Long-range correlations in nucleotide sequences.

DNA sequences have been analysed using models, such as an n-step Markov chain, that incorporate the possibility of short-range nucleotide correlations. We propose here a method for studying the stochastic properties of nucleotide sequences by constructing a 1:1 map of the nucleotide sequence onto a walk, which we term a 'DNA walk'. We then use the mapping to provide a quantitative measure of the correlation between nucleotides over long distances along the DNA chain. Thus we uncover in the nucleotide sequence a remarkably long-range power law correlation that implies a new scale-invariant property of DNA. We find such long-range correlations in intron-containing genes and in nontranscribed regulatory DNA sequences, but not in complementary DNA sequences or intron-less genes.     

Long-range restriction map around the Duchenne muscular dystrophy gene

Duchenne muscular dystrophy is an X-linked recessive disease affecting about 1 in 4,000 newborn boys. As in many other inherited diseases, the biochemical basis of the condition is unknown, and as yet there is no effective treatment. Translocations, deletions and other mutations leading to the DMD phenotype are distributed over a chromosomal area of large, but unknown size. Using pulsed-field gradient gel electrophoresis, we have now determined restriction maps of a major fraction of this area, covering two regions of three million basepairs in total, and used it to determine the position of several probes linked to DMD. The maps establish physical distances between structural changes associated with the DMD phenotype and provide evidence for a CpG-rich island proximal to the area containing translocations and deletions associated with the DMD phenotype.     

Stratified prokaryote network in the oxic-anoxic transition of a deep-sea halocline

The chemical composition of the Bannock basin has been studied in some detail. We recently showed that unusual microbial populations, including a new division of Archaea (MSBL1), inhabit the NaCl-rich hypersaline brine. High salinities tend to reduce biodiversity, but when brines come into contact with fresher water the natural haloclines formed frequently contain gradients of other chemicals, including permutations of electron donors and acceptors, that may enhance microbial diversity, activity and biogeochemical cycling. Here we report a 2.5-m-thick chemocline with a steep NaCl gradient at 3.3 km within the water column betweeen Bannock anoxic hypersaline brine and overlying sea water. The chemocline supports some of the most biomass-rich and active microbial communities in the deep sea, dominated by Bacteria rather than Archaea, and including four major new divisions of Bacteria. Significantly higher metabolic activities were measured in the chemocline than in the overlying sea water and underlying brine; functional analyses indicate that a range of biological processes is likely to occur in the chemocline. Many prokaryotic taxa, including the phylogenetically new groups, were confined to defined salinities, and collectively formed a diverse, sharply stratified, deep-sea ecosystem with sufficient biomass to potentially contribute to organic geological deposits.     

Membrane vesicles traffic signals and facilitate group activities in a prokaryote

Many bacteria use extracellular signals to communicate and coordinate social activities, a process referred to as quorum sensing. Many quorum signals have significant hydrophobic character, and how these signals are trafficked between bacteria within a population is not understood. Here we show that the opportunistic human pathogen Pseudomonas aeruginosa packages the signalling molecule 2-heptyl-3-hydroxy-4-quinolone (pseudomonas quinolone signal; PQS) into membrane vesicles that serve to traffic this molecule within a population. Removal of these vesicles from the bacterial population halts cell-cell communication and inhibits PQS-controlled group behaviour. We also show that PQS actively mediates its own packaging and the packaging of other antimicrobial quinolines produced by P. aeruginosa into vesicles. These findings illustrate that a prokaryote possesses a signal trafficking system with features common to those used by higher organisms and outlines a novel mechanism for delivery of a signal critical for coordinating group behaviour in P. aeruginosa.     

Origin of a gene regulatory mechanism in the evolution of echinoderms

A rich diversity of ancient sea urchin lineages survives to the present. These include several advanced orders as well as the cidaroids, which represent the group ancestral to all other sea urchins. Here we show that all advanced groups of sea urchins examined possess in their eggs a class of maternal messenger RNA (mRNA) encoded by the evolutionarily highly conserved alpha-subtype histone genes. The maternal histone mRNAs are unique in their time of accumulation in oogenesis, their localization in the egg nucleus and their delayed timing of translation after fertilization. Cidaroid sea urchins as well as other echinoderm classes, such as starfish and sea cucumbers, possess the genes but do not have maternal alpha-subtype histone mRNAs in their eggs. Thus, although all the echinoderms examined transcribe alpha-subtype histone genes during embryogenesis, the expression of these genes as maternal mRNAs is confined to advanced sea urchins. The fossil record allows us to pinpoint the evolution of this mode of expression of alpha-histone genes to the time of the splitting of advanced sea urchin lineages from the ancestral cidaroids in a radiation which occurred in a relatively brief interval of time approximately 190-200 Myr ago. The origin of a unique gene regulatory mechanism can thus be correlated with a set of macroevolutionary events.     

Altered nucleotide sequences of a translocated c-myc gene in Burkitt lymphoma

The nucleotide sequence of a translocated c-myc gene in a Burkitt lymphoma reveals multiple base changes in the coding region. Twenty-five base changes, generating 16 codon alterations, were found in the first coding exon; no changes occur in the second coding exon. These changes are probably the result of somatic mutations that occurred during and after translocation, and may contribute to oncogenesis by allowing synthesis of an altered c-myc gene product.     

基因调控网络研究进展

基因调控网络是一种连续而复杂多变的动态网络系统,是细胞内各种信号因子之间相互作用关系的整体表现.近些年来,很多物种全基因组测序的完成、高通量实验技术的发展以及高性能分子生物学工具的应用,使得构建一个复杂和相对完整的基因调控网络成为可能,从而使绘制整个活细胞内各种基因表达的调控网络成为当前研究的热点.作为系统生物学的核心领域,构建和分析基因调控网络将有利于我们更系统地剖析细胞的功能,更深刻地洞见生命的本质.综述关于基因调控网络研究的基本原理和方法,为今后进行更深入的研究和探讨打下良好的基础.     

由基因调控网络数据分析揭示振荡斑图的功能结构

自然和社会系统的许多实际问题都可以用复杂网络动力学来描述,特别是生物网络和社会网络的应用最为广泛.人们已经积累了各种网络行为的大量数据,如何提出合理的物理思想和有效的数学方法来分析这些数据、从中提取有用的信息;从这些信息出发,理解在许多实际过程中由复杂的网络拓扑结构产生的简单动力学关系,并辨识支持各种网络动力学行为的自组织结构,是一个重要的课题.本文综述了其中一种研究方法.以生物学基因调控网络(Gene Regulatory Network,GRN)为研究对象,提出了一种功能权重(Functional Weight,FW)计算方法.通过FW方法定量计算在GRN的振荡动力学中不同调控作用(称为作用边)的重要性.进一步研究发现在各种GRN中这种FW的分布普遍极不均匀,绝大部分作用边具有很小权重(弱作用边),只有少数边具有大的权重(强作用边).而这些强作用边构成的子网络比原网络简单得不可比拟,但它们揭示了网络节点之间的相互作用关系并控制着整个网络的动力学行为.由这些强作用边构成的网络,我们可以辨识GRN的功能骨架和振荡核心子网络.振荡核心起到网络振荡源的作用,而振荡骨架则成为网络中信号传播的主要路径.FW方法可以广泛应用到不同尺寸、不同调控规则(AND,OR等形式)和不同动力学行为(周期振荡、混沌动力学和暂态过程)的GRNs,并且由FW分析出发我们可以对GRN动力学进行有效调控.     

Integration of mitochondrial gene sequences within the nuclear genome during senescence in a fungus

Cellular senescence in the ascomycete fungus Podospora anserina is associated with the appearance of an altered mitochondrial genome. Discrete mitochondrial DNA sequences are excised and amplified and isolated as multimerically arranged, head-to-tail repetitions. We have referred to the most frequently observed excision/amplification product as alpha-event senDNA. It is a 2.6-kilobase pair (kbp) monomeric unit (see refs 1, 3, 7) and is often found in senescent mitochondria in conjunction with other excision products. At the final stage of senescence these plasmids constitute virtually all of the DNA present in senescent mitochondria; they have replicated to high copy number at the expense of the young native genome. Because P. anserina is characterized by race-specific timing of senescence (that is, a programme of senescence), we have begun to contrast rapidly and slowly senescing races in terms of senDNA. Here we present evidence that young mitochondria of the rapidly senescing race, A+, possess an extremely high copy number of alpha-event senDNA plasmid in contrast to the more slowly senescing races s+ or s-. Moreover, we observe that during senescence the alpha-event senDNA and the beta-event senDNA (a 9.8-kbp monomer) are transposed to the nucleus and integrated into nuclear DNA. These plasmids contain the coding information for subunits I and III (respectively) of the mitochondrial cytochrome c oxidase. This constitutes the first clear evidence for the active mobilization of genetic elements from the mitochondrion to the nucleus.     

Muscle-specific gene expression controlled by a regulatory element lacking a MyoD1-binding site

Muscle-specific expression of the gene encoding the delta subunit of the acetylcholine receptor is controlled by a 54-base-pair region that does not contain a binding site for MyoD1, a protein involved in activation of the myogenic program. A MyoD1-binding site is present in the proximal promoter region of the gene encoding the delta-subunit, but is neither sufficient nor necessary for muscle-specific expression in transfected muscle cells.     

Emerging properties of animal gene regulatory networks

Gene regulatory networks (GRNs) provide system level explanations of developmental and physiological functions in the terms of the genomic regulatory code. Depending on their developmental functions, GRNs differ in their degree of hierarchy, and also in the types of modular sub-circuit of which they are composed, although there is a commonly employed sub-circuit repertoire. Mathematical modelling of some types of GRN sub-circuit has deepened biological understanding of the functions they mediate. The structural organization of various kinds of GRN reflects their roles in the life process, and causally illuminates both developmental and evolutionary process.     

Spatial cooperativity in soft glassy flows

Amorphous glassy materials of diverse nature-concentrated emulsions, granular materials, pastes, molecular glasses-display complex flow properties, intermediate between solid and liquid, which are at the root of their use in many applications. A general feature of such systems, well documented yet not really understood, is the strongly nonlinear nature of the flow rule relating stresses and strain rates. Here we use a microfluidic velocimetry technique to characterize the flow of thin layers of concentrated emulsions, confined in gaps of different thicknesses by surfaces of different roughnesses. We find evidence for finite-size effects in the flow behaviour and the absence of an intrinsic local flow rule. In contrast to the classical nonlinearities of the rheological behaviour of amorphous materials, we show that a rather simple non-local flow rule can account for all the velocity profiles. This non-locality of the dynamics is quantified by a length, characteristic of cooperativity within the flow at these scales, that is unobservable in the liquid state (lower emulsion concentrations) and that increases with concentration in the jammed state. Beyond its practical importance for applications involving thin layers (for example, coatings), these non-locality and cooperativity effects have parallels in the behaviour of other glassy, jammed and granular systems, suggesting a possible fundamental universality.     

纤维素降解混合培养物的16S rRNA基因序列分析

以牦牛瘤胃内容物为接种物,以滤纸为唯一碳源富集到一个降解纤维素的混合培养物.构建混合培养物的16S rRNA基因文库,共获得49个序列,分为7个OTU.其中19个序列与已培养细菌的16S rRNA基因相似性97%,占总序列的38.8%;2个古菌的序列与甲烷菌的16S rRNA基因相似性分别为99%和98%,占总序列的4.1%;28个序列属于未培养细菌,占总序列的57.1%.未培养的序列形成4个独立的系统发育分支,其中3个未培养分支与在其他环境中的黏附在纤维素上的瘤胃细菌的16S rRNA基因序列相似性97%,推测这3类微生物可能与纤维素降解相关.