基于RAD-seq技术的鹅掌楸基因组SNP标记开发

【目的】开发大量可靠的SNP标记,为鹅掌楸高密度遗传连锁图谱的构建和基于基因组的林木选择育种提供分子基础。【方法】从北美鹅掌楸NK基因型为母本、鹅掌楸LS基因型为父本的F1代杂交群体中,选取198株个体为作图群体。用限制性内切酶EcoR I对包括2个亲本和198个子代在内的200个单株的基因组DNA进行酶切,构建RAD(restriction-site associated DNA)文库并进行RAD-seq测序。采用读长为91 bp的双末端测序。2个亲本的平均测序深度为2×,198个子代的平均测序深度为0.8×,平均产量为1.94 Gb,共获得约387.21 Gb数据。用Stacks软件将每个样品的RAD-reads作生物信息学分析,对候选位点进行卡方检验和缺失率检验,再将符合孟德尔遗传的标记及与之相对应的RAD-tag序列和鹅掌楸参考基因组序列进行比对。最后,从本研究开发的SNP标记中选取27个候选SNP位点,设计引物,对随机挑选的16个F1代进行PCR扩增并将结果进行测序,同时验证SNP的有效性。【结果】从候选群体中共鉴定到22 019个SNP位点,符合孟德尔遗传规律的标记为4 233个,最终获得3 501个候选SNP标记。SNP验证中,共有293个SNP标记完成测序并能判读结果,所有位点都为SNP位点,共有194(66.2%)个SNP变异类型得到了验证。 【结论】基于RAD-seq技术和鹅掌楸参考基因组序列为基础的策略,能够作为一种快速有效的手段,实现大规模的分子标记开发,可用于鹅掌楸等林木的高密度遗传图谱的构建。     

基于序列拼接的基因组长插入变异集成检测方法研究

针对目前基于测序的结构变异检测方法检测效果较差的问题，提出了基于序列拼接的长插入变异（ISALins）检测方法。首先融合3种不同检测工具初始的检测结果，然后在初始的预测可疑断点附近分析和提取最可能包含插入信息的高质量软切片段，并比对失败的片段；将这些候选片段利用基于De Bruijn图的方法进行拼接后完成长插入变异的检测。仿真数据和真实数据的实验结果表明：与直接融合多个单一工具检测结果相比，本文方法可以在确保检测敏感度的前提下大幅提高长插入变异的检测精度。     

利用泛素分裂系统筛选AtTR1相互作用蛋白质

以AtTR1作为诱饵蛋白利用泛素分裂系统在拟南芥cDNA文库中筛选与拟南芥AtTR1基因相互作用的蛋白质.运用营养缺陷型培养基和X-Gal显色、PCR扩增及酶切分析等实验排除假阳性,并对阳性克隆进行序列测定和比对.通过泛素分裂系统筛选到可靠的AtTR1相互作用蛋白质,测序比对后,选取HMA与AtTR1通过GST pull-down进行进一步的验证,结果证明它们确实存在相互作用,这对进一步研究AtTR1及其相互作用蛋白质在植物耐热中的作用和耐热分子机制奠定了基础.     

基于感兴趣区域AdaBoost分类器的视频车辆检测研究

近年来基于视频的车辆自动检测作为城市智能交通系统的一项重要技术一直受到关注.针对AdaBoost分类器目标检测所存在的漏检、误检和计算量过大等问题,提出一种基于混合高斯模型运动区域提取和Haar-like特征的AdaBoost级联分类器的交通视频车辆检测算法,首先通过建立混合高斯模型对运动目标的总体区域进行检测,进而提取基于车辆运动的感兴趣区域,再对其进行基于Haar-like特征的区域AdaBoost级联分类,实现对运动车辆的检测.由于采用了基于运动区域提取和分类相结合的检测模式,通过混合高斯背景模型较准确的提取出ROI作为车辆的候选区域,约束了每帧的搜索区域,使AdaBoost分类器的目标检测更具针对性,提高了检测的准确性,降低了漏检率;同时也减少了分类算法滑动窗口扫描所需要的时间,提高了检测速度.实验结果验证了所提出算法对复杂交通环境车辆检测的适应性和有效性.     

高良姜及其混淆品rDNA ITS序列的分析与鉴别

用聚合酶链式反应(PCR)直接测序法测定和分析不同产地野生和农家品种的高良姜及其3种混淆品(山姜、华山姜和大高良姜)的核糖体DNA内转录间隔区(rDNA ITS)序列,为高良姜种质资源研究和真伪鉴别提供分子数据.ITS序列分析结果表明:高良姜种内序列同源性达100%,测序结果中发现杂合位点,且广西样品杂合位点的两个碱基所占的比例与其它地方样品的不同.高良姜及其混淆品经测序、比对、排序得到的812bp序列中有61个变异位点,60个是信息位点,同源性达96.32%,其中ITS1和ITS2区中的11个位点在高良姜及其混淆品中差别明显,可以鉴别高良姜及其混淆品.同时发现,基于DNA序列的高良姜及其混淆品的系统分类结果与形态学的分类结果不完全一致,有待进一步研究探讨.     

中国四个小型猪品种生长激素基因克隆测序及分子进化研究

研究对中国四个小型猪五指山猪、贵州香猪、滇南小耳猪和藏猪的生长激素基因(pGH,porcine growth hormone)进行了克隆测序及构建分子进化树,考察该激素对小型猪体型的影响。通过筛选合适的引物,采用PCR技术,扩增了四个小型猪品种的pGH基因全序列,并对其进行了克隆测序分析。4个小型猪品种pGH基因全长为2006bp,包括5个外显子和4个内含子,CDS全长为648bp。将4个品种小型猪和长白猪、雅南猪、内江猪进行了核苷酸序列比对,共有63处发生了变异,变异率为2.9%,其中外显子有12处变异,全部为转换;内含子有51处发生了变异,包括转换、颠换和缺失。聚类结果基本符合其地方猪种的地理位置分布原则。     

基于双肤色模型及AdaBoost算法的人脸检测

针对复杂背景和可变光照条件下,彩色静止图像的人脸检测问题,综合利用YCbCr和HSI颜色空间下的肤色模型,先进行肤色分割,定位出候选人脸,再用AdaBoost级联分类器进行检测验证,有利于提高检测效率,降低误检率。     

黑胸大蠊浓核病毒基因组末端序列测定与分析

利用构建的黑胸大蠊浓核病毒（ＰｆＤＮＶ）全且竽组抽粒（ＰｆＤＮＶ－ｐＵＣ１１９）以及一系列完整缺失克隆，通过全自动测序方法了ＰｆＤＮＶ两末端各７２８ｂｐ和７３０ｂｐ核苷酸序列的测定，通过计算机软件分析发现，ＰｆＤＮＶ末端２０１ｎｔ为倒置重复序列，其中最末端１２２ｎｔ为回序列，能形成典型的发夹结构，并与同科其它病毒末端序列进行了核苷酸序列回同源性比较。     

应用3’RACE技术扩增仿刺参C型凝集素基因及实验条件的优化

从GenBank上调取刺参C型凝集素（C-type Lectin）基因序列EST,根据此序列设计RACE引物,采用PCR扩增技术得到了仿刺参C-type Lectin基因序列（EST）,根据这段EST序列设计1个基因特异引物（GSPF）,与通用引物（UPM）扩增,成功地克隆到了该基因的3’末端序列.同时,对仿刺参C型凝集素基因3’克隆的实验条件进行了优化.该扩增片段长度为670bp,与已知序列重叠部分为417bp.经测序和比对发现该段序列与预期的目标基因的序列一致.     

用5′加尾长引物进行AFLP片段的直接测序

现有的AFLP标记片段测序方法比较费时,成本也较高.设计一个包括EcoRI接头引物和5′端加36个额外核苷酸的长引物AF2SC,用该引物再扩增时可AFLP片段末端增加36个碱基.再利用这36个碱基的末端序列进行测序,只需一次反应就能获得AFLP标记片段的全序列.该方法缩短了AFLP片段测序所需时间,也降低了实验成本.     

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.     

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     

Journal of Donghua University ( English Edition) Contents of Volume 31

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