基于Diurnal在线软件分析拟南芥生物节律基因对GABA的响应

Diurnal是一个基于网络的在线分析工具,利用该工具可以得到几种模式植物基因组范围内的昼夜和生物钟节律基因表达的变化规律。这一在线分析软件是一个可供搜索的数据库,它提供了几个基于网络的界面友好的数据挖掘工具,其结果以一种易于理解的方式呈现。在该研究中首先介绍了这个在线软件的使用方法,然后分析了几个拟南芥生物钟节律基因和开花基因在长日照条件下的表达模型,这些结果可以以图形和数字的方式下载用于后续的特定研究。结合在线数据,该研究表明,γ-氨基丁酸（GABA在1.0mmol/L）可以改变3个生物钟核心节律基因（TOC1,CCA1和LHY）的表达模式,这种模式的改变主要是增加了这些基因表达的幅度。     

氯虫苯甲酰胺干扰桃小食心虫交配的转录组分析

【目的】探明氯虫苯甲酰胺处理后桃小食心虫(Carposina sasakii)成虫的转录组差异,了解该药剂影响桃小食心虫交配的基因在功能分类和代谢通路等方面的生物学特征,挖掘与交配相关的功能基因。【方法】通过生物学实验观察氯虫苯甲酰胺干扰桃小食心虫成虫交配及繁殖情况。采用Illumina Hi SeqTM2500高通量测序技术对刚羽化的桃小食心虫雌雄成虫、羽化后4—6 h进入交配高峰期的雌雄成虫和经氯虫苯甲酰胺处理4—6 h的雌雄成虫进行转录组测序,利用Trinity软件对所得序列进行de novo组装及评估,之后对获得的有效序列进行功能注释,并利用q RT-PCR技术分析氯虫苯甲酰胺处理后相关基因的时空表达变化。【结果】氯虫苯甲酰胺处理后,桃小食心虫的交配率显著降低,寿命缩短,产卵量减少。通过合并组装桃小食心虫转录组有效序列共获得102 831条unigene,其中34 526个有注释信息。根据筛选标准,氯虫苯甲酰胺处理过程中,雌雄虫中分别有122个和147个基因发生变化,其中相同差异基因31个。对所存在的234个差异基因进行GO功能注释和富集分析结果显示,分子功能过程中的催化活性和结合活性及生物学过程中与代谢过程、单一生物体过程和细胞过程相关的5类基因占主导地位。KEGG分类结果显示,富集到代谢通路的最多,有25个,包括昆虫激素合成、药物代谢等。通过比对分析,鉴定c64662.graph_c0为桃小食心虫鱼尼丁受体基因,其长度为15 637 bp,与已报道Cs Ry R的一致性为99.0%。此外,在234个差异基因中,鉴别羧酸酯酶unigene 3个、细胞色素P450 unigene 4个、肌钙蛋白unigene3个、气味结合蛋白unigene 1个和生物钟unigene 1个。细胞色素P450 c40709.graph_c0参与昆虫激素生物合成。根据转录组中基因表达分析,12个基因在雌雄虫中的表达均出现不同变化趋势。q RT-PCR结果显示,氯虫苯甲酰胺诱导羧酸酯酶c51998.graph_c0基因上调表达;药剂处理后,雌雄虫的c57480.graph_c0和c53794.graph_c0的表达分别呈现显著的上调和下调变化,而c40709.graph_c0基因仅在雄虫中显著下调,处理6 h后c53281.graph_c0只在雌虫中上调表达;氯虫苯甲酰胺处理后3个肌钙蛋白基因在整个试验阶段均表现明显的下调趋势;雄虫中的生物钟unigene c60883.graph_c0和气味结合蛋白unigene c45675.graph_c0的变化趋势较为一致,进入暗期后立即上调,但均受氯虫苯甲酰胺的抑制。雌虫体内Ry R的表达量显著上调,而雄虫初次到达求偶高峰期前Ry R的表达量与对照差异不显著,到第2个求偶高峰期时,Ry R表达显著下调。除细胞色素P450c57480.graph_c0、c40709.graph_c0和c53281.graph_c0外,其余基因在雄虫中的表达均高于雌虫。且触角酯酶基因c54944.graph_c0、生物钟基因c60883.graph_c0和气味结合蛋白基因c45675.graph_c0在黑暗光照交替变化时,表达发生明显地上调或下调。【结论】通过转录组测序发现氯虫苯甲酰胺干扰桃小交配的作用机制是由靶标基因、嗅觉相关基因、代谢基因、生物钟基因等相互作用引起的。     

Nuclear receptor Rev-erbalpha is a critical lithium-sensitive component of the circadian clock

Lithium is commonly used to treat bipolar disorder, which is associated with altered circadian rhythm. Lithium is a potent inhibitor of glycogen synthase kinase 3 (GSK3), which regulates circadian rhythm in several organisms. In experiments with cultured cells, we show here that GSK3beta phosphorylates and stabilizes the orphan nuclear receptor Rev-erbalpha, a negative component of the circadian clock. Lithium treatment of cells leads to rapid proteasomal degradation of Rev-erbalpha and activation of clock gene Bmal1. A form of Rev-erbalpha that is insensitive to lithium interferes with the expression of circadian genes. Control of Rev-erbalpha protein stability is thus a critical component of the peripheral clock and a biological target of lithium therapy.     

Vision and development in Trichoderma atroviride

Phototropism, the induction of carotenogenesis and reproductive structures, and resetting of the circadian rhythm are controlled by blue light. Trichoderma is used as a photomorphogenetic model due to its ability to conidiate upon exposure to light. In total darkness, T. atroviride grows indefinitely as a mycelium provided that nutrients are not limiting. However, nutrient deprivation and light trigger the conidiation process. A pulse of blue light given to a radially growing colony induc…     

Mapping the core of the Arabidopsis circadian clock defines the network structure of the oscillator

In many organisms, the circadian clock is composed of functionally coupled morning and evening oscillators. In Arabidopsis, oscillator coupling relies on a core loop in which the evening oscillator component TIMING OF CAB EXPRESSION 1 (TOC1) was proposed to activate a subset of morning-expressed oscillator genes. Here, we show that TOC1 does not function as an activator but rather as a general repressor of oscillator gene expression. Repression occurs through TOC1 rhythmic association to the promoters of the oscillator genes. Hormone-dependent induction of TOC1 and analysis of RNA interference plants show that TOC1 prevents the activation of morning-expressed genes at night. Our study overturns the prevailing model of the Arabidopsis circadian clock, showing that the morning and evening oscillator loops are connected through the repressing activity of TOC1.     

Control mechanism of the circadian clock for timing of cell division in vivo

Cell division in many mammalian tissues is associated with specific times of day, but just how the circadian clock controls this timing has not been clear. Here, we show in the regenerating liver (of mice) that the circadian clock controls the expression of cell cycle-related genes that in turn modulate the expression of active Cyclin B1-Cdc2 kinase, a key regulator of mitosis. Among these genes, expression of wee1 was directly regulated by the molecular components of the circadian clockwork. In contrast, the circadian clockwork oscillated independently of the cell cycle in single cells. Thus, the intracellular circadian clockwork can control the cell-division cycle directly and unidirectionally in proliferating cells.     

The pseudo-response regulator Ppd-H1 provides adaptation to photoperiod in barley

Plants commonly use photoperiod (day length) to control the timing of flowering during the year, and variation in photoperiod response has been selected in many crops to provide adaptation to different environments and farming practices. Positional cloning identified Ppd-H1, the major determinant of barley photoperiod response, as a pseudo-response regulator, a class of genes involved in circadian clock function. Reduced photoperiod responsiveness of the ppd-H1 mutant, which is highly advantageous in spring-sown varieties, is explained by altered circadian expression of the photoperiod pathway gene CONSTANS and reduced expression of its downstream target, FT, a key regulator of flowering.     

黄曲条跳甲JH诱导蛋白基因的克隆与表达分析

【目的】克隆黄曲条跳甲保幼激素诱导蛋白（Juvenile hormone-inducible protein,Ps-jhip-1）基因,并分析其表达特征。【方法】克隆黄曲条跳甲Ps-jhip-1基因,对其进行系统发育分析,并对其编码蛋白进行生物信息学分析。利用荧光定量PCR方法分析Ps-jhip-1基因在黄曲条跳甲不同组织器官及1个生物钟周期内表达量的变化趋势。【结果】成功克隆了Ps-jhip-1全长cDNA,其长度为1 252 bp,开放阅读框为1 230 bp,编码409个氨基酸。Ps-jhip-1基因编码蛋白具有典型的类蛋白激酶C超家族的蛋白功能域,不具备保幼激素膜受体分子的特征。系统发育分析结果表明,Ps-jhip-1与同为鞘翅目昆虫赤拟谷盗的8种JH诱导蛋白基因聚为一支。荧光定量PCR结果表明,Ps-jhip-1基因mRNA在黄曲条跳甲雌雄成虫的多种组织器官中都有表达,其中在触角和头部的表达量相对较高,而在中足和后足的表达量相对较低,约为触角表达量的6%;Ps-jhip-1基因mRNA表达水平在1个生物钟周期内存在4个下调表达时段,但并未表现出明显的节律性特征。【结论】成功克隆了黄曲条跳甲Ps-jhip-1基因,并分析了其在不同组织及1个生物钟周期内表达量的变化。     

The ecoresponsive genome of Daphnia pulex

We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than a third of Daphnia's genes have no detectable homologs in any other available proteome, and the most amplified gene families are specific to the Daphnia lineage. The coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random, and the analysis of gene expression under different environmental conditions reveals that numerous paralogs acquire divergent expression patterns soon after duplication. Daphnia-specific genes, including many additional loci within sequenced regions that are otherwise devoid of annotations, are the most responsive genes to ecological challenges.     

Searching for genes underlying behavior: lessons from circadian rhythms

The success of forward genetic (from phenotype to gene) approaches to uncover genes that drive the molecular mechanism of circadian clocks and control circadian behavior has been unprecedented. Links among genes, cells, neural circuits, and circadian behavior have been uncovered in the Drosophila and mammalian systems, demonstrating the feasibility of finding single genes that have major effects on behavior. Why was this approach so successful in the elucidation of circadian rhythms? This article explores the answers to this question and describes how the methods used successfully for identifying the molecular basis of circadian rhythms can be applied to other behaviors such as anxiety, addiction, and learning and memory.     

Resetting of circadian time in peripheral tissues by glucocorticoid signaling

In mammals, circadian oscillators reside not only in the suprachiasmatic nucleus of the brain, which harbors the central pacemaker, but also in most peripheral tissues. Here, we show that the glucocorticoid hormone analog dexamethasone induces circadian gene expression in cultured rat-1 fibroblasts and transiently changes the phase of circadian gene expression in liver, kidney, and heart. However, dexamethasone does not affect cyclic gene expression in neurons of the suprachiasmatic nucleus. This enabled us to establish an apparent phase-shift response curve specifically for peripheral clocks in intact animals. In contrast to the central clock, circadian oscillators in peripheral tissues appear to remain responsive to phase resetting throughout the day.     

蝗虫节律基因pdp的克隆和功能分析

[目的]研究不同条件下蝗虫（Locusta migratoria）节律基因pdp（Pyruvate dehydrogenase phosphatase）的mRNA表达水平,进一步揭示蝗虫节律的分子机制。[方法]通过中国科学院动物研究所内的转录组数据库中找出pdp基因的原型来设计引物,以群居型东亚飞蝗的头部的反转录cDNA为模板,克隆出pdp基因的全序列。把一天24小时等分成八个点,进行定时取样,以qRT-PCR技术进行不同时段pdp基因表达量的测定;并在不同处理条件下,测定pdp基因的表达量。[结果]节律基因pdp在蝗虫的不同处理条件下变化不大。[结论]该研究对了解飞蝗节律规律﹑种族特点及有效防虫具有重要的现实意义。     

光照对小鼠下丘脑视上核及乳腺组织钟基因Clock表达的影响

分析光照对泌乳期小鼠下丘脑视上核(SCN)及乳腺组织内生物钟基因Clock表达的影响.采用荧光定量RT-PCR法测定不同光照条件下SCN和乳腺组织中Clock基因的昼夜表达规律.试验发现Clock基因的mRNA不但在SCN,而且在乳腺组织也具有昼夜节律性表达.在光照-黑暗交替光制下,SCN和乳腺组织Clock基因的mRNA表达的峰值相位存在约6 h的相位差;在全黑暗条件下,Clock基因的mRNA表达存在昼夜节律,SCN和乳腺组织Clock基因的mRNA表达的峰值相位基本同步.结果显示,Clock基因的昼夜节律表达具内源性特征;光照影响Clock基因mRNA的表达.     

水稻幼苗响应褐飞虱和稻瘿蚊的转录组分析

【目的】筛选出同时响应褐飞虱和稻瘿蚊取食的基因,揭示水稻幼苗应对2种害虫时基因表达层面的差异,为后续挖掘广谱抗虫基因和解析水稻抗虫机制打下理论基础。【方法】以水稻品种9311为供试植物,分别对15日龄的水稻幼苗进行褐飞虱和稻瘿蚊接虫处理,观测幼苗表型,并通过转录组测序技术分别对褐飞虱接入后24 h和稻瘿蚊接入后7 d的水稻幼苗进行转录组测序。以水稻日本晴基因组作为参考基因组进行对比,利用FPKM法计算基因表达量,设定参数（|log₂ FC|>1且P<0.05）筛选差异表达基因。结合基因差异表达分析和功能富集分析,研究水稻响应2种害虫的机制异同点。【结果】鉴定出响应褐飞虱取食的差异表达基因3963个,响应稻瘿蚊取食的差异表达基因1206个,有251个差异表达基因同时响应2种害虫,其中108个具有相同表达模式,143个具有相反表达模式。GO功能注释分析表明,褐飞虱取食显著影响植物体内细胞壁合成和缺水响应,而稻瘿蚊取食则对植物光合作用的影响更显著,具有相同表达模式的差异表达基因主要富集在光合作用、水杨酸合成、茉莉酸信号转导和伤害响应等生物学功能,而具有相反表达模式的差异表达基因仅富集在乙醛酸循环。KEGG信号通路富集分析表明,褐飞虱和稻瘿蚊取食均显著影响植物体内次生代谢物的合成,相同表达模式的差异表达基因富集到MAPK信号通路、植物激素信号转导通路及光合作用等6个通路,而相反表达模式的差异表达基因没有富集的通路。【结论】水稻应对褐飞虱和稻瘿蚊的基因表达调控存在相同点和不同之处,共响应2种害虫的调控通路可能在水稻抗虫过程中发挥重要作用。     

Regulation of spontaneous intestinal tumorigenesis through the adaptor protein MyD88

Inflammation is increasingly recognized as an important component of tumorigenesis, although the mechanisms and pathways involved are not well understood. Tumor development is regulated by products of several modifier genes, but instructions for their tumor-specific expression are currently unknown. We show that the signaling through the adaptor protein MyD88 has a critical role in spontaneous tumor development in mice with heterozygous mutation in the adenomatous polyposis coli (APC) gene. We found that MyD88-dependent signaling controls the expression of several key modifier genes of intestinal tumorigenesis and has a critical role in both spontaneous and carcinogen-induced tumor development. This study thus reveals the important role of an innate immune signaling pathway in intestinal tumorigenesis.