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.

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.

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.

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

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.

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.

Helicobacter pylori infection- recent developments in diagnosis

Considering the recommended indications for Helicobacter pylori(H.pylori)eradication therapy and the broad spectrum of available diagnostic methods,a reliable diagnosis is mandatory both before and after eradication therapy.Only highly accurate tests should be used in clinical practice,and the sensitivity and specificity of an adequate test should exceed 90%.The choice of tests should take into account clinical circumstances,the likelihood ratio of positive and negative tests,the cost-effectiveness of the testing strategy and the availability of the tests.This review concerns some of the most recent developments in diagnostic methods of H.pylori infection,namely the contribution of novel endoscopic evaluation methodologies for the diagnosis of H.pylori infection,such as magnifying endoscopy techniques and chromoendoscopy.In addition,the diagnostic contribution of histology and the urea breath test was explored recently in specific clinical settings and patient groups.Recent studies recommend enhancing the number of biopsy fragments for the rapid urease test.Bacterial culture from the gastric biopsy is the gold standard technique,and is recommended for antibiotic susceptibility test.Serology is used for initial screening and the stool antigen test is particularly used when the urea breath test is not available,while molecular methods have gained attention mostly for detecting antibiotic resistance.

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.

Evaluation of Free Radicals and Antioxidant Properties of Virus Infected Food Crops in Azerbaijan

Abstract： Viral diseases are an important limiting factor in many crop production systems in Azerbaijan. Symptomatic plants in main crop-producing areas were tested by ELISA （enzyme-linked immunosorbent assay） using specific monoclonal and polyclonal antibodies. Then RCA （rolling circle amplification） of circular DNA and PCR using different specific primer pairs have indicated that the tested symptomatic plant samples were completely infected by the following viruses： Luteovirus [BLRV （Bean leaf roll virus）], Potyviruses [BCMV （Bean common mosaic virus）, BYMV （Bean yellow mosaic virus）], Bromovirus [（AMV） Alfa-alfa mosaic virus], Geminiviruses [CpCDV （ Cickpea chlorotic dwarf virus） and TYLCV （Tomato yellow leaf curl virus）] and Nanoviruses [two different FBNYV （Faba bean necrotic yellow virus） and FBNSV （Faba bean necrotic stunt virus）]. At the same time generation sites of superoxide and hydrogen peroxide radicals and activity of antioxidant enzymes were studied in the naturally infected plants.

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.

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.

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

The molecular geometries,heats of formation and electronic structures of three trinitrobenzenes(1,2,3TNB,1,2,4TNB and 1,3,5TNB)and their chloro derivatives were studied by using the quantum chemical MO AM1 method at the RHF level and ab initio method at the HF/321G level.The decompositions of the title compounds were investigated by using the AM1 method at the UHF level.The decomposition activation energies were obtained and the order of the relative stabilities of the title compounds is found.The substituent effects on the structures and properties and on the decompositions of the title compounds are discussed in the present paper.