The diversity of small non-coding RNAs in the diatom Phaeodactylum tricornutum

Background

Marine diatoms constitute a major component of eukaryotic phytoplankton and stand at the crossroads of several evolutionary lineages. These microalgae possess peculiar genomic features and novel combinations of genes acquired from bacterial, animal and plant ancestors. Furthermore, they display both DNA methylation and gene silencing activities. Yet, the biogenesis and regulatory function of small RNAs (sRNAs) remain ill defined in diatoms.

Results

Here we report the first comprehensive characterization of the sRNA landscape and its correlation with genomic and epigenomic information in Phaeodactylum tricornutum. The majority of sRNAs is 25 to 30 nt-long and maps to repetitive and silenced Transposable Elements marked by DNA methylation. A subset of this population also targets DNA methylated protein-coding genes, suggesting that gene body methylation might be sRNA-driven in diatoms. Remarkably, 25-30 nt sRNAs display a well-defined and unprecedented 180 nt-long periodic distribution at several highly methylated regions that awaits characterization. While canonical miRNAs are not detectable, other 21-25 nt sRNAs of unknown origin are highly expressed. Besides, non-coding RNAs with well-described function, namely tRNAs and U2 snRNA, constitute a major source of 21-25 nt sRNAs and likely play important roles under stressful environmental conditions.

Conclusions

P. tricornutum has evolved diversified sRNA pathways, likely implicated in the regulation of largely still uncharacterized genetic and epigenetic processes. These results uncover an unexpected complexity of diatom sRNA population and previously unappreciated features, providing new insights into the diversification of sRNA-based processes in eukaryotes.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-698) contains supplementary material, which is available to authorized users.     

Distribution of Elements in Rat Peripheral Axons and Nerve Cell Bodies Determined by X-Ray Microprobe Analysis

X-ray microprobe analysis was used to determine concentrations (millimoles of element per kilogram dry weight) of Na, P, Cl, K, and Ca in cellular compartments of frozen, unfixed sections of rat sciatic and tibial nerves and dorsal root ganglion (DRG). Five compartments were examined in peripheral nerve (axoplasm, mitochondria, myelin, extraaxonal space, and Schwann cell cytoplasm), and four were analyzed in DRG nerve cell bodies (cytoplasm, mitochondria, nucleus, and nucleolus). Each morphological compartment exhibited characteristic concentrations of elements. The extraaxonal space contained high concentrations of Na, Cl, and Ca, whereas intraaxonal compartments exhibited lower concentrations of these elements but relatively high K contents. Nerve axoplasm and axonal mitochondria had similar elemental profiles, and both compartments displayed proximodistal gradients of decreasing levels of K, Cl, and, to some extent, Na. Myelin had a selectively high P concentration with low levels of other elements. The elemental concentrations of Schwann cell cytoplasm and DRG were similar, but both were different from that of axoplasm, in that K and Cl were markedly lower whereas P was higher. DRG cell nuclei contained substantially higher K levels than cytoplasm. The subcellular distribution of elements was clearly shown by color-coded images generated by computer-directed digital x-ray imaging. The results of this study demonstrate characteristic elemental distributions for each anatomical compartment, which doubtless reflect nerve cell structure and function.     

LTSE—新的大肠菌群快速检测法

本文报道快速简易、结果准确、应用广泛、效益明显,总大肠菌群和粪大肠菌群在15～18小时内同时检出,费用比部颁三步发酵法(GB)节省75～84%的大肠菌群检测新方法。笔者研究出 Lactose-Tryptone-Sodium Dodecyl sulfate-Trace Elements[简称 LTSE]培养基,加上几种鉴定验证试验的 LTSE 法,用来快速检测水质、食品、冷饮、餐具等各类样品703件,结果与国标法(GB)对照总符合率为99.3%;同时与美国《水和废水标准检验法》(16版1985年)新发展的现行标准检测粪大肠菌群的正式 A-1法相比较特异性强,灵敏度高,能提高检出率,并节约经费38.1%.     

On the Use of Infinite Elements for the Determination of Optimal Closure Patterns based on Stress Analysis

Solid infinite elements are used in conjunction with finite elements to compute the stress and displacement distribution resulting from the suturing of wounds of symmetric and nonsymmetric shapes in orthotropic, abdominal human skin. The optimal pattern of suturing of wounds are investigated from a stress perspective. Highly accurate, quantitative and qualitative improvements over the use of finite elements to approximate distant boundaries are obtained. Numerical results quantitatively agree with analytic results computed using complex analysis techniques. The technique used and the results obtained will aid surgeons in closing nonsymmetrical wounds on regions of the body that exhibit orthotropy.     

香紫苏叶片表面微区元素成分分析研究

目的:对药用植物和香料植物香紫苏叶片表面结构进行观察,同时对叶片表面的元素种类和含量进行分析。方法:利用Quanta 200扫描电镜对香紫苏叶片表面进行观察,利用EDAX-9100能谱仪对选定区域进行元素种类和含量的线扫描和面扫描分析。结果:香紫苏叶片表面被覆大量表皮毛,且香紫苏叶片表皮毛中的C、O和K元素含量明显高于其他部位,其他元素分布则比较均匀。结论:电子探针可以快速对叶片表面特定区域以及特殊结构进行元素种类和含量分析。     

Automatic classification within families of transposable elements: Application to the mariner Family

The higher levels of the classification of transposable elements (TEs) from Classes to Superfamilies or Families, is regularly updated, but the lower levels (below the Family) have received little investigation. In particular, this applies to the Families that include a large number of copies. In this article we propose an automatic classification of DNA sequences. This procedure is based on an aggregation process using a pairwise matrix of distances, allowing us to define several groups characterized by a sphere with a central sequence and a radius. This method was tested on the mariner Family, because this is probably one of the most extensively studied Families. Several Subfamilies had already been defined from phylogenetic analyses based on multiple alignments of complete or partial amino-acid sequences of the transposase. The classification obtained here from DNA sequences of 935 items matches the phylogenies of the transposase. The rate of error from a posteriori re-assignment is relatively low.     

环境科学国际合作的理论机制研究

迄今科学界尚无形成系统的国际科学合作理论,也鲜有就环境科学国际合作进行理论研究。首次从全球资源配置的角度来看待环境科学国际合作。通过国际合作,环境科学在内在科学动力和外在社会动力的驱动下,促使全球科学资源和社会资源向有利于环境学科自身发展的方向流动和积聚。其中,配置科学资源遵循"最优要素选择原则",配置社会资源遵循"最小省力原则",两种内在动力和两个调节手段共同构成了环境科学国际合作的理论机制。     

英罗港红树植物群落不同演替阶段植物元素分布及其与土壤肥力的关系

 根据广西英罗港红树植物群落的演替过程, 研究了5个主要演替阶段红树植物群落优势种地上部分的7种元素 （N、P、K、Ca、Mg、Na、Cl）含量、群落元素积累量及其与土壤肥力的关系。结果表明：1）红树植物不同器官元素含量大小为：N、P、K均为花果＞叶＞枝＞皮＞干,Ca为皮＞枝、叶＞花果＞干,Mg为花果＞叶＞皮＞枝＞干, Na、Cl为叶、花果＞皮＞枝＞干;2）同一器官中各元素含量均以Cl、Na最多, 其次是N、Ca、K, 然后是Mg, 最少是P;3）随着进展演替, 红树植物群落优势种的N、P、K含量呈明显减少