应用量子化学方法研究茶多酚类抗氧化剂的构效关系

采用分子力学和量子化学从头计算方法,研究了不同结构茶多酚（Green tea polyphenol,GTP)抗氧化活性的构效关系。计算结果表明,茶多酚类的抗氧化活性与其释放活泼氢生成苯氧自由基的能力有关,添生大小与O－H间的Mulliken集居数、前线轨道能量、反应终态能量下降量及苯氧自由基稳定性有关。     

正确理解和应用经济阈值

分析了害虫经济阈值制定与应用中的若干常见问题。制定问题主要来自试验和计算两方面。试验方面涉及虫量设置的梯度和范围、模拟为害、考察时间和供试虫龄以及样本大小等 ,计算方面涉及虫量计算、理论产量和防治效果等。阈值应用的问题涉及防治行动时间、多项投资选择、害虫自然存活率以及作物产量水平等。为避免这些陷阱 ,作者提出个人见解。     

蛋白质序列的矩阵图谱表达

基于经典HP模型,利用蛋白质序列的矩阵图谱表达法(MGR)及数值刻画的思想提出了一种新的蛋白质序列的比对方法,通过观察蛋白质序列的数值刻画图及计算两蛋白质序列之间的欧氏距离d,对木聚糖酶两家族的蛋白质序列进行了相似性分析.发现被划分为同一木聚糖酶家族的蛋白质序列之间的相似性更大,而且蛋白质序列的相似性程度与分子大小、结构和分子进化相关.     

计算任务男女性别差异的fMRI研究

目的:用功能磁共振(functional Magnetic Resonance Imaging,FMRI)探讨男女不同性别在计算任务时脑活动的差异。方法:对10例男性、8例女性正常年青受试者进行简单及复杂任务的功能MRI扫描,采用SPM2软件进行数据分析和脑功能区定位。结果:计算任务中男女主要激活区域均为额前区、顶叶、枕叶及小脑,男性额前区及顶叶等计算功能区激活范围较女性广,其中以复杂计算为著。结论:相同的计算任务,男性激活的脑功能区范围多于女性。     

用于寡核苷酸二级结构预测的热力学数据库研究进展

基于核酸分子杂交的生物技术（如PCR）在病原微生物检测、临床诊断等诸多领域中应用广泛,此类技术的可靠性在于寡核苷酸分子与其靶点结合的高稳定性与特异性,而精确预测寡核苷酸与靶分子结合的二级结构是分析其稳定性与特异性的关键。其中,基于热力学的最近邻模型是寡核苷酸二级结构预测最为可靠的计算方法,但其精确性强烈依赖于精确的热力学参数。由于寡核苷酸分子二级结构的复杂性,除了完美匹配外,还需要错配、内环、膨胀环、末端摇摆、CNG重复、GU摆动等特殊结构的热力学数据。本文综述了近年来用于寡核苷酸二级结构预测的有效热力学数据库及相关计算方法,并指出当前热力学数据库的局限及未来发展方向。     

基因功能注释的计算方法

对未知功能的基因进行注释的通常的方法是依据序列同源性分析。近年来,出现了多种不基于序列同源性的基因注释的计算方法,这些方法不依赖于核酸或蛋白质序列的相似性,所能预测的基因的功能属性也有所扩展,如,能够预测基因间相互作用关系。这些方法有效地减少实验材料、时间消耗。该文综述了几种这样的计算方法,包括原理、方法评估及存在的问题。     

计算生态学的形成与发展

1　计算生态学产生的背景1998年在意大利召开的统计生态学国际大会上 ,与会者普遍认为 ,随着计算机技术的普及和计算方法的推广 ,数字化、模型化、智能化、可视化技术已经被广泛地应用到生态学计算领域中 ,依托计算机技术而进行的生态学计算正蓬勃兴起并迅速发展 ,在生态学中起着越来越重要的作用 ,已经形成了一个新的生态学分支计算生态学 (ｃｏｍｐｕｔｉｎｇｅｃｏｌ ｏｇｙ)。计算生态学的概念一经提出就倍受重视 ,各国的生态学家 ,目前正在努力发展和完善这一新兴学科领域。与其它科学相比 ,计算生态学的产生具有特殊的历史背景。一方…     

分子信标DNA计算模型的研究进展与展望

由于分子信标具有结构简单,灵敏度高及反应迅速等优点,因此,利用分子信标进行数学问题的求解将成为可能.通过对分子信标的计算模型进行详细的介绍,并对分子信标的计算模型的研究思路进行了展望,据此思路,可以建立多种组合优化问题及逻辑门的分子信标计算模型.     

复杂疾病靶基因识别与网络重建的计算系统生物研究

复杂疾病相关靶基因的识别、构建疾病驱使相关基因网络及进行疾病机制研究,是功能基因组学研究中非常重要的科学问题。文章以计算系统生物学的观点和三维的角度,综述了基于生物谱（SNP遗传谱、芯片表达谱和2D-PAGE蛋白质谱等）的复杂疾病靶基因识别、多水平（SNPs虚拟网络、基因调控网络、蛋白质互作网络等）遗传网络逆向重构方法,及不同水平的网络之间在生物学和拓扑学上的纵向映射关系,并给出复杂疾病靶基因识别与网络关系的计算系统生物方法研究的未来展望。     

计算生物学在RNA研究中的应用

计算生物学在非编码RNA(non-coding RNA, ncRNA)研究领域中发挥着重要的作用.计算生物学是利用计算机科学方法来研究和理解生命科学问题的交叉学科,而ncRNA作为一类数目庞大且功能多样的RNA分子,参与了广泛的生物学过程.本文对RNA计算生物学中的常用算法和工具进行综述,并着重介绍专家系统、机器学习、深度学习等计算生物学研究策略在ncRNA鉴定、ncRNA靶标预测、RNA修饰、RNA二级结构检测、RNA-蛋白质互作及RNA功能预测中的应用.     

激光扫描共聚焦显微镜在蛋白质晶体生长研究中的应用

激光扫描共聚焦显微镜与普通光学显微镜相比,其分辨率高,同时具有可对样品进行非侵入性无损伤断层扫描,以及对样品形貌进行三维成建等特点,因此,可作为研究晶体生长强有利的工具。本文介绍了其在定量测量晶体的个数,重组三维图像以获得晶体生长的过程信息及测定晶体生长台阶动态变化等方面的应用。还对激光扫描共聚焦显微镜在晶体生长研究的其它方面应用前景作了展望。     

同义密码子使用模式对多肽链共翻译折叠的影响研究进展

同义密码子使用模式作为核苷酸与氨基酸的纽带,其多样性介导了核糖体扫描速率,同时扩充了基因的遗传信息存储量。随着新型技术的应用,发现特异性密码子和密码子结合力可调节核糖体扫描速率并影响蛋白质构象。同义密码子使用模式通过多种方式在不同环节影响着核糖体扫描速率,同时还影响着自身mRNA的稳定性。本文简述了密码子使用模式如何在核糖体扫描翻译mRNA的过程中实现对多肽链翻译延伸的调控,为今后生物工程学领域如何优化蛋白高效表达提供可参考的思路与理念。     

Scanning of polyacrylamide gel electrophoresis columns for detection of unstained protein zones and for their localization relative to enzyme activities.

Background disturbances which often confuse 280-nm scans of polyacrylamide gels, can be distinguished from true protein peaks by scanning also at a wavelength where the proteins do not absorb (for instance 310 nm).A scanning technique has been used also for precise localization of spectrophotometrically detectable enzyme activities relative to protein zones. After electrophoresis the gel is transferred to a specially designed quartz cuvette and scanned at 280 nm for protein detection. The substrate is then allowed to diffuse into the gel and the activity is located by scanning at a wavelength absorbed by the product.Scanning of polyacrylamide gel electrophoresis columns can be used for the study of solute-solute interactions, as illustrated by a simple model experiment on the binding of bilirubin to albumin.     

Computational alanine scanning with linear scaling semiempirical quantum mechanical methods

Alanine scanning is a powerful experimental tool for understanding the key interactions in protein–protein interfaces. Linear scaling semiempirical quantum mechanical calculations are now sufficiently fast and robust to allow meaningful calculations on large systems such as proteins, RNA and DNA. In particular, they have proven useful in understanding protein–ligand interactions. Here we ask the question: can these linear scaling quantum mechanical methods developed for protein–ligand scoring be useful for computational alanine scanning? To answer this question, we assembled 15 protein–protein complexes with available crystal structures and sufficient alanine scanning data. In all, the data set contains ΔΔGs for 400 single point alanine mutations of these 15 complexes. We show that with only one adjusted parameter the quantum mechanics‐based methods outperform both buried accessible surface area and a potential of mean force and compare favorably to a variety of published empirical methods. Finally, we closely examined the outliers in the data set and discuss some of the challenges that arise from this examination. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

一种女贞叶抗冻蛋白的分离纯化

根据抗冻蛋白与冰结合的特性, 利用碎冰从女贞(Ligustrum lucidum)叶提取液中分离出抗冻蛋白。结果表明, 通过碎冰吸附、凝胶过滤和离子交换层析可以获得4个组分的蛋白质, 其中的1个经鉴定具有热滞活性。在蛋白质浓度为5 mg. mL-1时, 它的热滞活性(thermal hysteresis activity, THA)值为0.678°C, 对其进行全波长扫描(200-1 000 nm)发现在975nm处有吸收峰; 该蛋白亲水性氨基酸含量较高。     

Phosphatidylserine membrane domain clustering induced by annexin A2/S100A10 heterotetramer

By means of scanning force and fluorescence microscopy of artificial membranes immobilized on mica surfaces, the lateral organization of the annexin A2/S100A10 heterotetramer (annexin A2t) and its influence on the lateral organization of the lipids within the membrane have been elucidated. Planar lipid bilayers composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoserine (POPS) were prepared on atomically flat mica surfaces by the spreading of unilamellar vesicles. Fluorescence images of fluorescently labeled annexin A2t and scanning force microscopy images of nonlabeled protein bound to POPC/POPS bilayers show the formation of micrometer-sized lateral protein domains in the presence of 1 mM CaCl2. By means of scanning force microscopy, not only protein domains became discernible but also small membrane domains, which were attributed to POPS-enriched areas. A depletion of these POPS domains was observed in the vicinity of annexin A2t protein domains. These results indicate that annexin A2t is a peripheral membrane-binding complex capable of inducing lipid segregation.     

Fast scanning calorimetry of lysozyme unfolding at scanning rates from 5 K/min to 500,000 K/min

Background

Protein denaturation is often studied using differential scanning calorimetry (DSC). However, conventional instruments are limited in the temperature scanning rate available. Fast scanning calorimetry (FSC) provides an ability to study processes at much higher rates while using extremely small sample masses [ng]. This makes it a very interesting technique for protein investigation.

Evaluation of a cDNA scanning method concerning the fidelity and efficiency of cDNA selection using the YAC CIC3B1-S region of Arabidopsis thaliana chromosome 5.

We previously reported a cDNA selection method using DNA latex particles to identify expressed genes in specific regions of genomes and named this cDNA scanning method (Hayashida et al., 1995 Gene 155 161). We applied the cDNA scanning method to the YAC CIC3B1-S DNA on Arabidopsis thaliana chromosome 5, and constructed a region-specific sublibrary in which cDNAs for genes on the YAC CIC3B1-S DNA were concentrated. We isolated 545 cDNA clones from the sublibrary, and determined partial sequence of them to produce expressed sequence tags (ESTs) derived from the YAC region. In total, 74 nonredundant groups of cDNAs were obtained from 545 cDNA clones. Forty-seven percent of these EST clones had significant homology to functional proteins such as protein kinases, LON protease, nucleic acid binding protein and chloride channel protein. We compared the cDNA sequences isolated by the cDNA scanning method to the Arabidopsis genomic sequence corresponding to the YAC CIC3B1-S region, and found that 69% of the selected cDNAs are located in the region. We discuss the fidelity and efficiency of the cDNA scanning method for cloning region-specific cDNAs and its useful application in positional cloning.     

Ultraviolet scanning densitometry for detection, quantitation, and preparative elution of protein bands from unstained gels

Ultraviolet scanning of gel rods was used to identify and quantify protein bands in a nondestructive manner with good precision and sensitivity. This same technique, applied on a preparative scale, allowed quantitative protein elution, by reversed electrophoresis, from gel slices completely sealed in a dialysis bag. Protein recovery approached the theoretical yield (93.5 +/- 5%), with practically no interfering substances, and the entire preparative process (first electrophoresis, densitometric scanning, and reversed electrophoresis) could be performed in approximately 6 h. Its application to human growth hormone has shown no alteration in the biological activity of this protein.     

Isolation and Analysis of Protein Bodies from Cotyledons of Lablab purpureus and Phaseolus vulgaris (Leguminoseae)

Protein bodies, isolated by differential and isopycnic centrifugation, have been observed in transmission and scanning electron microscope and biochemically analysed. The powders of the axes and of the cotyledons contain numerous protein bodies, which in the scanning microscope appear to be surrounded by a more or less torn membrane. The proportion of intact, isolated protein bodies is influenced by the grinding methods, but even in the best conditions soaking disaggregates the majority of them. After isopycnic centrifugation, their debris gather in different density zones. Analyses of each zone have revealed that the caseinases are associated with particles of higher density than are peptidases and trypsin inhibitors. A minority population of small-size protein bodies resists the homogenization and fractioning modalities. A double origin of the protein bodies is considered.