金针菇菌柄发育的转录组与蛋白组分析

菌柄是金针菇等食用菌的主要商品部位,但其生长机制仍不明确。本研究对金针菇伸长期和成熟期菌柄进行了转录组联合蛋白组分析,结果显示,两样本显著性差异表达基因和蛋白分别为721个和61个,均以上调表达为主。GO（gene ontology）功能聚类分析表明：有72.41%的差异表达基因富集在催化活性（catalytic activity）条目下。细胞组分（cell part）和绑定结合（binding）条目同时富集了较多的差异表达基因和蛋白。KEGG通路富集分析显示：碳水化合物代谢通路（carbohydrate metabolism）和氨基酸代谢通路（amino acid metabolism）富集的差异表达基因较多。差异表达蛋白富集较多的通路是单环菌素生物合成（monobactam biosynthesis,ko00261）、链霉素生物合成（streptomycin biosynthesis,ko00521）和有机含硒化合物代谢（selenocompound metabolism,ko00450）等。内质网蛋白质加工（protein processing in endoplasmic reticulum,ko04141）和MAPK信号通路（MAPK signaling pathway-yeast,ko04011）在转录组和蛋白组的KEGG富集分析中均为差异通路。本研究联合转录组和蛋白组数据筛选了40个金针菇菌柄发育中差异表达基因,为深入研究揭示食用菌菌柄发育过程提供候选基因。     

DHR3 is required for the prepupal-pupal transition and differentiation of adult structures during Drosophila metamorphosis.

Pulses of the steroid hormone ecdysone activate genetic regulatory hierarchies that coordinate the developmental changes associated with Drosophila metamorphosis. A high-titer ecdysone pulse at the end of larval development triggers puparium formation and induces expression of the DHR3 orphan nuclear receptor. Here we use both a heat-inducible DHR3 rescue construct and clonal analysis to define DHR3 functions during metamorphosis. Clonal analysis reveals requirements for DHR3 in the development of adult bristles, wings, and cuticle, and no apparent function in eye or leg development. DHR3 mutants rescued to the third larval instar also reveal essential functions during the onset of metamorphosis, leading to lethality during prepupal and early pupal stages. The phenotypes associated with these lethal phases are consistent with the effects of DHR3 mutations on ecdysone-regulated gene expression. Although DHR3 has been shown to be sufficient for early gene repression at puparium formation, it is not necessary for this response, indicating that other negative regulators may contribute to this pathway. In contrast, DHR3 is required for maximal expression of the midprepupal regulatory genes, EcR, E74B, and betaFTZ-1. Reductions in EcR and betaFTZ-F1 expression, in turn, lead to submaximal early gene induction in response to the prepupal ecdysone pulse and corresponding defects in adult head eversion and salivary gland cell death. These studies demonstrate that DHR3 is an essential regulator of the betaFTZ-F1 midprepupal competence factor, providing a functional link between the late larval and prepupal responses to ecdysone. Induction of DHR3 in early prepupae ensures that responses to the prepupal ecdysone pulse will be distinct from responses to the late larval pulse and thus that the animal progresses in an appropriate manner through the early stages of metamorphosis.     

固始鸡1日龄和36周龄下丘脑高丰度差异性MiRNA的鉴定及功能预测分析

为鉴定鸡下丘脑发育相关特异性表达miRNA,基于固始鸡1日龄和36周龄下丘脑小RNA的Solexa测序数据,共鉴定到266种2个发育阶段共表达的miRNA,其中157种miRNA的表达水平被显著下调,22种被显著上调.聚类分析显示,鸡下丘脑高丰度差异性miRNA主要集中于let-7、mir-181、mir-30、mir-99、mir-1和mir-17等基因家族.另外,预测了10种高丰度差异性miRNA的靶基因,并进行了相应的GO分析和KEGG通路分析.结果显示,预测靶基因在发育过程、代谢过程、细胞过程和生物学过程调节等4个生物学过程以及细胞周期、粘着斑、TGF-beta信号通路和MAPK信号通路等通路中显著富集.研究结果为进一步揭示miRNA调控鸡下丘脑发育的分子机制提供了有益线索.     

Differences in heat shock protein 70 expression during larval and early spat development in the Eastern oyster, Crassostrea virginica (Gmelin, 1791)

For a variety of species, changes in the expression of heat shock proteins (HSP) have been linked to key developmental changes, i.e., gametogenesis, embryogenesis, and metamorphosis. Many marine invertebrates are known to have a biphasic life cycle where pelagic larvae go through settlement and metamorphosis as they transition to the benthic life stage. A series of experiments were run to examine the expression of heat shock protein 70 (HSP 70) during larval and early spat (initial benthic phase) development in the Eastern oyster, Crassostrea virginica. In addition, the impact of thermal stress on HSP 70 expression during these early stages was studied. C. virginica larvae and spat expressed three HSP 70 isoforms, two constitutive, HSC 77 and HSC 72, and one inducible, HSP 69. We found differences in the expression of both the constitutive and inducible forms of HSP 70 among larval and early juvenile stages and in response to thermal stress. Low expression of HSP 69 during early larval and spat development may be associated with the susceptibility of these stages to environmental stress. Although developmental regulation of HSP 70 expression has been widely recognized, changes in its expression during settlement and metamorphosis of marine invertebrates are still unknown. The results of the current study demonstrated a reduction of HSP 70 expression during settlement and metamorphosis in the Eastern oyster, C. virginica.     

Transcriptome analysis of differentially expressed genes in rabbits’ ovaries by digital gene-expression profiling

Reproduction is a complex physiological process that is regulated by multiple genes and pathways. Compared with studies of common livestock, fewer studies of genes related to the fertility of rabbits (Oryctolagus cuniculus) have been reported, and the molecular mechanism of their high productivity is still poorly understood. To identify candidate genes associated with development and prolificacy in rabbits, we analyzed gene expression differences among the ovaries of mature Californian rabbit (LC), and mature (HH) and immature Harbin white rabbit (IH) using digital gene expression technology. We detected 885 and 321 genes that were significantly differentially expressed in comparisons between HH/IH and HH/LC, respectively. The functions of the differentially expressed genes (DEGs) were determined by GO classification and KEGG pathway analysis. The results suggest that most of the DEGs between the mature and immature developmental stages were predominantly associated with DNA replication, cell cycle, and progesterone-mediated oocyte maturation, and most were up-regulated in the IH group compared with the HH group. The DEGs involved in disparate fecundities between HH and LC were associated with reproduction, fructose and mannose metabolism, steroid hormone biosynthesis, and pyruvate metabolism. Our results will contribute to a better understanding of changes in the regulatory network in ovary at different developmental stages and in different fertility of rabbit.     

Entrainment of eclosion and preliminary ontogeny of circadian clock gene expression in the flesh fly,Sarcophaga crassipalpis

Timing of circadian activities is controlled by rhythmic expression of clock genes in pacemaker neurons in the insect brain. Circadian behavior and clock gene expression can entrain to both thermoperiod and photoperiod but the availability of such cues, the organization of the brain, and the need for circadian behavior change dramatically during the course of insect metamorphosis. We asked whether photoperiod or thermoperiod entrains the clock during pupal and pharate adult stages by exposing flies to different combinations of thermoperiod and photoperiod and observing the effect on the timing of adult eclosion. This study used qRT-PCR to examine how entrainment and expression of circadian clock genes change during the course of development in the flesh fly, Sarcophaga crassipalpis. Thermoperiod entrains expression of period and controls the timing of adult eclosion, suggesting that the clock gene period may be upstream of the eclosion pathway. Rhythmic clock gene expression is evident in larvae, appears to cease during the early pharate adult stage, and resumes again by the time of adult eclosion. Our results indicate that both patterns of clock gene expression and the cues to which the clock entrains are dynamic and respond to different environmental signals at different developmental stages in S. crassipalpis.     

金针菇成熟期和伸长期菌盖的转录组与蛋白组比较分析

菌盖是大型真菌的重要组成部分,也是其产生有性孢子的部位,但是其发育机制仍不明确。本研究以金针菇Flammulina filiformis为材料,采用转录组和蛋白组联合分析的方法,比较分析了金针菇成熟期和伸长期菌盖的差异基因与蛋白,并对其进行GO (gene ontology)功能聚类分析、KEGG (Kyoto encyclopedia of genes and genomes)富集分析和蛋白互作网络分析。本研究筛选到差异表达基因有1 391个,差异表达蛋白147个,均以上调表达为主。GO功能聚类分析结果表明,催化活性(catalytic activity)条目富集基因最多,其次是细胞组分(cell part)、细胞过程(cellular process)和细胞器(organelle)。KEGG富集分析结果表明,差异表达基因和蛋白主要富集在碳水化合物代谢通路(carbohydrate metabolism)和氨基酸代谢通路(amino acid metabolism)等。本研究选取了9个关键的差异表达基因,使用实时荧光定量PCR (real-time quantitative PCR,RT-qPCR)对其表达量进行了验证。RT-qPCR验证结果与转录组测序结果相一致。蛋白互作网络分析表明,水解酶类、结构域类和转录调节类蛋白为互作网络的主要结点。本研究联合转录组、蛋白组测序数据,通过分析差异基因与蛋白,为深入了解金针菇菌盖发育机制提供数据参考。     

西方蜜蜂工蜂蛹响应低温胁迫的差异表达基因分析

【目的】本研究旨在从转录组水平筛选和分析西方蜜蜂Apis mellifera工蜂不同时期蛹对低温胁迫反应的差异表达基因(DEGs)。【方法】将西方蜜蜂工蜂封盖后3 d预蛹以及封盖后6和9 d蛹分别置于低温环境(20℃)和最适发育温度(35℃)中4 h,分别作为处理组和对照组,通过转录组学技术筛选低温处理组与对应的对照组之间的DEGs,并进行GO功能分类和KEGG通路分析。利用RT qPCR分别对封盖后3 d预蛹以及封盖后6和9 d蛹的8, 6和5个DEGs的表达谱进行验证。【结果】与对照组相比,封盖后3 d预蛹以及封盖后6和9 d蛹受低温胁迫后的DEGs分别有220, 50和26个;GO功能分类发现,DEGs富集数最多的条目为代谢进程、细胞进程、催化活性和结合,封盖后3 d预蛹的DEGs在生物学进程调控、细胞部分和细胞器等有较多富集。KEGG通路分析显示,处理组和对照组间西方蜜蜂各日龄DEGs在整体概述图、氨基酸代谢、信号转导、运输和分解代谢有富集。封盖后3 d预蛹以及封盖后6和9 d蛹受低温胁迫后共有的DEG 3-磷酸肌醇依赖性蛋白激酶1基因PDK1上调表达,同时富集在自噬-动物、mTOR和FoxO信号通路。低温胁迫后,封盖后3 d预蛹的胰岛素受体底物1-B基因IRS1-B和Kruppel同源物1基因Kr-h1上调表达,而核激素受体FTZ-F1基因Ftz-F1与蜕皮启动激素基因Eth显著下调表达,说明封盖后3 d预蛹响应低温细胞自噬和蜕皮受到抑制程度更大。在低温胁迫后封盖后6 d蛹中与昆虫角质层着色与免疫相关的酪氨酸羟化酶基因TyHyd下调表达;与对照组相比,在低温胁迫后封盖后9 d蛹中DEGs最少,说明在3个蛹期中,其受低温的影响较小。【结论】本研究测定了西方蜜蜂3个不同发育阶段蛹响应低温的DEGs,结果显示大部分DEGs为阶段特有,说明西方蜜蜂不同发育阶段响应低温的机制不同。一些共有DEGs以及阶段特有DEGs的功能研究和其作用机制是进一步研究蜜蜂对低温响应机制的重点内容,为探究蜜蜂蛹期响应低温胁迫的分子机制提供了基础数据。     

Tissue Damage Disrupts Developmental Progression and Ecdysteroid Biosynthesis in Drosophila

In humans, chronic inflammation, severe injury, infection and disease can result in changes in steroid hormone titers and delayed onset of puberty; however the pathway by which this occurs remains largely unknown. Similarly, in insects injury to specific tissues can result in a global developmental delay (e.g. prolonged larval/pupal stages) often associated with decreased levels of ecdysone – a steroid hormone that regulates developmental transitions in insects. We use Drosophila melanogaster as a model to examine the pathway by which tissue injury disrupts developmental progression. Imaginal disc damage inflicted early in larval development triggers developmental delays while the effects are minimized in older larvae. We find that the switch in injury response (e.g. delay/no delay) is coincident with the mid-3rd instar transition – a developmental time-point that is characterized by widespread changes in gene expression and marks the initial steps of metamorphosis. Finally, we show that developmental delays induced by tissue damage are associated with decreased expression of genes involved in ecdysteroid synthesis and signaling.