Molecular methods for detection of pathogenic viruses of respiratory tract——A review

Human respiratory system is harbored by a vast array of transient and normal microbial flora.A number of pathogenic viruses were diagnosed from samples in different occasions from mild to severe infections of respiratory tract.Molecular methods were developed for detection of these viruses during last two decades.Nucleic acid amplification methods were introduced for rapid and accurate diagnosis of pathogenic viruses.Multiplex detection systems were employed to identify a panel of pathogenic viruses,which requires specialized kits and instruments in some cases.This review summarizes different types of molecular approaches which were developed with time and applied for the detection of pathogenic viruses associated with infections of the respiratory system.

COMPUTERIZED SIMULATION OF MOLTEN SALT SOLUTION OF Li,KF,Cl SYSTEM BY MOLECULAR DYNAMIC METHOD

The structure and properties of molten salt solution o J Li,K|F,Cl system have been investiged by computerized simulation of molecular dynamic method.The partial RDF,the partial molar energy of mixing and the diffusion coeffients of Li^+,K^+,F^- and Cl^- have been calculated. The results are in agreement with the experimental values.The regularities of the distribution of ions and mieroscopic holes are discussed based on the results of computerized simulation.

A Modified Molecular Structural Mechanics Method for Analysis of Carbon Nanotubes

A modified molecular structural mechanics method, based on molecular mechanics and similar to the finite element method, was developed. The energy of a system was expressed by the force field functions of the molecular mechanics. Under the small deformation assumption and by the principle of minimum potential energy, the system function was established. The properties of tension and bending of single-walled carbon nanotubes were analyzed. The Young＇s modulus is about 0.36 TPa nm, which agrees perfectly with the results of previous analysis by other researchers. It is found, for the first time, that the Young＇s moduli, for Zigzag nanotubes, are different from each other when the system energy was expressed as the sum of two or three individual energy terms in molecular mechanics. Whereas, the Young＇s moduli were the same for the Armchair nanotubes. It is found, when simulating the bending, that the deflections are closer to the theoretical ones, of the classical elasticity, when the diameter of the carbon nanotube increases.

Establishment of Molecular Biological Method for Identification of Bacteria by 16S rDNA and gyrB Gene

[Objectives]The paper was to establish a molecular biological method for identification of bacterial strains.[Methods]The thalli of standard bacterial strains existing in the laboratory were collected and genomic DNA was extracted for amplification of 16S rDNA and gyrB gene.The 16S rDNA and gyrB gene sequences were obtained after sequencing.Sequences were aligned and analyzed via EzBioCloud and NCBI database,and phylogenetic trees were constructed to determine the species relationship of strains.Meantime,they were compared with known strains.[Results]This method could identify 5 standard strains accurately to the species level.The 16S rDNA and gyrB gene sequences were aligned and analyzed in EzBioCloud database and NCBI database.The strain with the max score was consistent with the known strain.And the query cover and ident were both above 99%.[Conclusions]The established molecular biological method for identification of bacterial strains by 16S rDNA and gyrB gene has good accuracy,which effectively solves the problem that the laboratory identification of bacteria relies on traditional methods and the accuracy can not be guaranteed,and further improves the identification ability of laboratory bacterial strains.

Clinical Observation on Treatment of 78 Patients of B-Thalassemla with Bushen Ylsul (补肾益髓) Method and Study on Its Molecular Mechanism

Objective: To study the treatment of B-Thalas-semia (ThE) with Chinese herbal medicine for Bushen Yisui (BSYS), its theoretical base and molecular mechanism. Methods: Seventy-eight patients with ThE were treated with BSYS recipe (consisted of 11 Chinese herbal drugs as Dogwood fruit, Fleeceflower root, prepared Rehmannia root and turtle shell, etc.) orally taken, 3 times per day, 10 g/time, 3 months as one therapeutic course. Hemoglobin (Hb), red blood cell (RBC), reticulocyte (Ret) and hemoglobin F (HbF) were checked every month. At the same time, PAGE, PVR, PCR-SSCP, RT-PCR, DNA series analysis, mRNA gene expression analysis techniques were used to conduct the systematic gene analysis in patients to study the molecular mechanism of TCM treatment from aspects of gene mutation, gene expression and control-regulation. Results: All the blood criteria in patients after BSYS treatment were improved significantly with clinical symptoms

An efficient method for mapping the 12C+12C molecular resonances at low energies

The 12C+12C fusion reaction is famous because of its complication of molecular resonances,and it plays an important role in both nuclear structural research and astrophysics. It is extremely difficult to measure the cross sections of 12C+12C fusions at energies of astrophysical relevance because of the very low reaction yields. To measure the complicated resonant structure that exists in this important reaction, an efficient thick target method has been developed and applied for the first time at energies Ec.m.<5.3 MeV. A scan of the cross sections over a relatively wide range of energies can be carried out using only a single beam energy. The result of measurement at Ec.m.=4.1 MeV is compared with results from previous work.This method will be useful for searching for potentially existing resonances of 12C+12C in the energy range 1 MeV<Ec.m.<3 MeV.

The LBFGS quasi-Newtonian method for molecular modeling prion AGAAAAGA amyloid fibrils

Experimental X-ray crystallography, NMR (Nuclear Magnetic Resonance) spectroscopy, dual polarization interferometry, etc. are indeed very powerful tools to determine the 3-Dimensional structure of a protein (including the membrane protein);theoretical mathematical and physical computational approaches can also allow us to obtain a description of the protein 3D structure at a submicroscopic level for some unstable, noncrystalline and insoluble proteins. X-ray crystallography finds the X-ray final structure of a protein, which usually need refinements using theoretical protocols in order to produce a better structure. This means theoretical methods are also important in determinations of protein structures. Optimization is always needed in the computer-aided drug design, structure-based drug design, molecular dynamics, and quantum and molecular mechanics. This paper introduces some optimization algorithms used in these research fields and presents a new theoretical computational method—an improved LBFGS Quasi-Newtonian mathematical optimization method—to produce 3D structures of prion AGAAAAGA amyloid fibrils (which are unstable, noncrystalline and insoluble), from the potential energy minimization point of view. Because the NMR or X-ray structure of the hydrophobic region AGAAAAGA of prion proteins has not yet been determined, the model constructed by this paper can be used as a reference for experimental studies on this region, and may be useful in furthering the goals of medicinal chemistry in this field.

Evaluation of Quantum Chemical Methods and Basis Sets Applied in the Molecular Modeling of Artemisinin

In this paper, we evaluate semiempirical methods (AM1, PM3, and ZINDO), HF and DFT (B3LYP) in different basis sets to determine which method best describes the sign and magnitude of the geometrical parameters of artemisinin in the region of the endoperoxide ring compared to crystallographic data. We also classify these methods using statistical analysis. The results of PCA were based on three main components, explaining 98.0539% of the total variance, for the geometrical parameters C3O13, O1O2C3, O13C12C12a, and O2C3O13C12. The DFT method (B3LYP) corresponded well with the experimental data in the hierarchical cluster analysis (HCA). The experimental and theoretical angles were analyzed by simple linear regression, and statistical parameters (correlation coefficients, significance, and predictability) were evaluated to determine the accuracy of the calculations. The statistical analysis exhibited a good correlation and high predictive power for the DFT (B3LYP) method in the 6-31G** basis set.

GALERKIN METHOD FOR COMPLETELY COMPRESSIBLE DISPLACEMENT WITH MOLECULAR DIFFUSION AND DISPERSION

In this paper, the numerical approximation by Galerkin method for completely compressible miscible displacement with molecular diffusion and dispersion in porous media is considered. Continuous time procedure is introduced and analysed. Some new techniques are applied to the analysis. Optimal error estimates in L ∞(J;H 1(Ω)) are proved, which implies an essential improvement to existed results. MR Subject Classification: 65N15,65N30.

GALERKIN METHOD FOR COMPRESSIBLE FLOW OF CONTAMINATION FROM NUCLEAR WASTE WITH MOLECULAR DIFFUSION AND DISPERSION

Abstract A system of quasilinear coupled equations which arise from simulation of contamination of geologic nulear waste in porous media is studied. We’ll discuss Galerkin method for the model of compressible flow with molecular diffusion and dispersion. Some new techniques are introcued to error analysis. Only one dimensional case is considered. The optimal error estimate in both L^2 and H^1 is proved. A contribution of this paper is how the dispersion term can be handled,

多光谱法研究二氢杨梅素对胰脂肪酶的抑制作用

藤茶中主要黄酮类物质——二氢杨梅素(DMY)具有多种生物活性,而其降血脂机理鲜有报道。采用紫外光谱研究了DMY对胰脂肪酶(PL)的抑制作用,结合荧光光谱、同步荧光光谱、三维荧光光谱及分子对接模拟法研究了二者之间的相互作用及机理。紫外光谱测得DMY对PL的半抑制浓度为2.6×10^(-4)mol·L^(-1),表明其对PL具有较好的抑制作用,采用Lineweaver-Burk方程得出该抑制剂为竞争性作用,其抑制常数为6×10^(-4)mol·L^(-1);通过Stern-Volmer方程和静态猝灭双对数公式对293和310 K两者互作的荧光光谱计算,结果表明DMY能猝灭PL的自发荧光,荧光猝灭方式为静态猝灭,猝灭常数K_(SV)与温度负相关;结合常数K a与温度正相关,结合位点数n约为1,说明DMY与PL结合并形成稳定的配位复合物;采用Van't Hoff方程求出结合过程中的热力学参数ΔS=0.2014 J·mol^(-1)·K^(-1),ΔH=32.311 kJ·mol^(-1),ΔG小于0,表明两者通过疏水作用力自发结合且放热;由F rster非辐射能量转移理论计算出结合距离r=1.475 nm,说明DMY与PL结合生成复合物时发生了非辐射能量转移;同步荧光光谱结果表明,DMY与PL的相互作用对PL的二级构象发生了明显改变,主要作用于色氨酸(Tyr)附近。紫外光谱进一步揭示DMY可使PL发生π→π跃迁,导致其氨基酸残基的微环境变化;三维荧光光谱显示DMY可使PL两个特征峰(peak1,peak2)分别红移10和5 nm,荧光强度分别下降51.38%和41.93%,证实两者发生疏水作用后PL的微环境极性增大,构象改变;分子对接模拟结果表明,DMY结合位点位于PL中由PHE77、PHE215、TYR114、ILE209、PRO180氨基酸形成的疏水口袋内,其A环C5、B环C4′、C环C3、C环C O的-OH分别与氨基酸HIS263、TYR114、SER152、PHE215形成氢键,与氨基酸LRU213、GLU179、ALA178、THR78产生范德华力。实验数据有助于深入解DMY的降血脂分子作用机制,其独特的结构为天然抑制剂的药物合成和筛选提供了理论依据。

Molecular detection of Helicobacter pylori antibiotic resistance in stool vs biopsy samples

AIM To compare(1) demographics in urea breath test(UBT) vs endoscopy patients; and(2) the molecular detection of antibiotic resistance in stool vs biopsy samples.METHODS Six hundred and sixteen adult patients undergoing endoscopy or a UBT were prospectively recruited to the study. The Geno Type Helico DR assay was used to detect Helicobacter pylori(H. pylori) and antibiotic resistance using biopsy and/or stool samples from CLOpositive endoscopy patients and stool samples from UBT-positive patients. RESULTS Infection rates were significantly higher in patients referred for a UBT than endoscopy(overall rates: 33% vs 19%; treatment-na?ve patients: 33% vs 14.7%, respectively). H. pylori-infected UBT patients were younger than H. pylori-infected endoscopy patients(41.4 vs 48.4 years, respectively, P < 0.005), with a higher percentage of H. pylori-infected males in the endoscopy-compared to the UBT-cohort(52.6% vs 33.3%, P = 0.03). The Geno Type Helico DR assay was more accurate at detecting H. pylori infection using biopsy samples than stool samples [98.2%(n = 54/55) vs 80.3%(n =53/66), P < 0.005]. Subset analysis using stool and biopsy samples from CLO-positive endoscopy patients revealed a higher detection rate ofresistance-associated mutations using stool samples compared to biopsies. The concordance rates between stool and biopsy samples for the detection of H. pylori DNA, clarithromycin and fluoroquinolone resistance were just 85%, 53% and 35%, respectively. CONCLUSION Differences between endoscopy and UBT patients provide a rationale for non-invasive detection of H. pylori antibiotic resistance. However, the Geno Type Helico DR assay is an unsuitable approach.

Comparison of Genomic DNA Extraction Methods for Chenopodium quinoa Willd

To rapidly obtain high-quality genomic DNA from Chenopodium quinoa Willd, the genomic DAN in different tissues （leaves, stems and roots） of Chenopodi- um quinoa Willd was extracted by modified CTAB method, SDS method and high- salt Iow-pH method, respectively. The quality and yield of extracted DNA was deter- mined using agarose gel electrophoresis and UV spectrophotometry. At the same time, the PCR-SSR and SSCP molecular detection was also performed. The results showed that the gel test strips, without obvious decomposition, of all the extraction methods were relatively obvious; the genomic DNA yield extracted by modified CTAB method was highest, followed by that by SDS method, and the genomic DNA extracted by high-salt Iow-pH method was lowest： the genomic DNA yields extracted by different methods from Chenopodium quinoa Wiltd leaves were all high- er than those from roots and stems; the quality of Chenopodium quinoa Willd ge- nomic DNA extracted by modified CTAB method and high-salt Iow-pH method was better, and polyphenols, polysaccharides and other impurities were removed more completely. The PCR-SSR and SSCP detection results showed that the genomic DNA extracted by different methods from different tissues of Chenopodium quinoa Willd all could be better amplified, and high-quality strips could be obtained. So the Chenopodium quinoa Willd genomic DNA extracted by the three methods all can be used for subsequent molecular biology research.

Maximum Overlap Symmetry Molecular Orbital Calculation under CNDO／2 Approximation

A basic calculation procedure for the MOSMO method under CNDO/2 approximation is presented in this paper,and performed by using the same parameters as those used in the ordinary CNDO/2 LCAO-MO calculation.The calculated results on the whole are close to those obtained by use of the ordinary CNDO/2 LCAO-MO calculation,illustrating that the presented procedure is reasonable.Due to its simplicity,the presented calculation procedure may be feasible even in very large molecular s ystems.

Molecular Replacement Studies of Cucurmosin from Cucurbita Moschata:Structure Homology with Trichosanthin

High diffraction quality crystals of cucurmosin, a type I ribosome inactivating protein isolated from the sarcocarp of Cucurbita moschata (pumpkin), have been grown under newly optimised conditions. With in-house rotating anode X-ray source, these crystals diffract to 1.65 ?resolution which is much higher than that of the previously reported crystals that diffracted only to 3 ?resolution. The crystals belong to space group P212121 with cell parameters a = 41.5, b = 58.4 and c = 99.3 . Molecular replacement studies indicate that the cucurmosin structure is homologous to trichosanthin. The initial structural model has been obtained and the model fitting/ refinement is in progress.

Molecular Clump Extraction Algorithm Based on Local Density Clustering

The detection and parameterization of molecular clumps are the first step in studying them.We propose a method based on the Local Density Clustering algorithm while physical parameters of those clumps are measured using the Multiple Gaussian Model algorithm.One advantage of applying the Local Density Clustering to the clump detection and segmentation,is the high accuracy under different signal-to-noise levels.The Multiple Gaussian Model is able to deal with overlapping clumps whose parameters can reliably be derived.Using simulation and synthetic data,we have verified that the proposed algorithm could accurately characterize the morphology and flux of molecular clumps.The total flux recovery rate in 13CO(J=1-0)line of M16 is measured as 90.2%.The detection rate and the completeness limit are 81.7%and 20 K km s-1 in 13CO(J=1-0)line of M16,respectively.

A constrained particle dynamics for continuum-particle hybrid method in micro- and nano-fluidics

A hybrid method of continuum and particle dynamics is developed for micro- and nano-fluidics, where fluids are described by a molecular dynamics （MD） in one domain and by the Navier-Stokes （NS） equations in another domain. In order to ensure the continuity of momentum flux, the continuum and molecular dynamics in the overlap domain are coupled through a constrained particle dynamics. The constrained particle dynamics is constructed with a virtual damping force and a virtual added mass force. The sudden-start Couette flows with either non-slip or slip boundary condition are used to test the hybrid method. It is shown that the results obtained are quantitatively in agreement with the analytical solutions under the non-slip boundary conditions and the full MD simulations under the slip bound- ary conditions.

Molecular Simulations of FCC Dry Gas Components Adsorption in Zeolite Y

Adsorption of FCC dry gas components, hydrogen(H_2), nitrogen(N_2), methane(CH_4), ethane(C_2H_6) and ethylene(C_2H_4) in zeolite Y was studied by performing the Grant Canonical Monte Carlo(GCMC) simulations at 298K and 823K and under a pressure range up to 10 MPa. Simulation results were analyzed using the Langmuir model, which presented fitting of dry gas components adsorption to be suggested as the monolayer adsorption. C_2H_4 presented most single adsorption amount, which reached 7.63 mol/kg at 298K under a pressure of 200kPa. Thermodynamic parameters of the Gibbs free energy change, enthalpy change and entropy change were analyzed based on adsorption equilibrium constant obtained from the GCMC simulations. The results suggested that it was more favorable for C_2H_4 to be adsorbed in zeolite Y. Adsorption molecules were in ordered arrangement in the zeolite, and C_2H_4 exhibited a more orderly arrangement than other components. Additionally, a competition in the adsorption of a mixture of dry gas components was found, and supercages were the priority adsorption space. The competition was favorable to CH_4 and C_2H_6, and the competitive power was affected by temperature.

Sorption and permeation of gaseous molecules in amorphous and crystalline PPX C membranes: molecular dynamics and grand canonical Monte Carlo simulation studies

Amorphous and crystalline poly （chloro-p-xytylene） （PPX C） membranes are constructed by using a novel com- putational technique, that is, a combined method of NVT＋NPT-molecular dynamics （MD） and gradually reducing the size （GRS） methods. The related free volumes are defined as homology clusters. Then the sorption and the permeation of gases in PPX C polymers are studied using grand canonical Monte Carlo （GCMC） and NVT-MD methods. The results show that the crystalline PPX C membranes provide smaller free volumes for absorbing or transferring gases relative to the amorphous PPX C area. The gas sorption in PPX C membranes mainly belongs to the physical one, and H bonds can appear obviously in the amorphous area. By cluster analyzing on the mean square displacement of gases, we find that gases walk along the x axis in the crystalline area and walk randomly in the amorphous area. The calculated permeability coefficients are close to the experimental data.

FINITE ELEMENT SIMULATIONS FOR COMPRESSIBLE MISCIBLE DISPLACEMENT WITH MOLECULAR DISPERSION IN POROUS MEDIA

We consider a nonlinear parabolic system describing compressible miscibledisplacement in a porous medium [5]. Continuous time and discrete time Galerkinmethods are introduced to approximate the solution and optimal H^1 error estimatesare obtained. One contribution of this paper is a demonstration of how moleculardispersion can be handled.