Overview of Molecular Typing Tools for The Characterization of Salmonella enterica in Malaysia

Salmonella is a member of the family Enterobacteriaceae. This genus comprises two species, namely Salmonella enterica and Salmonella bongori. Salmonella enterica is further divided into six subspecies, namely enterica, salamae, arizonae,

Establishment of a molecular tool for blood meal identification in Malaysia

Objective:To establish a polymerase chain reaction(PCR) technique based on cytochrome b {cytb) gene of mitochondria DNA(mtDNA) for blood meal identification.Methods:The PCR technique was established based on published information and validated using blood sample of laboratory animals of which their whole gene sequences are available in CenBank.PCR was next performed to compile gene sequences of different species of wild rodents.The primers used were complementary to the conserved region of the cytb gene of vertebrate's mtDNA.A total of 100 blood samples,both from laboratory animals and wild rodents were collected und analyzed.The obtained unknown sequences were compared with those in the GenBank database using BLAST program to identify the vertebrate animal species.Results:Gene sequences of 11 species of wild animals caught in 9 localities of Peninsular Malaysia were compiled using the established PCR. The animals involved were Rattus(rattus) tanezumi,Rattus tiomanicus,Leopoldamys sabanus, Tupaia glis,Tupaia minor,Niviventor cremoriventor,Rhinosciurus laticaudatus,Calloseiurus caniseps,Sundamys muelleri,Rattus rajah,and Maxomys whitelwadi.The BLAST results confirmed the host with exact or nearly exact matches(>89%identity).Ten new gene sequences have been deposited in CenBank database since September 2010.Conclusions:This study indicates that the PCR direct sequencing system using universal primer sets for vertebrate cytb gene is a promising technique for blood meal identification.

Development of A High-throughput Molecular Identification Method Suitable for Fungi

Fungi play a significant role in biology-related domains, and with the molecular biology technology advancing, identification of fungi at molecular level and verification of genetic transformant has become the necessary step of test. By far, however, there is no ideal high-throughput molecular identification method. In this paper, a high-throughput device was designed, and a novel PCR-mediated molecular identification method suitable for the device was developed. Through cloning of ccllulase encoding genes and regulatory genes on the genome of Trichoderma reesei, cloning of promoter of phesphoglycerate kinase gene 1 and xylanase encoding genes on the genome and expression vector of Saccharomyces cerevisiae, and ITS sequences cloning and RAPD analysis of T. reesei, S. cerevisiae, Penicil- lium oxalicum, Rhizopus stolonifer, Aspergillus niger, A. carbonarius and A. japonicas, the method turned out to be an effective one with wide application potential. The establishment of the method has worked out the bottleneck of high-throughput molecular identification.

Analysis on the Wear Performances of Cemented Carbide Tools Containing Ti in the Coatings When Machining Ti⁃6Al⁃4V Alloys

Because of the high affinity of the same element Ti,cemented carbide tools containing Ti seem to be non⁃optimal in machining titanium alloys.However,in practice,cemented carbide tools containing Ti are still widely used in machining titanium alloys.Cutting experiments were conducted in order to systematically explain the contradictions between the practice and theory.The diffusion process between titanium alloys and the cemented carbide tools was analyzed by auger electron spectroscopy detecting the cutting regions.It was also analyzed by Ti/Co diffusion behavior simulated by molecular thermodynamics.The experimental results and the simulation results showed that the mutual diffusion of Ti/Co atoms was the major reason for the diffusion wear.The dissolution⁃diffusion wear was one of the main wear mechanisms for the cemented carbide tools containing Ti in the coatings.Moreover,four types of cemented carbide tools and two other types of cermet tools were used to machine the Ti⁃6Al⁃4V alloys at different cutting speeds to further verify the high affinity of cutting tools containing Ti in the substrate/coating.The verification experiments results showed that the cemented carbide tools containing Ti generally cannot be used for machining titanium alloys,but could show less affinity in the cutting regions with reasonable cutting conditions.

New tools,new tick-borne diseases?

Tick-borne diseases(TBDs) are a major public health concern that has increased in the past three decades. Nevertheless, emerging or reemerging TBDs may be still misdiagnosed. Molecular biology techniques for the screening of ticks, use of "Omics" approaches and the incorporation of analytical methods such as mass spectrometry or nuclear magnetic resonance, to the study of ticks and their associated pathogens or potential pathogens are promising tools for a more accurate differential diagnosis of TBDs. However, this huge amount of data needs to be carefully interpreted before being incorporated to the routine of clinical practice. In the meantime, a clinical approach and high level of suspicion keep being essential for the diagnosis and proper handling of TBDs.

Purification and immunoglobulin E epitopes identification of low molecular weight glutenin:an allergen in Chinese wheat

As one of the most important cereals,wheat(Triticum aestivum)has high nutritional value and is widely cultivated in China.However,wheat can cause severe allergic reactions,and a growing number of people are developing allergies to Chinese wheat.Low molecular weight glutenin(LMW-GS),an important allergen in susceptible populations,is responsible for celiac disease and wheat contacts dermatitis.In this study,LMW-GS was highly purified from Chinese wheat(Xiaoyan 6)and further identified and characterized.In addition,8 peptides were predicted efficiently by 5 immunological tools,among which 5 peptides showed significant immunoglobulin E binding abilities.Two specific epitopes were found to be in the non-conserved region of the amino acid sequence of LMW-GS,which was speculated to be the specific epitope of Chinese wheat.This systematic research of LMW-GS may provide new insights into the prevention of wheat allergy and development of hypoallergenic wheat products.

Machine Learning-Assisted High-Throughput Virtual Screening for On-Demand Customization of Advanced Energetic Materials

Finding energetic materials with tailored properties is always a significant challenge due to low research efficiency in trial and error.Herein,a methodology combining domain knowledge,a machine learning algorithm,and experiments is presented for accelerating the discovery of novel energetic materials.A high-throughput virtual screening(HTVS)system integrating on-demand molecular generation and machine learning models covering the prediction of molecular properties and crystal packing mode scoring is established.With the proposed HTVS system,candidate molecules with promising properties and a desirable crystal packing mode are rapidly targeted from the generated molecular space containing 25112 molecules.Furthermore,a study of the crystal structure and properties shows that the good comprehensive performances of the target molecule are in agreement with the predicted results,thus verifying the effectiveness of the proposed methodology.This work demonstrates a new research paradigm for discovering novel energetic materials and can be extended to other organic materials without manifest obstacles.

The interaction between grain boundary and tool geometry in nanocutting of a bi-crystal copper

Anisotropy is one central influencing factor on achievable ultimate machined surface integrity of metallic materials.Specifically,grain boundary has a strong impact on the deformation behaviour of polycrystalline materials and correlated material removal at the microscale.In the present work,we perform molecular dynamics simulations and experiments to elucidate the underlying grain boundaryassociated mechanisms and their correlations with machining results of a bi-crystal Cu under nanocutting using a Berkovich tool.Specifically,crystallographic orientations of simulated bi-crystal Cu with a misorientation angle of 44.1°are derived from electron backscatter diffraction characterization of utilized polycrystalline copper specimen.Simulation results reveal that blocking of dislocation motion at grain boundaries,absorption of dislocations by grain boundaries and dislocation nucleation from grain boundaries are operating deformation modes in nanocutting of the bi-crystal Cu.Furthermore,heterogeneous grain boundary-associated mechanisms in neighbouring grains lead to strong anisotropic machining behaviour in the vicinity of the grain boundary.Simulated machined surface morphology and machining force evolution in the vicinity of grain boundary qualitatively agree well with experimental results.It is also found that the geometry of Berkovich tool has a strong impact on grain boundary-associated mechanisms and resultant ploughing-induced surface pile-up phenomenon.

油料作物育种的分子工具和技术创新

油料作物的主要育种目标是提高产量、品质和抗逆性。目前,就产量而言,全球主要油料作物依次为大豆、油菜、向日葵和花生。本文综述了这些主要油料作物育种的分子工具和技术创新,包括基因组选择、基因组编辑、分子设计育种等新技术,指出了当前在遗传研究和育种实践中存在的主要问题,并对技术进展和未来应用前景进行了展望,旨在为油料作物高产、优质、高效育种提供借鉴。

单晶硅纳米切削过程中微沟槽结构金刚石刀具切削性能的分子动力学模拟

基于分子动力学,利用LAMMPS和OVITO软件对单晶硅纳米切削过程进行模拟,研究了V形微沟槽结构对金刚石刀具切削性能的影响。结果表明,在金刚石刀具后刀面构建一定深度的V形微沟槽能够减少工件亚表面损伤,同时也对工件加工质量及刀具抗磨损性能产生了明显影响,当微沟槽深度为0.75 nm时,金刚石刀具切削性能最佳。

Advances in the development of molecular genetic tools for Mycobacterium tuberculosis

Mycobacterium tuberculosis, a Gram-positive bacterium of great clinical relevance, is a lethal pathogen owing to its complex physiological characteristics and development of drug resistance. Several molecular genetic tools have been developed in the past few decades to study this microorganism. These tools have been instrumental in understanding how M. tuberculosis became a successful pathogen. Advanced molecular genetic tools have played a significant role in exploring the complex pathways involved in M. tuberculosis pathogenesis. Here, we review various molecular genetic tools used in the study of M. tuberculosis. Further, we discuss the applications of clustered regularly interspaced short palindromic repeat interference（CRISPRi）, a novel technology recently applied in M. tuberculosis research to study target gene functions. Finally, prospective outcomes of the applications of molecular techniques in the field of M. tuberculosis genetic research are also discussed.

环境胁迫对海水青鳉( Oryzias melastigma )的毒性效应在基因组学和蛋白质组学上的研究进展

近年来,海水青鳉(Oryzias melastigma)已经被公认为海洋生态毒理学研究中的一种模式生物,其具有与淡水模式生物斑马鱼(Danio rerio)类似的研究特征优势,如世代时间短(3~4个月)、每日产卵、成鱼尺寸小(2.5~3.5 cm)、胚胎透明、性别二态性以及易于进行实验室规模化养殖等。在过去十余年中,国内外的研究者们对海水青鳉进行了广泛的基因组和蛋白质组研究。这些组学数据能够进一步帮助我们在分子层面了解环境胁迫对海洋生物的潜在影响及其可能的毒性机制。在这篇综述中,我们归纳了海水青鳉作为海洋生态毒理学研究模型的优势,介绍了当前用于海水青鳉基因/蛋白质组学的技术方法,整理了基因/蛋白质组学在研究不同种类的海洋环境压力源对海水青鳉毒性效应的应用现状。最后,我们对未来海水青鳉的研究提出了一定的预期与展望。

应用生理学方法和分子手段进行玉米抗旱育种

干旱是包括中国在内的世界上大多数玉米生产国家的重要农业灾害之一,解决干旱问题的有效途径包括培育抗旱型和节水型的玉米杂交种。多年来,通过常规手段进行玉米抗旱育种取得了一定进展,但由于多方面原因,其育种效率没有得到进一步提高。而与此同时,对玉米在干旱胁迫下的生理生化途径研究很多,其成果可以为抗旱育种提供理论指导;尤其是近年来应用分子标记技术和基因组学技术对玉米抗旱性进行了深入的遗传剖析,其研究结果也为玉米抗旱分子育种提供了新的手段和思路。同时评述了相关研究领域的进展,并讨论今后的发展趋势。

人工锌指核酸酶介导的基因组定点修饰技术

锌指核酸酶(ZFN)由锌指蛋白(ZFP)结构域和Fok I核酸内切酶的切割结构域人工融合而成,是近年来发展起来的一种可用于基因组定点改造的分子工具。ZFN可识别并结合特定的DNA序列,并通过切割这一序列的特定位点造成DNA的双链断裂(DSB)。在此基础上,人们可以对基因组的特定位点进行各种遗传操作,包括基因打靶、基因定点插入、基因修复等,从而能够方便快捷地对基因组实现靶向遗传修饰。这种新的基因组定点修饰方法的突出优势是适用性好,对物种没有选择性,并且可以在细胞和个体水平进行遗传操作。文章综述了ZFN技术的研究进展及应用前景,重点介绍ZFN的结构与作用机制、现有的靶点评估及锌指蛋白库的构建与筛选方法、基因组定点修饰的策略,以及目前利用这一技术已成功实现突变的物种及内源基因,为开展这一领域的研究工作提供参考。

纳米加工过程中金刚石刀具磨损研究的新进展

总结和分析了近几年来国内纳米加工过程中金刚石刀具磨损的研究方法,简要阐述了分子动力学模拟的基本原理及其应用情况,评述了分子动力学等模拟方法在金刚石刀具的热及化学磨损等方面的最新研究进展,指出了目前研究过程中存在的一些问题,以及今后研究中值得注意的几个发展方向.

线性改变切削深度对单晶铜纳米切削的影响

针对单晶铜纳米切削,利用分数阶微积分理论,建立了切削力主趋势分量对切削深度的依赖模型,以描述非线性的尺寸效应。利用近似熵测度,研究了在不同切削阶段中切削力高频扰动的复杂性。研究表明,在切入阶段,切削力经历了由负值到较大正值的突变,工件材料出现弹性失稳以及初期的弹塑性转变;在切削阶段,切削力的主趋势分量呈现明显的低频峰谷现象和非线性的尺寸效应。通过观测工件材料内部的位错形核及位错运动,详细地解释了切削力在线性改变切削深度条件下呈现这种演变特征的根本原因。

金刚石刀具机械研磨过程中材料的去除机理(英文)

从原子量级揭示了金刚石刀具机械研磨过程中材料的去除机理——研磨过程中,研磨区域原子的相变是材料去除的主要原因.使用分子动力学方法建立了金刚石刀具和刚性金刚石磨粒的三维模型.采用Tersoff势函数计算了所有原子之间的作用力,并以1.5个晶格的切深进行了研磨过程模拟.通过观测模型内部原子位置的变化发现,研磨区域刀具原子的晶胞在研磨过程中被压扁,发生了从金刚石体心立方结构向无定形碳结构的转变.计算了研磨区域原子研磨前后的径向分布函数,进一步验证了该相变过程.同时,使用X射线衍射方法分析了研磨实验过程中产生的碎屑,分析结果表明研磨过程中确实有相变发生.

分子纳米技术与金属有机分子纳米体系

基于超分子自组装的分子纳米技术是一种新兴的高新技术。本文从金属矢量操纵的自组装分子纳米体系、自组装的纳米微反应器与超分子催化和自组装金属超分子高分子纳米材料等三个方面评述了分子纳米技术及其在构筑金属有机分子纳米体系中的发展现状 ,进一步阐述了“金属矢量”的概念 ,并首次提出建立“自组装子工具箱” ,探讨了分子纳米技术的发展方向。

单晶硅纳米切削中C—C键断裂对金刚石刀具磨损的影响

本文基于分子动力学方法模拟金刚石刀具纳米切削单晶硅,从刀具的弹塑性变形、C—C键断裂对碳原子结构的影响以及金刚石刀具的石墨化磨损等方面对金刚石刀具的磨损进行分析,采用配位数法和6元环法表征刀具上的磨损碳原子.模拟结果表明:在纳米切削过程中,金刚石刀具表层C—C键的断裂使其两端碳原子由sp3杂化转变为sp2杂化,同时,表面上的杂化结构发生变化的碳原子与其第一近邻的sp2杂化碳原子所构成的区域发生平整,由金刚石的立体网状结构转变为石墨的平面结构,导致金刚石刀具发生磨损;刀具表面低配位数碳原子的重构使其近邻区域产生扭曲变形,C—C键键能随之减弱,在高温和高剪切应力的作用下,极易发生断裂;在切削刃的棱边上,由于表面碳原子的配位严重不足,断开较少的C—C键就可以使表面6元环中碳原子的配位数都小于4,导致金刚石刀具发生石墨化磨损.