AR） by norepinephrine, epinephrine and isoprote- renol using docking and molecular dynamics（MD） simulation. The simulation was done on the assumption that β2AR was surrounded with explicit water and infinite lipid bilayer membrane at body temperature. So the result should be close to that under the physiological conditions. We calculated the structure of binding sites in β2AR for the three ac- tivators. We also simulated the change of the conformation ofβ2AR in the transmembrane regions（TMs）, in the mo- lecular switches, and in the conserved DRY（Aspartic acid, Arginine and Tyrosine） motif. This study provides detailed information concerning the structure ofβ2AR during activation process.
基金Project supported by the National Natural Science Foundation of China(Grant Nos.11635003,11025524,and 11161130520)the National Basic Research Program of China(Grant No.2010CB832903)the European Commission’s 7th Framework Programme(Fp7-PEOPLE-2010-IRSES)(Grant Agreement Project No.269131)
文摘We present a systematic investigation of the impact of changing the geometry structure of the SPC/E water model by performing a series of molecular dynamic simulations at 1 bar （1 bar = 105 Pa） and 298.15 K. The geometric modification includes altering the H-O-H angle range from 90° to 115° and modifying the O-H length range from 0.90 A to 1.10 A in the SPC/E model. The former is achieved by keeping the dipole moment constant by modifying the O-H length, while in the latter only the O-H length is changed. With the larger bond length and angle, we find that the liquid shows a strong quadrupole interaction and high tetrahedral structure order parameter, resulting in the enhancement of the network structure of the liquid. When the bond length or angle is reduced, the hydrogen bond lifetime and self-diffusion constant decrease due to the weakening of the intermolecular interaction. We find that modifying the water molecular bond length leading to the variation of the intermolecular interaction strength is more intensive than changing the bond angle. Through calculating the average reduced density gradient and thermal fluctuation index, it is found that the scope of vdW interaction with neighbouring water molecules is inversely proportional to the change of the bond length and angle. The effect is mainly due to a significant change of the hydrogen bond network. To study the effect of water models as a solvent whose geometry has been modified, the solutions of ions in different solvent environments are examined by introducing NaCI. During the dissolving process, NaCI ions are ideally dissolved in SPC/E water and bond with natural water more easily than with other solvent models.
基金Project supported by the National Natural Science Foundation of China(Grant Nos.11374217,11135012,and 11375262)the Joint Fund of the National Natural Science Foundation of Chinathe China Academy of Engineering Physics(Grant No.11176020)
文摘Thermodynamic and chemical properties of liquid carbon dioxide and nitrogen（CO_（2~–）N_2） mixture under the conditions of extremely high densities and temperatures are studied by using quantum molecular dynamic（QMD） simulations based on density functional theory including dispersion corrections（DFT-D）. We present equilibrium properties of liquid mixture for 112 separate density and temperature points, by selecting densities ranging from ρ = 1.80 g/cm^3 to 3.40 g/cm^3 and temperatures from T = 500 K to 8000 K. In the range of our study, the liquid CO_（2~–）N_2 mixture undergoes a continuous transition from molecular to atomic fluid state and liquid polymerization inferred from pair correlation functions（PCFs）and the distribution of various molecular components. The insulator–metal transition is demonstrated by means of the electronic density of states（DOS）.
文摘The purpose of this overview is to provide a concise introduction to the methodology and current advances in molecular dynamics(MD) simulations. MD simulations emerged as a powerful and popular tool to study dynamic behavior of proteins and macromolecule complexes at the atomic resolution. This approach can extend static structural data, such as X-ray crystallography, into dynamic domains with realistic timescales(up to millisecond) and high precision, therefore becoming a veritable computational microscope. This perspective covers current advances and methodology in the simulation of protein folding and drug design as illustrated by several important published examples Overall, recent progress in the simulation field points to the direction that MD will have significant impact on molecular biology and pharmaceutical science.
文摘目的:基于网络药理学方法筛选固本平喘剂(补骨脂、地龙、防风)中的主要活性成分,探讨其治疗支气管哮喘的作用机制。方法:通过中药系统药理学数据库TCMSP数据库、中药与化学成分数据库,筛选固本平喘剂的活性成分及靶标。利用Genecards、OMIM数据库获得支气管哮喘的潜在靶标基因。将两者靶基因进行映射后通过Cytoscape3.6.1软件构建“成分-靶标”网络、结合String数据库构建蛋白质相互作用网络扩充核心靶点。依托功能注释生物信息学分析平台DAVID数据库对固本平喘剂的作用靶点进行基因本体(gene ontology,GO)生物学过程和基因组百科全书(kyoto encyclopedia of genes and genomes,KEGG)通路富集注释分析,通过Autodock vina软件进行分子对接以验证结果。结果:符合筛选条件的共有53个活性成分,补骨脂18个,地龙17个,防风18个,筛选得到固本平喘剂关键成分,包括补骨脂黄酮类、补骨脂查耳酮类、汉黄芩素、补骨脂酚、β-谷甾醇等;通过GenCards、OMIM数据库剔除重复后,共收集支气管哮喘潜在靶点2358个。将固本平喘剂和支气管哮喘靶点进行映射取交集共得到237个交叉靶点,即固本平喘剂治疗支气管哮喘潜在作用靶点。以degree值大于二倍均值的靶点为PTGS2、ESR1、ACHE、ESR2、PTGS1、DPP4、ADORA3,degree值排名前5的靶蛋白为PIK3CA、MAPK3、MAPK1、TP53、AKT1。主要涉及PI3K-Akt信号通路、TNF信号通路、趋化因子信号通路、FoxO信号通路、MAPK信号通路、Toll样受体信号通路、T细胞受体信号通路等。结论:固本平喘剂治疗支气管哮喘潜在作用靶点有PTGS2、ESR1、ACHE、ESR2、PTGS1、DPP4、ADORA3、PIK3CA、MAPK3、MAPK1、TP53、AKT1,可能通过抗感染、调节免疫、抑制气道重塑等发挥作用。
