Discovering common combinatorial histone modification patterns in the human genome

Histone modifications play a crucial role in regulating gene expression and cell lineage determination and maintenance at the epigenetic level. To systematically investigate this phenomenon, this paper presented a statistical hybrid clustering algorithm to identify common combinatorial histone modification patterns. We applied the algorithm to 39 histone modification marks in human CD4 + T cells and detected 854 common combinatorial histone modification patterns. Our results could cover 211 (76.17%) patterns among 277 patterns identified by the tandem mass spectrometry experiments. Based on the frequency statistical analysis, it was found that the co-occurrence frequencies of 20 backbone modifications are greater than or close to 0.2 in the 854 patterns. we also found that 15 modifications (H2BK120ac, H4K91ac, H2BK20ac, etc.), three histone acetylations (H2AK9ac, H4K16ac, and H4K12ac) and five histone methylations (H3K79me1, H3K79me2, 3K79me3, H4K20me1, and H2BK5me1) were most likely prone to coexist respectively in these patterns. In addition, we found that DNA methylation tends to combine with histone acetylation rather than histone methylation.     

糙皮侧耳(Pleurotus ostreatus)的AFLP指纹图谱分析

在对糙皮侧耳(Pleurotus ostreatus)的AFLP分析条件进行优化的基础上,利用该技术建立了14株产自不同地区的糙皮侧耳：DNA指纹图谱,并进行了数据分析。结果表明,在合成的14条引物的不同组合中,引物对E-3／M-3可以产生较多的DNA多态片段,E-AGC／M-CAT引物对的扩增效果最好,共获得184条DNA扩增带,其中多态性条带i101条,占54．89％。利用UPGMA法对所获数据进行聚类分析,计算得到糙皮侧耳菌株之间的遗传距离,发现不同品种间遗传距离差异较大,从0．192到0．754,说明糙皮侧耳的遗传多样性比较丰富。绘制的指纹分析树状图表明,14个糙皮侧耳菌株被分为6个组群,其中P17和杂3的相似性系数最高,达到了81．2％,而侧5与其他菌株的亲缘关系相对最远。     

光合作用氧释放机理研究进展

植物在光合作用过程中不仅为同化CO2提供能量和还原力,同时裂解水放出氧气。放氧反应主要由光系统Ⅱ(PSⅡ)氧化侧的4个锰原子组成的锰簇催化完成的。因此,锰簇在光合放氧过程中起看至关重要的作用。文章概述了对锰簇及其微环境的结构和功能的研究进展。     

BIOACOUSTIC PUBLICATIONS, 1986

ABSTRACT

A common task for researchers of animal vocalisations is statistically comparing repertoires, or sets of vocalisations. We evaluated five methods of comparing repertoires of ‘codas’, short repeated patterns of clicks, recorded from sperm whale (Physeter macrocephalus) groups. Three of the methods involved classification of codas—human observer classification, k-means cluster analysis using Calinski and Harabasz's (1974) criterion to determine k, and a divisive k-means clustering procedure using Duda and Hart's (1973) criterion to determine k. Two other methods used multivariate distances to calculate similarity measures between coda repertoires. When used on a sample coda dataset, observer classification failed to produce consistent results. Calinski and Harabasz's criterion did not provide a clear signal for determining the number of coda classes (k). Divisive clustering using Duda and Hart's criterion performed satisfactorily and, encouragingly, gave similar results to the multivariate similarity measures when used on our data. However, the relative performance of the k-means techniques is likely data dependent, so one method is not likely to perform best in all circumstances. Thus results should be checked to ensure they extract logical clusters. Using these techniques concurrently with multivariate measures allows the drawing of relatively robust conclusions about repertoire similarity while minimising uncertainties due to questionable validity of classifications.     

沙芥属植物染色体数及核型分析

以沙芥属植物根尖为材料,采用常规压片法,对其染色体数及其核型进行分析,结果表明:本属植物间期核特征为前染色体核型;染色体均为二倍体,沙芥染色体数为2n=2x=22,基数为x=11,宽翅沙芥、斧形沙芥、距果沙芥和齿冠沙芥染色体数为2n=2x=20,基数为x=10;染色体有亚中部着丝点染色体(sm)和中部着丝点染色体(m)2种;沙芥、距果沙芥属于2A型,宽翅沙芥、斧形沙芥、齿冠沙芥属于1A型,本属植物的核型均为首次报道。根据核型特征进行聚类分析,将染色体数为2n=2x=20的沙芥属4种植物分为两类:第一类距果沙芥;第二类包括宽翅沙芥、斧形沙芥、齿冠沙芥。     

Multivariate morphometric study of theCardamine pratensis group (Cruciferae) in the Carpathian and Pannonian area

A multivariate morphometric study of theCardamine pratensis group is presented, based on 84 population samples collected from the Carpathian and Pannonian area in the Czech Republic, Slovakia, Poland, Ukraine, Hungary, and Romania. Among the multivariate methods, principal component analysis, cluster analysis, and classificatory and canonical discriminant analysis were used. The analysis of chromosome numbers from all populations studied showed wide variation. The morphometric study showed that not all groups of populations characterised by their chromosome numbers and geographical criteria are morphologically, and thus taxonomically, distinguishable. Besides the morphologically well characterised speciesCardamine dentata andC. rivularis, the following species were recognised in the area studied:C. matthioli, C. majovskii andC. pratensis. Within the last species, besides the typical populations, two diploid types are provisionally recognised: type ucranica and type rivularis auct..     

单端孢霉烯族毒素的产生及分子调控机制

禾谷镰刀菌复合种(Fusarium graminearum species complex,FGSC)引起的赤霉病是小麦生产上危害最为严重的病害之一。赤霉病除了造成减产外,感病籽粒中含有多种镰刀菌毒素,如单端孢霉烯族的呕吐毒素,可引起人畜中毒和重大疾病,给食品安全构成严重威胁。过去20年,随着禾谷镰刀菌全基因组序列的公布和遗传转化体系的成熟,禾谷镰刀菌Fusarium graminearum的功能基因组学的研究取得了较大进展,单端孢霉烯族毒素的产生、调控机制及网络研究成为热点。本文综述国内外单端孢霉烯族毒素的生物合成和分子调控机制,包括合成基因簇及决定不同产毒化学型的基因、产毒调控元件、环境因子调控产毒的分子机制,可为小麦抗赤霉病的育种提供新思路,为新型药剂的研发提供分子靶标,为赤霉病的持续防控和毒素污染的有效治理提供理论依据。     

基于文献计量的凋落物研究现状及热点分析

在生态学中,凋落物作为过渡层的研究价值日趋重要。为进一步探究凋落物的现存特征以及热点问题,基于文献计量学的相关方法分析,分别以中国知网数据库(CNKI)和Web of Science核心数据库集合中的文献作为基础数据源。运用Bibexcel、Ucinet、和Netdraw等软件得出研究文献中的高频词共词矩阵和关键词网络化图谱。再利用SPSS进行聚类分析,将研究内容分为五大群集,据此分析枯落物的特性及未来研究方向。研究结果表明:①就文献发文量来看国内外对凋落物的研究,国际上开始的时间较早,国内的研究比国际滞后10年左右,但国内的发文量和增长速度要明显高于国际上;两者都在21世纪开始趋于成熟稳定发展。②国内的凋落物研究以森林生态系统内部的各因子之间的联系为主;国外更偏向于把研究凋落物的分解、土壤营养元素归还以及化学元素转变所带来的气候改变和对环境的污染程度作为该领域研究热点。③经过共现网络化可视分析得出,国内凋落物研究中一定程度上可将凋落物、凋落物分解、生物量、人工林、土壤养分、氮沉降等词作为该领域研究热点和未来延伸发展方向。④通过聚类分析,国内外的研究有相近的部分,都涉及到凋落物的分解方...     

Application of Multivariate Analysis for the Selection of Candidates for Biological Control Agents

A survey of natural enemies ofSenna obtusifolia(Leguminosae: Cesalpinaceae) was made in 46 localities in Brazil. Twenty-one preselected insect species were used in a multivariate analysis in a search for potential biocontrol agents, based on frequency of occurrence of each species, degree of insect/host association, and damage level. Insect communities were organized in a binary matrix (presence/absence of the species); measures of distance and similarities were based on the Jaccard coefficient, and cluster analysis was then conducted. Construction of a dendogram showed similarities among geographically close localities where phenological stages of sicklepod plants were similar. Analysis of correspondence based on the correlation matrix showed that Eigen values of the three first axes explain only 40.1% of the observed variation. Correlation among the scores produced by species Eigenvectors in each locality on axis 1 and the latitude, altitude, and phenological stage showed that only phenological stage was correlated (r = 0.45,P = 0.02). The results indicate that weather will not be a limiting factor for the establishment of these insect species in an environmental gradient similar to that of the surveyed area (12 to 22° latitude and 6 to 1200 m altitude). Distribution in the ordinal space of axes 1 and 2 showed thatAgrilus oceanicum(Buprestidae),Fundella argentina(Pyralidae),Thyphedanus undulatus(Hesperidae), andPhoebis sennae(Pieridae) are grouped and separated from the others in axis 2, suggesting that these species co-occur with each other. Based on their feeding guilds, multiple introduction of these species can be considered. Multivariate analysis showed potential to be used as an additional tool to help in the selection of candidates for biocontrol agents.