药用真菌子实体多糖SEC—HPLC图谱的相似度定量评价研究

目的：对灵芝属Ganoderma下4个种共7个菌株及灰树花Grifola ffondosa和云芝Trametes versicolor共9种子实体粗多糖进行了体积排阻HPLC色谱（SEC—HPLC）,并分析了相似度。方法：各样品水提物的HPLC图谱用平方欧氏距离法计算了相似度,用离差平方和法进行聚类分析。结果：灵芝属内各样品聚类距离为8,灰树花与云芝的聚类距离为16,它们与灵芝属的距离为25,说明同一灵芝属内的不同种及同种不同菌株所产生的多糖分子量分布近似度远高于来自树花菌属的灰树花或栓菌属的云芝。结论：此方法可量化描述不同多糖间SEC—HPLC的相似关系,有作为真菌多糖样品质量控制手段的潜在能力。     

Constraints-based genome-scale metabolic simulation for systems metabolic engineering

Random mutagenesis and selection approaches used traditionally for the development of industrial strains have largely been complemented by metabolic engineering, which allows purposeful modification of metabolic and cellular characteristics by using recombinant DNA and other molecular biological techniques. As systems biology advances as a new paradigm of research thanks to the development of genome-scale computational tools and high-throughput experimental technologies including omics, systems metabolic engineering allowing modification of metabolic, regulatory and signaling networks of the cell at the systems-level is becoming possible. In silico genome-scale metabolic model and its simulation play increasingly important role in providing systematic strategies for metabolic engineering. The in silico genome-scale metabolic model is developed using genomic annotation, metabolic reactions, literature information, and experimental data. The advent of in silico genome-scale metabolic model brought about the development of various algorithms to simulate the metabolic status of the cell as a whole. In this paper, we review the algorithms developed for the system-wide simulation and perturbation of cellular metabolism, discuss the characteristics of these algorithms, and suggest future research direction.     

Organization and possible origin of the Bari-1 cluster in the heterochromatic h39 region of Drosophila melanogaster

The molecular organization of the heterochromatic h39 region of the Drosophila melanogaster second chromosome has been investigated by studying two BAC clones identified both by Southern blotting and by FISH experiments as containing tandem arrays of Bari1, a transposable element present only in this region. Such BAC clones appear to contain different portions of the h39 region since they differ in the DNA sequences flanking the Bari1 repeats on both sides. Thus, the 80 Bari1 copies estimated to be present in the h39 region are split into at least two separated subregions. On the basis of the analysis of the flanking sequences a possible mechanism depending on an aberrant activity of the Bari1 transposase is proposed for the genesis of the heterochromatic tandem arrays of the element.     

大穗和中华结缕草的群落特征及种内分异研究

大穗结缕草为盐生植物,主要生长在沿海潮沟两侧的滨海盐土地带上,其区系组成绝大多数种类属于盐生植物,为海滩原生植物群落。中华结缕草为耐盐的优良草坪植物,其野生群落主要分布在沿海2~40m的滨海阶地上。其生态幅较宽,土壤pH在7.2~9.2之间。中华结缕草群落为单优群落,盖度多在60%~90%。中华结缕草种内存在十分丰富的变异,采用模糊聚类的方法将17份草样划分为6类,各类间差异很大。主分量分析表明有性繁殖器官如果穗高度和营养器官特征如叶长和匍匐茎扩展速度是研究中华结缕草种内分异的重要指标。这2种植物可作为沿海城市建植草坪的优良植物。     

14个黄皮品种(系)的RAPD分析

对14个黄皮(Clausena lansium)品种(系)进行RAPD分析,从150个随机引物中筛选出16个能在种质间表现出多态性的引物,共扩增出87条谱带,其中多态性带47条,多态性比例为54.0%。结果表明,除龙川无核黄皮、龙山无核黄皮和冰糖黄皮外,其它11个品种(系)间的遗传距离较近(D≤0.1),说明大多数黄皮品种遗传差异较小,亲缘关系较近。UPGMA聚类分析表明,14个黄皮品种(系)在遗传距离0.15处可划分为3个类群,基本反映了黄皮品种间的遗传多样性。     

基于小波包变换的基因微阵列数据预处理方法

目的:基于阿尔茨海默病微阵列基因表达数据,分析研究微阵列基因表达数据预处理的新的有效方法。方法:首先采用标准差滤波、FSC(特征记分准则)和WPT-SAM(小波包变换-微阵列数据显著性分析)方法对微阵列基因表达数据进行预处理,比较处理后获得的基因数和FDR值;然后采用分类聚类方法对处理后的数据进行分类聚类和分层决策聚类,比较分类聚类结果。结果:标准差滤波和FSC方法获得的初筛基因数据较WPT-SAM方法多,但FDR值也高、后续分类聚类结果较WPT-SAM方法差。结论:WPT-SAM方法在预处理微阵列基因表达数据中,是比较灵活理想的分析方法。     

一种新的EST聚类方法

该研究发展了一种EST（expressed sequence tag）聚类方法（ESTClustering）,用于分析大规模EST测序中所产生的大量数据,以获得高质量,非重复表达序列,该方法在聚类过程中采用MEGABLAST工具对一致序列进行序列同源比较,并用phrap程序对每一EST簇进行拼接检验。这一聚类策略能降低测序错误带来的影响,有效识别基因家族成员,并避免选择性剪接的干扰,与NCB（National Center for Biotechnology Information）的UniGene clustering）方法相比,ESTClustering的聚类结果可以更好地反映表达序列的多样性,用ESTClustering对112256条拟南芥EST聚类测试,产生23581个EST簇,其中13597个EST簇有对应拟南芥基因组编码序列,与该基因组中有EST作为依据的预测基因数目接近。应用该方法对收集的147191条水稻EST序列进行聚类,形成33896个EST簇。     

生物网络研究进展述评

生物网络是一类典型的复杂适应性系统,包含了许多个体的多层次的各种相互作用和关系,在过去的十年里,利用复杂网络理论对生物网络进行研究引起了人们的注意并获得了快速发展.本文首先从从度分布、聚类系数及鲁棒性等角度对现阶段生物网络性质的研究进行了简要介绍,后进一步对生物网络的聚类算法及主要建模理论做出了概括.今后的研究趋势在于如何建立合理的生物网络模型,以深入研究生物网络的各种性质.     

基于遗传算法的谷氨酸发酵动力学参数估计

把遗传算法应用于求解谷氨酸分批发酵动力学模型参数,取交叉概率Pc=0．8、变异概率Pm=0．06、初始种群为20、遗传世代数为200代,能进一步提高谷氨酸分批发酵过程状态变量的计算值与实验值的吻合程度。模拟值与实验值对比显示,该动力学模型能很好地反映谷氨酸分批发酵过程。     

Integrated analysis of multiple data sources reveals modular structure of biological networks

It has been a challenging task to integrate high-throughput data into investigations of the systematic and dynamic organization of biological networks. Here, we presented a simple hierarchical clustering algorithm that goes a long way to achieve this aim. Our method effectively reveals the modular structure of the yeast protein-protein interaction network and distinguishes protein complexes from functional modules by integrating high-throughput protein-protein interaction data with the added subcellular localization and expression profile data. Furthermore, we take advantage of the detected modules to provide a reliably functional context for the uncharacterized components within modules. On the other hand, the integration of various protein-protein association information makes our method robust to false-positives, especially for derived protein complexes. More importantly, this simple method can be extended naturally to other types of data fusion and provides a framework for the study of more comprehensive properties of the biological network and other forms of complex networks.