水稻microRNA及其靶基因的系统鉴定

miRNA在植物生长发育和环境胁迫中发挥着重要的作用.本研究基于49个水稻小RNA 测序数据,系统分析了已知miRNA的表达,并鉴定到了新的水稻miRNA.我们发现,miRBase上注释的水稻miRNA中,只有39％具有可检测的表达. 此外,对水稻降解组数据的分析鉴定到一些新的miRNA靶基因,包括两个新的miR444靶基因,它们分别编码WD40蛋白和热休克因子型DNA结合蛋白.     

miR164a及其靶基因PeNAC1相互作用研究

miRNA参与了生物体重要的基因表达调控过程,其中miR164通过对标靶NAC(NAM/ATAF/CUC)基因家族的精细调控,在植物激素信号传导、生长发育以及胁迫应答中起着重要作用。为了验证杨树中miR164a和其预测靶基因PeNAC1间是否也存在这一相互作用,笔者采用PCR技术克隆了毛果杨(Populus trichocarpa)miR164a的前体序列Ptc-MIR164a,并通过RNA fold(http://rna.tbi.univie.ac.at/)在线软件对其进行了miRNA二级结构分析。结果表明:该序列能形成典型的二级茎环结构,预示其在细胞内能被加工为成熟的miR164a。进一步借鉴动物细胞miRNA研究中荧光素酶报告基因法,利用高效的杨树原生质体瞬时表达体系,验证了Ptc-MIR164a对其预测靶基因PeNAC1的标靶作用; 同时,也建立了一种比较简单、直观的植物miRNA靶标基因的鉴定方法。     

RACK1依赖的miRNA途径参与调节植物叶绿素的生物合成

为深入探索活化C激酶受体1(receptor of activated C kinase 1,RACK 1)在调节植物microRNA(miRNA)的生物发生,以及其靶基因中的关键作用,对在美国国家生物技术信息中心(National Center for Biotechnology Information,NCBI)网站上共享的基因表达综合数据库(Gene Expression Omnibus,GEO)中有关rack1突变体的小RNA序列数据重新进行了系统分析和挖掘,找到了19个新miRNA.通过解析差异miRNA表达,鉴定到了特异调控叶绿素合成相关基因HEMA和HEMC表达的miRNA,为今后深入系统地研究RACK1在调节叶绿体发育和光合作用机理提供了关键的理论依据,也为利用公共数据库挖掘潜在的数据信息提供了基本的研究设想和思路.     

基于金纳米粒子的催化发夹DNA组装检测microRNA

结合金纳米粒子和催化发夹DNA组装,发展了一种检测microRNA(miRNA)的新方法.首先,在金纳米粒子表面修饰荧光素标记的发夹DNA探针P1,P1荧光被金纳米粒子猝灭.当加入目标miRNA分子时,其与P1杂交并形成P1-miRNA中间体,同时打开P1发夹结构.继而P1-miRNA与P2发夹探针结合,形成稳定的P1-P2双链结构,导致P1上的荧光素远离金纳米粒子而释放荧光,同时顶替下miRNA.随后,miRNA又可以引发金纳米粒子表面多个P1与P2探针的组装,如此循环,实现了对miRNA的放大检测.方法中miRNA在50pmol/L~2nmol/L之间呈现良好的线性关系,最低检出限为39pmol/L.方法简便,成本低,应用于HeLa细胞和HepG 2细胞中miRNA的检测,结果满意.     

miRNA在肿瘤发生、诊断及治疗中的研究进展

对微小RNA(microRNA,miRNA)的产生与肿瘤的关系及其在肿瘤诊断、预后和治疗方面的潜在作用进行了综述.研究表明,miRNA可以调节癌基因和/或抑癌基因,与肿瘤的发生存在着紧密关系;同时miRNA在肿瘤的诊断、预后及治疗方面也发挥着重要的作用.该领域未来研究将主要集中在新miRNA靶标分子的识别、miRNA参与疾病发生分子机制的研究及作为某些疾病诊断、预后和治疗的特异性miRNA分子的筛选及鉴定等.     

基于Gene Ontology的MicroRNA功能聚类

MicroRNA(miRNA)的许多生物过程是通过影响靶基因的转录后表达.miRNA与靶标之间的互补程度和性质决定其基因调控作用.结构相似性可以作为一个强有力的方法推断分子功能的相似性.然而,结构比对的方法来度量miRNA之间的相似性通常不太准确,而且时间开销大.对这些表达差异的miRNA的靶标基因进行聚类,可以很好地理解miRNA的功能.提出一个新的GO(gene Ontology)语义相似性的方法来区分miRNA功能组.该方法采用项信息和边的权重来度量GO项的权重.此外,2个GO图的共同项和非共同项还被用来度量这2个图之间的相似度.对于2个miRNA,它们之间的相似性可以用它们靶标基因标注的GO项的相似性来计算.实验结果表明此方法不仅可以将相似功能的miRNA聚在一起,而且可以预测未知miRNA的功能.     

非小细胞肺癌外周血有核细胞miRNA表达特点研究

miRNA在非小细胞肺癌的发生发展中发挥重要作用,为了解非小细胞肺癌患者外周血有核细胞的miRNA表达特征及其作用,采用第二代高通量测序技术对7例非小细胞肺癌患者和7例对照的外周血有核细胞miRNA表达水平进行检测,比较非小细胞肺癌患者与对照的外周血有核细胞miRNA表达特征,分析两者miRNA表达水平差异情况,共鉴定出非小细胞肺癌患者与对照的外周血有核细胞中有显著表达差异的miRNA 209种,其中肺癌样本miRNA表达上调的有138种,表达下调的有71种.研究结果显示非小细胞肺癌患者与对照样本的外周血有核细胞中miRNA表达具有显著差异,其中部分已被证实参与肿瘤发生、发展等过程.     

基于MiRfilter系统的毛果杨miRNA预测

从参数训练、参数范围训练、候选成熟体打分等方面改进miRNA预测系统MiRfilter,使其适应拥有更长前体的植物miRNA的预测.预测毛果杨基因组上的miRNA,并对系统进行精度检验.利用MiRfilter系统共预测出3 860条候选miRNA;在110个正样本中,正确识别91条前体和80条成熟体,前体预测精度为82.73%,成熟体预测精度为72.73%;在毛果杨第4号染色体（LG_Ⅳ）上得到的1 968个负样本中,有12个数据可认为是miRNA,假阳性率为0.61%.     

microRNA: 一种潜在新型诊断结核病的生物标志物

为了阐述miRNA作为新型生物标记物在结核病诊断中的潜在应用的可能性和优势,文章对结核病的流行态势、诊断现状以及结核病中特异表达miRNA的研究进展了进行总结.结核病的高感染率、高死亡率及耐药菌株的出现严重威胁人类公共卫生事业.现有的结核病诊断技术无法满足快速、低成本、非侵袭性并易推广的诊断要求.miRNA作为一种新的诊断疾病的生物标志物已经在癌症、心脏疾病、妊娠、糖尿病、精神疾病以及多种感染性疾病等领域有研究.大量研究结果显示,在结核病人体内miRNA 21、miRNA 29a、miRNA 99b、miRNA 125b、miRNA 144和miRNA 144*、miRNA 155、miRNA 424表达上调,miRNA 142 3p、miRNA 146表达下调,而miRNA 223及miRNA let 7家族在结核病人不同部位表达存在差异.     

miRNAs在不同物种进化中序列保守性的研究

miRNAs在不同物种的进化中存在保守性,不仅单独在动物或是植物中存在保守性,而且在动植物之间也同样存在．本研究在人和动物的不同组织中克隆到了同源性很高的序列,将所得结果与已发表的成熟的miRNAs比对,发现克隆到的序列与植物中miRNA319家族的相似性较高,并且保守区靠近其5’端,推测新miRNAs可能与miRNA319扮演相似的角色,而这些序列的保守性跨越不同进化阶段的物种,也为miRNAs广泛的保守性增加新的证据,显示miRNAs在物种进化过程中发挥着重要的功能．     

Markedness and its Interpretation in Language Use

Language markedness is a common phenomenon in languages, and is reflected from hearing, vision and sense, i.e. the variation in the three aspects such as phonology, morphology and semantics. This paper focuses on the interpretation of markedness in language use following the three perspectives, i.e. pragmatic interpretation, psychological interpretation and cognitive interpretation, with an aim to define the function of markedness.     

Features of Women's language

Language is a means of verbal communication. People use language to communicate with each other. In the society, no two speakers are exactly alike in the way of speaking. Some differences are due to age, gender, statue and personality. Above all, gender is one of the obvious reasons. The writer of this paper tries to describe the features of women＇s language from these perspectives： pronunciation, intonation, diction, subjects, grammar and discourse. From the discussion of the features of women＇s language, more attention should be paid to language use in social context. What＇s more, the linguistic phenomena in a speaking community can be understood more thoroughly.     

低渗透非均质砂岩油藏启动压力梯度研究

理论推导与室内实验相结合,建立了低渗透非均质砂岩油藏启动压力梯度确定方法。首先借助油藏流场与电场相似的原理,推导了非均质砂岩油藏启动压力梯度计算公式。其次基于稳定流实验方法,建立了非均质砂岩油藏启动压力梯度测试方法。结果表明:低渗透非均质砂岩油藏的启动压力梯度确定遵循两个等效原则。平面非均质油藏的启动压力梯度等于各级渗透率段的启动压力梯度关于长度的加权平均;纵向非均质油藏的启动压力梯度等于各渗透率层的启动压力梯度关于渗透率与渗流面积乘积的加权平均。研究成果可用于有效指导低渗透非均质砂岩油藏的合理井距确定,促进该类油藏的高效开发。     

On Tragic Consciousness In The Works By Ernest Hemingway

As an American modern novelist who were famous in the literary world, Hemingway was not a person who always followed the trend but a sharp observer. At the same time, he was a tragedy maestro, he paid great attention on existence, fate and end-result. The dramatis personae's tragedy of his works was an extreme limit by all means tragedy on the meaning of fearless challenge that failed. The beauty of tragedy was not produced on the destruction of life, but now this kind of value was in the impact activity. They performed for the reader about the tragedy on challenging for the limit and the death.     

Achieving Unusual States of Matter Under High Pressure

正The periodicity of the elements and the non-reactivity of the inner-shell electrons are two related principles of chemistry,rooted in the atomic shell structure.Within compounds,Group I elements,for example,invariably assume the+1 oxidation state,and their chemical properties differ completely from those of the p-block elements.These general rules govern our understanding of chemical structures and reactions.Using first principles calcula-     

Exchange-Correlation and Electronic Excitation Energies from Pairing Matrix Fluctuations

We have developed an adiabatic connection to formulate the ground-state exchange-correlation energy in terms of pairing matrix linear fluctuations.This formulation of the exchange-correlation energy opens a new channel for density functional approximations based on the many-body perturbation theory.We illustrate the potential of such approaches with an approximation based on the particle-particle Random Phase Approximation(pp-RPA).This re-     

Density Functional Theory for the Response of Periodic Systems to Electric Fields Based on the Vector Potential Approach

正The electronic and nuclear(structural/vibrational)response of 1D-3D nanoscale systems to electric fields gives rise to a host of optical,mechanical,spectral,etc.properties that are of high theoretical and applied interest.Due to the computational difficulty of treating such large systems it is convenient to model them as infinite and periodic(at least,in first approximation).The fundamental theoretical/computational problem in doing so is that     

On the Thermodynamic Limit for Responses to Static Electromagnetic Fields

For molecular systems,the quantum-mechanical treatment of their responses to static electromagnetic fields usually employs a scalar-potential treatment of the electric field and a vector-potential treatment of the magnetic field.Although the potential for each field separately is associated with the choice of an(unphysical)origin,the precise choice of the origin for the electrostatic field has little consequences for the results.This is different for the     

An affordable accurate evaluation of the binding conformations predicted by molecular docking studies in bio-system

Franck-Condon factors bridge the gap between theoretical modeling and experimental observations for molecular electronic spectroscopy and electron transfer.Under the displaced harmonic oscillator approximation,multidimensional Franck-Condon factors are decomposed into a product of many one-dimensional(1D)Franck-Condon(FC)factors,and each 1D-FC factor is associated with one Huang-Rhys factor that determines the leading contribution of     

Call for Papers

<正>"The Journal of Shanghai Normal University:Mathematics"is published by Shanghai Normal University as regular issues of The Journal of Shanghai Normal University each year from 2014 in English.The editors-in-chief of the issues are professors Yuhao Cong and Maoan Han.The Journal of Shanghai Normal University was started in 1958 with