Bioinformatics analysis of structure and function in the MRP gene family and its expression in response to various drugs in Bursaphelenchus xylophilus

Genes homologous to members of the MRP gene family in Caenorhabditis elegans are important in drug resistance.To further explore the molecular mechanism of drug resistance in pine wood nematode(Bursaphelenchus xylophilus),we used bioinformatics approaches to analyze genomic data for B.xylophilus and identified Bx-MRP genes.We predicted the structure and function of the genes and encoded proteins.Using bioinformatics programs to predict and analyze various properties of the predicted proteins,including hydrophobicity,transmembrane regions,phosphorylation sites,and topologically isomeric structures,of these Bx-MRP genes,we determined that they function in transmembrane transport.From the results of RT-qPCR,the Bx-MRP family members confer significant differential resistance to different drug treatments.After treatment with different concentrations of emamectin benzoate,avermectin and matrine,the expression of each gene increased with increasing drug concentrations,indicating that the family members play a positive role in the regulation of multidrug resistance.

Topology and Vortex Structures of Turbine Cascade with Different Tip Clearances

This paper uses the topology theory to analyze the surface flowspectrums of straight, positively curved and negatively curvedcascades with relative tip clearances of 0.023 and 0.036, findsapparent differences of topology and vortex structures in the bladetip and the suction side wall corner of single type of cascade withthis two clearances, and studies the mechanism of the differenceformation as well as their effects o the energy loss.

TOPOLOGY AND VORTEX STRUCTURES OF A CURVING TURBINE CASCADE WITH TIP CLEARANCE (Ⅰ)- EXPERIMENTAL MODEL AND TOPOLOGICAL FLOW PATTERNS ON BOTH ENDWALLS AND BLADE SURFACES

By means of ink trace visualization of the flows in conventional straight, positively curved and negatively curved cascades with tip clearance, and measurement of the aerodynamic parameters in the transverse section, and by appling topology theory, the structures on both endwalls and blade surfaces were analyzed. Compared with conventional straight cascade, blade positive curving eliminates the separation line of the upper passage vortex and leads the secondary vortex to change from close separation to open separation, while blade negative curving effects merely the positions of singular points and the intensities and scales of vortex.

TOPOLOGY AND VORTEX STRUCTURES OF A CURVING TURBINE CASCADE WITH TIP CLEARANCE (Ⅱ)- TOPOLOGICAL FLOW PATTERN AND VORTEX STRUCTURE IN THE TRANSVERSE SECTION OF A BLADE CASCADE

By means of ink trace visualization of the flows in conventional straight, positively curved and negatively curved cascades with tip clearance, and measurement of the aerodynamic parameters in transverse section, and by appling topology theory, the topological structures and vortex structure in the transverse section of a blade cascade were analyzed. Compared with conventional straight cascade, blade positive curving eliminates the separation line of the upper passage vortex, and leads the secondary vortex to change from close separation to open separation, while blade negative curving effects merely the positions of singular points and the intensities and scales of vortex.

Field structure at mode Ⅲ dynamically propagating crack tip in elastic-viscoplastic materials

An elastic-viscoplastic mechanics model is used to investigate asymptotically the mode Ⅲ dynamically propagating crack tip field in elastic-viscoplastic materials. The stress and strain fields at the crack tip possess the same power-law singularity under a linear-hardening condition. The singularity exponent is uniquely determined by the viscosity coefficient of the material. Numerical results indicate that the motion parameter of the crack propagating speed has little effect on the zone structure at the crack tip. The hardening coefficient dominates the structure of the crack-tip field. However, the secondary plastic zone has little influence on the field. The viscosity of the material dominates the strength of stress and strain fields at the crack tip while it does have certain influence on the crack-tip field structure. The dynamic crack-tip field degenerates into the relevant quasi-static solution when the crack moving speed is zero. The corresponding perfectly-plastic solution is recovered from the linear-hardening solution when the hardening coefficient becomes zero.

Analysis of the Protein Structure and Function of HpaG_(Xoo)

[Objective] The study was to analyze the structure and function of HpaGXoo and the relationship between the two.[Method] Some related bioinformatics analysis software on internet such as NPSA,Swiss-Model,SAPS and InterPro Scan were adopted to analyze the structure and predict its function.[Result] HpaGXoo consists of 139 amino acids,and has many alpha-helical and coiled structure,no signal peptide on N-terminal and no transmembrane structure.It locates in bacterial cytoplasm.[Conclusion] The study will lay ...

The Evolutionary Computation Techniques for Protein Structure Prediction:A Survey

In this paper, the applications of evolutionary algorithm in prediction of protein secondary structure and tertiary structures are introduced, and recent studies on solving protein structure prediction problems using evolutionary algorithms are reviewed, and the challenges and prospects of EAs applied to protein structure modeling are analyzed and discussed.

Tertiary structure-based protein classificationby virtual-bond-angles series

Structure-based protein classification can be based on the similarities in primary, second or tertiary structures of proteins. A method using virtual-bond-angles series that transformed the protein space configuration into a sequence was used for the classification of three-dimensional structures oi proteins. By transforming the main chains formed by C^a atoms of proteins into sequences, the series of virtual-bond-angles corresponding to the tertiary structure of the proteins were constructed. Then a distance-based hierarchical clustering method similar to Ward method was introduced to classify these virtual-bond-angles series of proteins. 200 files of protein structures were selected from Brookheaven protein data bank, and 11 clusters were classified.

Identification and bioinformatics analysis of lactate dehydrogenase genes from Echinococcus granulosus

Objective:To identify full length cDNA sequence of lactate dehydrogenase(LDH) from adult Echinococcus granulosus(E.granulosus) and to predict the structure and function of its encoding protein using bioinformatics methods.Methods:With the help of NCBI,EMBI, Expasy and other online sites,the open reading frame(ORF),conserved domain,physical and chemical parameters,signal peptide,epitope,topological structures of the protein sequences were predicted and a homology tertiary structure model was created:Vector NT1 software was used for sequence alignment,phylogenetic tree construction and tertiary structure prediction. Results:The target sequence was 1 233 bp length with a 996 bp biggest ORF encoding 331 amino acids protein with typical L-LDH conserved domain.It was confirmed as full length cDNA of LDH from E.granulosus and named as EgLDH(GenBank accession number:HM748917).The predicted molecular weight and isoelectric point of the deduced protein were 3 5516.2Da and 6.32 respectively.Compared with LDHs from Taenia solium,Taenia saginata asiatica,Spirometra erinaceieuropaei.Schistosoma japonicum,Clonorchis sinensis and human,it showed similarity of 86% ,85% ,55% ,58% ,58% and 53% ,respectively.EgLDH contained 3 putative transmembrane regions and 4 major epitopes(54aa-59aa.81aa-87aa,97aa-102aa,307aa-313aa),the latter were significant different from the corresponding regions of human LDH.In addition,some NAD and substrate binding sites located on epitopes 54aa-59aa and 97aa-102aa,respectively.Tertiary structure prediction showed that 3 key catalytic residues 105R,165D and 192H forming a catalytic center near the epitope 97aa-102aa,most NAD and substrate binding sites located around the center.Conclusions:The full length cDNA sequences of EgLDH were identified.It encoded a putative transmembrane protein which might be an ideal target molecule for vaccine and drugs.

Effects of Inflow Conditions on Wind Turbine Performance and near Wake Structure

Knowledge about the structure and development of wakes behind wind turbines is important for power optimization of wind power farms. The high turbulence levels in the wakes give rise to undesired unsteady loadings on the downstream turbines, which in the long run might cause fatigue damages. In the present study, the near wake behind a small-scale model wind turbine was investigated experimentally in a wind tunnel. The study consists of measurements with particle image velocimetry using two different inlet conditions: a freely developing boundary layer, causing an almost uniform inflow across the rotor disc, and an inflow with strong shear across the rotor disc, in order to model the atmospheric boundary layer. The results show a faster recovery of the wake in the case with shear inflow, caused by the higher turbulence levels and enhanced mixing of momentum. The increased inlet turbulence levels in this case also resulted in a faster breakdown of the tip vortices as well as different distributions of the streamwise and vertical components of the turbulence intensity in the wake. An analysis comparing vortex statistics for the two cases also showed the presence of strong tip vortices in the case with lower inlet turbulence, while the case with higher inlet turbulence developed a different distribution of vortices in the wake.

Research Progress on the Structure of DCAF7 Gene and Its Effects on Growth and Development

DNA damage binding protein 1(DDB1) and CUL4-associated factor 7(DCAF7), also known as WDR68, regulate a series of biological activities such as growth and development of organisms. In this paper, the nucleotide sequence and the secondary structure and tertiary structure of the encoded protein were analyzed by an online bioinformatics program, and the biological function, deletion effects and expression level of the gene in different tissues were reviewed, in order to provide reference for the study of this gene as a genetic marker affecting livestock production performance.

Field-assisted tunneling enabled pressure-sensitive composites/sensors for smart concrete structures

Spiky spherical nickel powder with sharp nano-tips on its surface is a kind of excellent fillers for developing pressure-sensitive cement-based composites/sensors for traffic detection,structural health monitoring,and border and military security.The sharp nano-tips on the surface of spiky spherical nickel particles can induce field emission and tunneling effects,which leads to the ultrahigh pressure-sensitive responses of the cement-based composites.In this paper,we systematically introduce research on nanotip-induced ultrahigh pressure-sensitive cement-based composites/sensors,with attentions to their pressure-sensitive property and sensing mechanism,pressure-sensitive characteristic model,and smart structure system for traffic detection.

Experimental Study on the Film Cooling Characteristics of Three Complex Tip Structures

The turbine blades of aircrafts must be properly cooled to prevent engine failure.Thus,to investigate the influence of the tip structure on the film cooling effect,pressure-sensitive paint test technology was used to determine the adiabatic film cooling effectiveness in this study.The experiment was completed in a cascade comprising three straight blades.The effects of the blowing ratio,density ratio,tip clearance,and tip structure on film cooling efficiency were analyzed.The experimental results demonstrated that,as the blowing ratio increased,the film coverage area and film cooling efficiency increased under most experimental conditions.However,the film cooling efficiency was found to initially increase,and subsequently decrease,as the blowing ratio increased.The respective influences of the density ratio and tip clearance on the film cooling efficiency were found to be significant.The density ratio experiments revealed that a high-density ratio can result in better film coverage than the low-density-ratio air.The tip clearance experimental results indicated that a small tip clearance promotes an increase in film cooling efficiency;this is because the small tip clearance negatively affects the main stream leakage flow,which can reduce the film coverage area.Under the conditions of the Base case 2 configuration,a blowing ratio of 2.1,and a tip clearance of 0.6%h,the average film cooling efficiency of the blade tip was 0.22.Among the three blade tip structures applied in this study,Base case 2 demonstrated higher film cooling efficiency than the other two blade tip structures under the conditions of the same blowing ratio,tip clearance,and density ratio.

A Combined Computational and Experimental Study on the Structure-Regulation Relationships of Putative Mammalian DNA Replication Initiator GINS

GINS, a heterotetramer of SLD5, PSF1, PSF2, and PSF3 proteins, is an emerging chromatin factor recognized to be involved in the initiation and elongation step of DNA replication. Although the yeast and Xenopus GINS genes are well documented, their orthologous genes in higher eukaryotes are not fully characterized. In this study, we report the genomic structure and transcriptional regulation of mammalian GINS genes. Serum stimulation increased the GINS mRNA levels in human cells. Reporter gene assay using putative GINS promoter sequences revealed that the expression of mammalian GINS is regulated by 17β-Estradiolstimulated estrogen receptor a, and human PSF3 acts as a gene responsive to transcription factor E2F1. The goal of this study is to present the current data so as to encourage further work in the field of GINS gene regulation and functions in mammalian cells.

Bioinformatics Analysis of Antifungal Peptide 25a2 of Cotton Verticillium Wilt

Protein 25a2 is the antifungal peptide of cotton Verticillium wilt which was isolated from Bacillus amyloliquefaciens. The amino acid sequence of antifungal peptide 25a2 was analyzed using bioinformatics tools, and the characters of signal peptides, transmembrane topological structura, physicochemical signatures, protein domain, secondary and tertiary structure of protein were predicted. The results showed that 25a2 was a secreted protein, the sequence of which included a signal peptide in N end and a transmembrane domain in C end. The predicted secondary structure showed that the antibacterial peptide was mainly free random coils, belonging to mixed protein, three-dimensional model of 25a2 was a compact ball. These results showed that the most possible action mechanism of antifungal peptide 25a2 might be ＂carpet＂ model.

Comparative Analysis of Different Evaluation Functions for Protein Structure Prediction Under the HP Model

The HP model for protein structure prediction abstracts the fact that hydrophobicity is a dominant force in the protein folding process. This challenging combinatorial optimization problem has been widely addressed through metaheuristics. The evaluation function is a key component for the success of metaheuristics; the poor discrimination of the conventional evaluation function of the HP model has motivated the proposal of alternative formulations for this component. This comparative analysis inquires into the effectiveness of seven different evaluation functions for the HP model. The degree of discrimination provided by each of the studied functions, their capability to preserve a rank ordering among potential solutions which is consistent with the original objective of the HP model, as well as their effect on the performance of local search methods are analyzed. The obtained results indicate that studying alternative evaluation schemes for the HP model represents a highly valuable direction which merits more attention.

Computational Challenges in Deciphering Genomic Structures of Bacteria

This article addresses how the functionalities of the cellular machinery of a bacterium might have constrained the genomic arrangement of its genes during evolution and how we can study such problems using computational approaches, taking full advantage of the rapidly increasing pool of the sequenced bacterial genomes, potentially leading to a much improved understanding of why a bacterial genome is organized in the way it is. This article discusses a number of challenging computational problems in elucidating the genomic structures at multiple levels and the information that is encoded through these genomic structures, gearing towards the ultimate understanding of the governing rules of bacterial genome organization.

Dendritic tip selection during solidification of alloys:Insights from phase-field simulations

The effect of undercooling DT and the interface energy anisotropy parameter e4 on the shape of the equiaxed dendritic tip has been investigated by using a quantitative phase-field model for solidification of binary alloys.It was found that the tip radius r increases and the tip shape amplitude coefficient A4 decreases with the increase of the fitting range for all cases.The dendrite tip shape selection parameter sdecreases and then stabilizes with the increase of the fitting range,and sincreases with the increase of e4.The relationship between sand e4 follows a power-law function sµea 4,and a is independent of DT but dependent on the fitting range.Numerical results demonstrate that the predicted sis consistent with the curve of microscopic solvability theory(MST)for e4<0.02,and sobtained from our phase-field simulations is sensitive to the undercooling when e4 is fixed.

A multirate DSP structure for the identification of protein-coding regions

The identification of protein-coding regions in DNA sequence using digital signal process- ing methods is one of the central issues in bioinformatics. In this paper, a multirate struc- ture is proposed for the identification of protein-coding regions whose input sampling rate is same as output sampling rate. The multirate structure consists of cascade com- bination of decimation filter, kernel filter and interpolation filter. The decimation filter is a complex filter, the kernel filter is an FIR lowpass filter and the interpolation filter is a moving average filter. Polyphase decomposition is applied on both decimation filter and interpolation filter for computationally efficient implementation. The potential of the proposed method is evaluated in comparison with existing methods using standard datasets. The results show that the proposed method improves the identification accu- racy of protein-coding regions to a great extent compared to its counterparts.

Study on flow behavior and structure over chined fuselage at high angle of attack

A study of leeward vortex structure over chined fuselage and the effects of micro tip perturbation on its vortex flow have been carried out in wind tunnel experiments at Reynolds numbers from 1.26×105 to 5.04×105 with PIV and pressure measurement techniques.Firstly,the experiment results have proved that micro tip perturbation has no effects on the vortex flow and its aerodynamic characteristics over chined fuselage at high angle of attack,in which there are not any non-deterministic flow behaviors.Secondly,the evolution of leeward vortex structure over chined fuselage along the axis of model can be divided into four flow regimes:linear conical developed regime,decay regime of leeward vortex intensity,asymmetric leeward vortex break down regime and completely break down regime.And a correlation between leeward vortex structure and sectional aerodynamic force was also revealed in the present paper.Thirdly,the experiment results show the behavior of leeward vortex core trajectories and zonal characteristics of leeward vortex structure with angles of attack.Finally,the experiment results of Reynolds number effect on the leeward vortex flow have further confirmed research conclusions from previous studies:the flows over chined fuselage at high angles of attack are insensitive to variation of Reynolds number,and there is a little effect on the secondary boundary layer separation and the suction peak induced by leeward vortex.