Viral metagenomic analysis of feces of wild small carnivores

Background: Recent studies have clearly demonstrated the enormous virus diversity that exists among wild animals. This exemplifies the required expansion of our knowledge of the virus diversity present in wildlife, as well as the potential transmission of these viruses to domestic animals or humans. Methods: In the present study we evaluated the viral diversity of fecal samples (n = 42) collected from 10 different species of wild small carnivores inhabiting the northern part of Spain using random PCR in combination with next-generation sequencing. Samples were collected from American mink (Neovison vison), European mink (Mustela lutreola), European polecat (Mustela putorius), European pine marten (Martes martes), stone marten (Martes foina), Eurasian otter (Lutra lutra) and Eurasian badger (Meles meles) of the family of Mustelidae; common genet (Genetta genetta) of the family of Viverridae; red fox (Vulpes vulpes) of the family of Canidae and European wild cat (Felis silvestris) of the family of Felidae. Results: A number of sequences of possible novel viruses or virus variants were detected, including a theilovirus, phleboviruses, an amdovirus, a kobuvirus and picobirnaviruses. Conclusions: Using random PCR in combination with next generation sequencing, sequences of various novel viruses or virus variants were detected in fecal samples collected from Spanish carnivores. Detected novel viruses highlight the viral diversity that is present in fecal material of wild carnivores.

离体诱发水稻核质互作雄性不育突变的研究

本研究通过离体培养在正常籼稻品种IR26,IR54中获得雄性不育突变, 并建立了不育系及相应的三系配套, 证实通过离体培养、体细胞无性系变异可以获得核质互作的雄性不育突变。这一研究为解决我国杂交水稻生产中长期存在的不育系之细胞质源单一化的问题提供了新的途径。本研究在Theoratical and Applied Genet及遗传学报等著名学术刊物上发表论文10余篇。

根茎克隆植物羊草分株种群对去叶干扰的生长对策

克隆植物具有多种不同于非克隆植物的生长和繁殖策略。本研究首先综述了这些生长与繁殖策略之中，与我们的实验研究相关的尤其是对于去叶干扰适应策略的四个方面，包括克隆整合、克隆分株大小与密度之权衡( tradeoff)过程、碳水化合物贮备与利用、营养繁殖和芽种群(bud population)调节等。预测克隆植物选择什么样的对策以及某种对策发生作用的条件及程度如何，对克隆植物生态学研究者来说，将是富有挑战意味的课题。 羊草(Leymus chinensis (Trin,) Tzvel.)是禾本科的一种多年生根茎型克隆植物，常常处于由放牧或刈割造成的去叶干扰( defoliation)的胁迫下。在我们的第一个实验（2002年）中，考察了去叶干扰和根茎切割( rhizome severing)是否影响根茎本身和分株地上部分的生长、以及营养繁殖芽的数量特征。同时我们检验如下的假设：直接受到去叶干扰的分株除了会受益于可能的补偿作用之外，还会受益于克隆整合作用，即与之保持根茎联系的未受去叶处理的分株将转移碳水化合物或养分给受去叶干扰的分株，使之得以尽快恢复光合组织。实验结果显示：单次去叶干扰影响根茎生长和芽的产生，而对地上部分的生长影响甚微。只有重度去叶干扰才显著影响营养繁殖芽的产生，而轻度去叶干扰作用不明显。所以，当去叶强度不大时，补偿作用机制将弥补植物由于去叶干扰而受到的损失。我们的实验并未检测到克隆整合的发生，可能的原因是本实验持续的时间不足够长或者是由于根茎中的碳水化合物贮备在去叶干扰发生后发挥了作用，缓解了去叶干扰对羊草分株生长及芽生产的所造成的冲击。 在第二个实验（200 3年）中，为了考查相继数次的去叶干扰是否能够启动羊草分株间的克隆整合，以及启动克隆整合所需达到的去叶干扰的频次，我们将实验样方设计为两部分：核心区( Core section)和外围区(Periphery section)。不同频次的去叶处理（0去叶，作为对照; 1次去叶;3次去叶;5次去叶）仅施加于实验样方的核心区。结果表明，经历3次和5次去叶处理的样方外围区的生物量及水溶性碳水化合物( wsc)含量均明显少于经历1次去叶处理及0去叶处理的样方外围区，这意味着克隆整合在3次去叶和5次去叶两种处理中发生了，而在其它两种处理中没有发生。此外，分株的大小一数目之权衡可能在基株(genet)水平上发生，因此，一个克隆植物基株，当部分分株受到去叶干扰后，将增加其分株数目，但优先增加未受到去叶干扰部分的分株数目。我们将羊草的这种行为视为克隆基株试图逃避干扰的“逃逸行为”( escaping behavior)。 同时在实验中，我们监测了实验样方核心区分株的wsc浓度，目的是查明羊草枝条与根茎中wsc浓度随时间的变化格局及其对去叶干扰的响应，意在发现羊草枝条地上、地下部分和根茎中wsc浓度的时间变化之间的联系。在生长旺季，对照处理（即O去叶处理）的wsc浓度显著降低，这是由于植物在此时期的高生长速率和高呼吸速率所致;相比之下，其它经历去叶干扰的三个处理中羊草wsc浓度降低不如对照处理那么明显和迅速，甚至在高频次去叶处理中还有所上升，其原因大概是由于去叶而使叶面积减小，引起枝条的总呼吸下降所致。羊草枝条中最终的wsc浓度没有受到单次去叶处理的显著影响，却很可观地受到相继数次去叶干扰（3次和5次去叶处理）的影响。去叶干扰可能加速了碳水化合物在气温降低时自地上向地下的转移。枝条的地下部分wsc浓度比地上部分更稳定。在地上部分受到去叶干扰后，根茎中的wsc必然向上输出到地上枝条，而强烈的生长会消耗wsc，但可能的克隆整合（通常在相对频繁的去叶干扰条件下发生）将在一定程度上缓解这种wsc消耗。 在此实验中，我们还监测了羊草平均每分株所拥有的芽的数目，包括每分株分蘖节芽（tiller bud）数目和根茎芽(thizomatous bud)数目。从平均每分株芽数目的时间动态来看，各种去叶处理之间的差异程度不大，这主要是羊草在受到去叶干扰后补偿作用的贡献。与对照处理相比，受不同频次去叶干扰的三个处理的根茎芽具有相对于分蘖节的更强的增长优势。去叶干扰对根茎芽生长的促进作用大于对分蘖节芽的促进作用。我们认为这种反应是羊草克隆基株的一种逃避干扰的适应性努力，可视为一种“逃逸行为”，也可看作克隆植物觅养行为(foraging behavior)的一种特殊形式。芽的增长在中等频度的去叶干扰条件下最强，似乎同样符合中度干扰理论。有趣的是，特定频度的去叶干扰可能会造成芽种群中两大类型芽之间比例（根茎芽／分蘖节芽）的振荡现象（Oscillation）。 最后展望了对于羊草今后应继续开展的工作主要集中在两大方面：一是有性繁殖与无性繁殖之间在不同生境或不同干扰条件下的权衡关系;二是处于不同斑块对比度( patch contrast)的生境中的羊草克隆分株之问的生理整合，及其强度与斑块对比度的定量关系。

The need for winter in the switch to flowering.

Vernalization is the process whereby the floral transition is promoted through exposure of plants to long periods of cold temperature or winter. A requirement for vernalization aligns flowering with the seasons to ensure that their reproductive phase occurs in favorable conditions. The mitotic stability of vernalization, suggestive of an epigenetic mechanism, has intrigued researchers for many years. Genetic analysis of the vernalization requirement in Arabidopsis has identified key floral repressor genes, FRI and FLC. The action of these floral repressors is antagonized by vernalization and the activity of a set of genes grouped into the autonomous floral pathway. Analysis of the vernalization pathway has defined a series of epigenetic regulators crucial for "cellular-memory" of the cold signal, whereas the autonomous pathway appears to function in part through posttranscriptional mechanisms. The mechanism of the vernalization requirement, which is now being explored in a range of plant species, should uncover the evolutionary origins of this key agronomic trait.

Gardening the genome: DNA methylation in Arabidopsis thaliana.

DNA methylation has two essential roles in plants and animals - defending the genome against transposons and regulating gene expression. Recent experiments in Arabidopsis thaliana have begun to address crucial questions about how DNA methylation is established and maintained. One cardinal insight has been the discovery that DNA methylation can be guided by small RNAs produced through RNA-interference pathways. Plants and mammals use a similar suite of DNA methyltransferases to propagate DNA methylation, but plants have also developed a glycosylase-based mechanism for removing DNA methylation, and there are hints that similar processes function in other organisms.

Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning.

Small RNAs have several important biological functions. MicroRNAs (miRNAs) and trans-acting small interfering RNAs (tasiRNAs) regulate mRNA stability and translation, and siRNAs cause post-transcriptional gene silencing of transposons, viruses and transgenes and are important in both the establishment and maintenance of cytosine DNA methylation. Here, we study the role of the four Arabidopsis thaliana DICER-LIKE genes (DCL1-DCL4) in these processes. Sequencing of small RNAs from a dcl2 dcl3 dcl4 triple mutant showed markedly reduced tasiRNA and siRNA production and indicated that DCL1, in addition to its role as the major enzyme for processing miRNAs, has a previously unknown role in the production of small RNAs from endogenous inverted repeats. DCL2, DCL3 and DCL4 showed functional redundancy in siRNA and tasiRNA production and in the establishment and maintenance of DNA methylation. Our studies also suggest that asymmetric DNA methylation can be maintained by pathways that do not require siRNAs.

Dynamic regulation of ARGONAUTE4 within multiple nuclear bodies in Arabidopsis thaliana.

DNA methylation directed by 24-nucleotide small RNAs involves the small RNA-binding protein ARGONAUTE4 (AGO4), and it was previously shown that AGO4 localizes to nucleolus-adjacent Cajal bodies, sites of snRNP complex maturation. Here we demonstrate that AGO4 also localizes to a second class of nuclear bodies, called AB-bodies, which are found immediately adjacent to condensed 45S ribosomal DNA (rDNA) sequences. AB-bodies also contain other proteins involved in RNA-directed DNA methylation including NRPD1b (a subunit of the RNA Polymerase IV complex, RNA PolIV), NRPD2 (a second subunit of this complex), and the DNA methyltransferase DRM2. These two classes of AGO4 bodies are structurally independent--disruption of one class does not affect the other--suggesting a dynamic regulation of AGO4 within two distinct nuclear compartments in Arabidopsis. Abolishing Cajal body formation in a coilin mutant reduced overall AGO4 protein levels, and coilin dicer-like3 double mutants showed a small decrease in DNA methylation beyond that seen in dicer-like3 single mutants, suggesting that Cajal bodies are required for a fully functioning DNA methylation system in Arabidopsis.

Epigenetic remodeling of meiotic crossover frequency in Arabidopsis thaliana DNA methyltransferase mutants.

Meiosis is a specialized eukaryotic cell division that generates haploid gametes required for sexual reproduction. During meiosis, homologous chromosomes pair and undergo reciprocal genetic exchange, termed crossover (CO). Meiotic CO frequency varies along the physical length of chromosomes and is determined by hierarchical mechanisms, including epigenetic organization, for example methylation of the DNA and histones. Here we investigate the role of DNA methylation in determining patterns of CO frequency along Arabidopsis thaliana chromosomes. In A. thaliana the pericentromeric regions are repetitive, densely DNA methylated, and suppressed for both RNA polymerase-II transcription and CO frequency. DNA hypomethylated methyltransferase1 (met1) mutants show transcriptional reactivation of repetitive sequences in the pericentromeres, which we demonstrate is coupled to extensive remodeling of CO frequency. We observe elevated centromere-proximal COs in met1, coincident with pericentromeric decreases and distal increases. Importantly, total numbers of CO events are similar between wild type and met1, suggesting a role for interference and homeostasis in CO remodeling. To understand recombination distributions at a finer scale we generated CO frequency maps close to the telomere of chromosome 3 in wild type and demonstrate an elevated recombination topology in met1. Using a pollen-typing strategy we have identified an intergenic nucleosome-free CO hotspot 3a, and we demonstrate that it undergoes increased recombination activity in met1. We hypothesize that modulation of 3a activity is caused by CO remodeling driven by elevated centromeric COs. These data demonstrate how regional epigenetic organization can pattern recombination frequency along eukaryotic chromosomes.

Effects of melatonin on ovarian follicles

Objective: To evaluate the histomorphometry and expression of Ki-67 and c-kit in ovarian follicles of pinealectomized or melatonin-treated pinealectomized rats.Study design: Forty adult rats were randomly divided into four groups of 10 animals: Group I - control; Group II - sham-pinealectomized; Group III - pinealectomized (Px), and Group IV - Px treated with melatonin (10 mu g/night, per animal). After two months' treatment, on the night of proestrous, the animals were placed in metabolic cages for night urine collection and subsequent measurement of 6-sulfatoxymelatonin (6-SMT). the rats were anesthetized, blood samples were taken for estrogen and progesterone determinations, and they were then euthanized. the ovaries were dissected out for further histological and immunohistochemical analyses. Data were first submitted to analysis of variance (ANOVA) complemented with the Tukey-Kramer test for multiple comparisons (P < 0.05).Results: the urinary levels of 6-SMT and serum progesterone were lower in the Px group (GIII). Exogenous melatonin treatment restored both blood melatonin and 6-SMT urinary levels. the histomorphometric data in Group III revealed a significant increase of degenerating antral and nonantral follicles with regard to the other groups. in addition no corpora lutea were observed in this group. No significant differences were noticed regarding the number of corpora lutea among the other groups (I, II and IV), but the number of cells and the thickness of the theca interna of Px animals (Group III) were higher than in the other groups. Conversely, the density of progesterone receptors (fmol/g) in the ovaries of Group III was significantly lower than in the other groups.Conclusion: Our data indicate that melatonin exerts a role on the maintenance of a proper follicular function, and is thus important for ovulation and progesterone production. (C) 2012 Elsevier Ireland Ltd. All rights reserved.