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.

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.

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.

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.

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.

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.

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

Molecular dynamics simulation on generalized stacking fault energies of FCC metals under preloading stress

Molecular dynamics(MD) simulations are performed to investigate the effects of stress on generalized stacking fault(GSF) energy of three fcc metals(Cu, Al, and Ni). The simulation model is deformed by uniaxial tension or compression in each of [111], [11-2], and [1-10] directions, respectively, before shifting the lattice to calculate the GSF curve. Simulation results show that the values of unstable stacking fault energy(γusf), stable stacking fault energy(γsf), and unstable twin fault energy(γutf) of the three elements can change with the preloaded tensile or compressive stress in different directions.The ratio of γsf/γusf, which is related to the energy barrier for full dislocation nucleation, and the ratio of γutf/γusf, which is related to the energy barrier for twinning formation are plotted each as a function of the preloading stress. The results of this study reveal that the stress state can change the energy barrier of defect nucleation in the crystal lattice, and thereby can play an important role in the deformation mechanism of nanocrystalline material.

A molecular dynamics simulation of segregation behaviours of horizontally vibrated binary granular mixture

This paper performs the two-dimensional, soft-sphere molecular dynamics simulations to study the granular segregation in a binary granular mixture with the same size but different density in the container with the sawtooth base under horizontal vibration. The segregation phase diagram is presented in the acceleration-frequency space. When the acceleration is high enough to result in relative motions of the particles, the system can be in various states （mixed state, vertical and horizontal segregation state）, which depend on both acceleration and frequency. Due to the sawtooth base there is stratified flow effect besides density effect. The density effect raises the light particles. The stratified flow drives the particles in the upper levels to the right and the particles in the lower particles to the left, resulting in the appearance of the left segregation state. The left segregation state can be changed to the right segregation by changing the shape of the sawtooth. As the vibration frequency increases, the stratified flow effect becomes weaker and weaker, so at high vibration frequencies the vertical segregation state appears instead of the left segregation state.

Directional mechanical and thermal properties of single-layer black phosphorus by classical molecular dynamics

Black phosphorus （BP） has received attention due to its own higher carrier mobility and layer dependent electronic properties, such as direct band gap. Interestingly, the single layer black phosphorus （SLBP） has had large popularity in applications related to thermoelectric, optoelectronic, and electronic devices. Here, we investigate the phonon spectrum, thermal conductivities, and stress strain effects. Robust anisotropy was mainly observed in the thermal conductivities together with the alongside zigzag （ZZ） direction value, compared to the armchair （AC） directions. We also investigated the attitude of stress that was anisotropic in both directions, and the stress effects were two times greater across the ZZ path than those in the AC direction at a low temperature. We obtained a ~oung＇s modulus of 63.77 and 20.74 GPa in the AC and ZZ directions, respectively, for a strain range of 0.01. These results had good agreement with first principle calculations. Our study here is useful and significant for the thermal tuning of phosphorus-based nanoelectronics and thermalelectric applications of phosphorus.

Molecular Dynamics Simulation of Interaction of Short Lysine Brush and Oppositely Charged Semax Peptides

The possibility of complex formation by short lysine brush and therapeutic Semax peptides was investigated using molecular dynamics method. Lysine dendrimers and polymer brushes are used for drug and other (e.g., DNA, peptides, and polysaccharides) molecules delivery to different target cells. It is known that they could penetrate blood brain barrier. Since short lysine brush is nontoxic, a system containing of such brush and 8 oppositely charged Semax peptides was studied. It was obtained that stable complexes consisting of brush and peptides formed and structures of these complexes were investigated. Such complex can be used in future for delivery of Semax peptides to brain since these peptides have significant antioxidant, antihypoxic and neuroprotective effects.

Detection of two pathogenic marine ciliates Ancistrum haliotis and A. crassum(Ciliophora: Scuticociliatia) by fluorescence in situ hybridization

The scuticociliatid ciliates Ancistrum haliotis and A.crassum are parasites that may cause high mortality in the cultured abalone Haliotis spp.and the bivalve Ruditapes philippinarum.Traditional identification with silver staining methods is hampered by their morphological similarities to closely related species and the complicated procedures of morphological analysis.We designed two SSU rRNA-targeted oligonucleotide probes labeled with a fluorochrome,and optimized the fluorescence in situ hybridization(FISH)protocols for identification of A.halioti and A.crassum,respectively.The assays resulted in a clear identification by strong fluorescence signals from the oligonucleotide probes.The method can be used for quick and accurate quantitative analysis of A.haliotis and A.crassum infections on host molluscs.

Atomistic simulation of free transverse vibration of graphene,hexagonal SiC, and BN nanosheets

Free transverse vibration of monolayer graphene, boron nitride (BN), and silicon carbide (SiC) sheets is investigated by using molecular dynamics finite element method. Eigenfrequencies and eigenmodes of these three sheets in rectangular shape are studied with different aspect ratios with respect to various boundary conditions. It is found that aspect ratios and boundary conditions affect in a similar way on natural frequencies of graphene, BN, and SiC sheets. Natural frequencies in all modes decrease with an increase of the sheet’s size. Graphene exhibits the highest natural frequencies, and SiC sheet possesses the lowest ones. Missing atoms have minor effects on natural frequencies in this study.

MD simulation of a copper rod under thermal shock

In this paper, thermoelastic problem of onedimensional copper rod under thermal shock is simulated using molecular dynamics method by adopting embedded atom method potential. The rod is on axis x, the left outermost surface of which is traction free and the right outermost surface is fixed. Free boundary condition is imposed on the outermost surfaces in direction y and z. The left and right ends of the rod are subjected to hot and cold baths, respectively. Temperature, displacement and stress distributions are obtained along the rod at different moments, which are shown to be limited in the mobile region, indicating that the heat propagation speed is limited rather than infinite. This is consistent with the prediction given by generalized thermoelastic theory. From simulation results we find that the speed of heat conduction is the same as the speed of thermal stress wave. In the present paper, the simulations are conducted using the large-scale atomic/molecular massively parallel simulator and completed visualization software.

Quantum Chemical Investigations on the Structures,Stabilities and Decompositions of Trinitrobenzenes and Their Chloro Derivatives

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Angular Effects on F＋ Etching SiC： MD Study

Molecular dynamics （MD） simulations were performed to investigate F＋ continuously bombarding SiC surfaces with energies of 100 eV at different incident angles at 300 K. The simulated results show that the steady-state uptake of F atoms increases with increasing incident angle. With the steady-state etching established, a Si-C-F reactive layer is formed. It is found that the etching yield of Si is greater than that of C. In the F-containing reaction layer, the SiF species is dominant with incident angles less than 30°. For all incident angles, the CF species is dominant over CF2 and CF3.

Phase behaviour of polyethylene knotted ring chains

The phase behaviour of polyethylene knotted ring chains is investigated by using molecular dynamics simulations. In this paper, we focus on the collapse of the polyethylene knotted ring chain, and also present the results of linear and ring chains for comparison. At high temperatures, a fully extensive knot structure is observed. The mean-square radius of gyration per bond （S2）/（Nb2） and the shape factor （（δ＊） depend on not only the chain length but also the knot type. With temperature decreasing, chain collapse is observed, and the collapse temperature decreases with the chain length increasing. The actual collapse transition can be determined by the specific heat capacity Cv, and the knotted ring chain undergoes gas-liquid-solid-like transition directly. The phase transition of a knotted ring chain is only one-stage collapse, which is different from the polyethylene linear and ring chains. This investigation can provide some insights into the statistical properties of knotted polymer chains.

Energy barrier for configurational transformation of graphene nanoribbon on nanotube

A graphene nanoribbon （GNR） has two basic configurations when winding on the outer surface of a carbon nanotube （CNT）： helix and scroll. Here the transformation between the two configurations is studied utilizing molecular dynamics simulations. The energy barrier during the transformation as well as its relationship with the interfacial energy and the radius of CNT are investigated. Our work offers further insights into the formation of desirable helix/scroll of GNR winding on nanotubes or nanowires, and thus can enable novel design of potential graphene-based electronics.

Crystal Structure of Crotin Ⅱ at 2.5 Resolution

Crotin Ⅱ is one of the ribosome inactivating proteins (RIPs). It belongs to RNA hydrolase. The crystals of crotin Ⅱ are hexagonal with a=b= 94. 62, c=28. 44 A, space group P61, Mr= 14900 Da. The structure was solved by molecularreplacement methed using the molecular structure of RNase T1 as a search model andrefined to R= 0. 25 for the reflections within 10- 2. 5 A resolution range. The refinedmodel cotains one α-helix, one two-strand antiparallel β-sheet and one five-strand an-tiparallel β-sheet. Four conservative residues His47, Glu77, Arg102 and His117 gathering in the cleft of the structure form the possible active site of crotin Ⅱ.

Perspective for aggregation-induced delayed fluorescence mechanism:A QM/MM study

To enhance the potential application of thermally activated delayed fluorescence(TADF)molecular materials,new functions are gradually cooperated to the TADF molecules.Aggregation induced emission can effectively solve the fluorescence quenching problem for TADF molecules in solid phase,thus aggregation-induced delayed fluorescence(AIDF)molecules were recently focused.Nevertheless,their luminescent mechanisms are not clear enough.In this work,excited state properties of an AIDF molecule DMF-BP-DMAC[reported in Chemistry-An Asian Journal 14828(2019)]are theoretically studied in tetrahydrofuran(THF)and solid phase.For consideration of surrounding environment,the polarizable continuum method(PCM)and the combined quantum mechanics and molecular mechanics(QM/MM)method were applied for solvent and solid phase,respectively.Due to the increase of the transition dipole moment and decrease of the energy difference between the first single excited state(S1)and the ground state(S0),the radiative rate is increased by about 2 orders of magnitude in solid phase.The energy dissipation of the non-radiative process from S1 to S0 is mainly contributed by low-frequency vibrational modes in solvent,and they can be effectively suppressed in aggregation,which may lead to a slow non-radiation process in solid phase.Both factors would induce enhanced luminescence efficiency of DMF-BP-DMAC in solid phase.Meanwhile,the small energy gap between S1 and triplet excited states results in high reverse intersystem crossing(RISC)rates in both solvent and solid phase.Therefore,TADF is confirmed in both phases.Aggregation significantly influences both the ISC and RISC processes and more RISC channels are involved in solid state.The enhanced delayed fluorescence should be induced by both the enhanced fluorescent efficiency and ISC efficiency.Our calculation provides a reasonable explanation for experimental measurements and helps one to better understand the luminescence mechanism of AIDF molecules.