Evolution of the gene network underlying wing polyphenism in ants

Wing polyphenism in ants evolved once, 125 million years ago, and has been a key to their amazing evolutionary success. We characterized the expression of several genes within the network underlying the wing primordia of reproductive (winged) and sterile (wingless) ant castes. We show that the expression of several genes within the network is conserved in the winged castes of four ant species, whereas points of interruption within the network in the wingless castes are evolutionarily labile. The simultaneous evolutionary lability and conservation of the network underlying wing development in ants may have played an important role in the morphological diversification of this group and may be a general feature of polyphenic development and evolution in plants and animals.     

有翅型与无翅型棉蚜发育及繁殖能力比较研究

在室内采用网罩盆栽苗研究有翅型与无翅型棉蚜若虫及成虫发育历期、繁殖能力、成虫寿命、产仔能力、体重.有翅型与无翅型棉蚜若虫发育历期之间无显著差异.二者成虫寿命、第一次产仔数量、平均每次产仔数差异不显著,而生殖前期、产仔次数、净增殖率与内禀增长率均存在极显著差异(P<0.01).有翅型棉蚜的产仔次数极显著小于无翅型,而有翅型棉蚜生殖前期显著长于无翅型棉蚜.无翅型棉蚜净增殖率显著大于有翅型棉蚜.无翅型棉蚜可能可以将用于翅发育和飞行的能量转而用于繁殖.     

荞麦ARF基因家族的鉴定及生物信息学分析

生长素响应因子(auxin response factor, ARF)基因应答了生长素信号,在植物生长发育中具有重要的调控作用。以荞麦基因组数据库为基础,利用BlastP比对程序共鉴定了21个荞麦ARF基因,并对其基因结构、编码蛋白理化性质、保守结构域、保守基序、亚细胞定位、潜在磷酸化位点及系统进化关系进行了分析。基因结构分析表明,21个荞麦ARF基因均含有内含子,且不同基因间内含子数目存在较大差异。保守结构域分析显示,21个ARF蛋白均含有保守的B3和ARF结构域,部分ARF蛋白还含有Aux/IAA结构域。蛋白保守基序分析表明,21个ARF蛋白共有10个保守基序,基序长度在13~55个氨基酸之间。亚细胞定位分析表明,大多数ARF蛋白定位于细胞核,个别定位于叶绿体。潜在磷酸化位点分析显示,所有ARF蛋白均含有潜在的丝氨酸(Ser)、苏氨酸(Thr)和酪氨酸(Tyr)磷酸化位点,但各蛋白的不同磷酸化位点的数目差异较大。系统进化分析表明,21个ARF基因可以分为Ⅰ、Ⅱ、Ⅲ三个亚家族,其中,Ⅰ亚家族可以进一步分为Ⅰa和Ⅰb两个家族,Ⅱ亚家族可以进一步分为Ⅱa和Ⅱb两个家族。研究结果为进一步克隆荞麦ARF基因及深入研究它们在荞麦中的功能提供了参考。     

Bidirectional transmembrane signaling by cytoplasmic domain separation in integrins

Although critical for development, immunity, wound healing, and metastasis, integrins represent one of the few classes of plasma membrane receptors for which the basic signaling mechanism remains a mystery. We investigated cytoplasmic conformational changes in the integrin LFA-1 (alphaLbeta2) in living cells by measuring fluorescence resonance energy transfer between cyan fluorescent protein-fused and yellow fluorescent protein-fused alphaL and beta2 cytoplasmic domains. In the resting state these domains were close to each other, but underwent significant spatial separation upon either intracellular activation of integrin adhesiveness (inside-out signaling) or ligand binding (outside-in signaling). Thus, bidirectional integrin signaling is accomplished by coupling extracellular conformational changes to an unclasping and separation of the alpha and beta cytoplasmic domains, a distinctive mechanism for transmitting information across the plasma membrane.     

Cabbage aphid: effect of isolation on form and on endocrine activity

Isolated wingless cabbage aphids, Brevicoryne brassicae (L.), produced only wingless young. Aphids isolated from birth all became wingless, whereas over 50 percent of grouped controls developed wings. Isolation caused hyperactivity of the corpus allatum; this hyperactivity may have caused the wingless form.     

Origins of bilateral symmetry: Hox and dpp expression in a sea anemone

Over 99% of modern animals are members of the evolutionary lineage Bilateria. The evolutionary success of Bilateria is credited partly to the origin of bilateral symmetry. Although animals of the phylum Cnidaria are not within the Bilateria, some representatives, such as the sea anemone Nematostella vectensis, exhibit bilateral symmetry. We show that Nematostella uses homologous genes to achieve bilateral symmetry: Multiple Hox genes are expressed in a staggered fashion along its primary body axis, and the transforming growth factor-beta gene decapentaplegic (dpp) is expressed in an asymmetric fashion about its secondary body axis. These data suggest that bilateral symmetry arose before the evolutionary split of Cnidaria and Bilateria.     

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.     

Initiation of proximal-distal patterning in the vertebrate limb by signals and growth

Two broad classes of models have been proposed to explain the patterning of the proximal-distal axis of the vertebrate limb (from the shoulder to the digit tips). Differentiating between them, we demonstrate that early limb mesenchyme in the chick is initially maintained in a state capable of generating all limb segments through exposure to a combination of proximal and distal signals. As the limb bud grows, the proximal limb is established through continued exposure to flank-derived signal(s), whereas the developmental program determining the medial and distal segments is initiated in domains that grow beyond proximal influence. In addition, the system we have developed, combining in vitro and in vivo culture, opens the door to a new level of analysis of patterning mechanisms in the limb.     

Functional genomic analysis of the Wnt-wingless signaling pathway

The Wnt-Wingless (Wg) pathway is one of a core set of evolutionarily conserved signaling pathways that regulates many aspects of metazoan development. Aberrant Wnt signaling has been linked to human disease. In the present study, we used a genomewide RNA interference (RNAi) screen in Drosophila cells to screen for regulators of the Wnt pathway. We identified 238 potential regulators, which include known pathway components, genes with functions not previously linked to this pathway, and genes with no previously assigned functions. Reciprocal-Best-Blast analyses reveal that 50% of the genes identified in the screen have human orthologs, of which approximately 18% are associated with human disease. Functional assays of selected genes from the cell-based screen in Drosophila, mammalian cells, and zebrafish embryos demonstrated that these genes have evolutionarily conserved functions in Wnt signaling. High-throughput RNAi screens in cultured cells, followed by functional analyses in model organisms, prove to be a rapid means of identifying regulators of signaling pathways implicated in development and disease.     

苏博美利奴羊毛囊发育相关lncRNA与mRNA共表达网络的构建

【目的】 随着高通量测序技术的发展和完善,海量的转录组测序数据随之涌现,基因网络的方法也越来越多被用于研究中;细毛羊毛囊发育受多个基因及lncRNA共同调控,单独研究某一分子并不足以发现其调控机制,本研究旨在构建毛囊发育相关lncRNA和mRNA的共表达网络,挖掘细毛羊毛囊发育的潜在候选基因。【方法】 以苏博美利奴羊胎龄65 d（D65）、85 d（D85）、105 d（D105）、135 d（D135）的胎儿以及出生后7 d（A7）、30 d（A30）的羔羊肩胛部皮肤组织,每个时期有3个生物学重复,共18个样本,进行转录组测序以获得6个不同发育时期的lncRNA与mRNA表达谱数据,筛选出相邻时期的差异表达lncRNA与mRNA,运用加权基因共表达网络分析（weighted gene co-expression network analysis,WGCNA）方法构建共表达模块,使用DAVID在线工具进行GO（gene ontology）和 KEGG pathway富集分析以找到与毛囊发育相关的模块,最后从目标模块筛选高连通度的lncRNA与mRNA使用Cytoscape软件进行网络可视化。【结果】 从表达谱数据中筛选得到9 070个差异表达的lncRNA与mRNA,运用WGCNA方法得到11个模块,使用DAVID富集分析发现honeydew1、paleturquoise、skyblue2模块中的基因富集在皮肤发育、毛囊发育、毛囊形态发生、Wnt信号通路负调控、细胞粘附等生物过程,以及Wnt信号通路、TGF-β信号通路、Hedgehog信号通路、紧密连接、MAPK信号通路、ECM-受体相互作用等毛囊发育相关的信号通路,并筛选这3个模块中连通度高的lncRNA和mRNA构建了子网络,得到包括TGFB2、CTSB、SFN、SPINT1、FAM83G、GSDMA、MPZL3、VIM、CRABP1在内的毛囊发育相关基因,预测出ENSOART00000029117、TCONS_00489976、TCONS_00376759等24个lncRNA的可能靶基因。【结论】 首次运用WGCNA方法构建了苏博美利奴羊毛囊发育相关lncRNA与mRNA的共表达网络,鉴别出3个毛囊发育相关的共表达模块,发现多个与毛囊发育相关的潜在候选基因,并预测出24个lncRNA可能的靶基因。     

苏尼特羊不同生长时期肌肉组织lncRNA的差异表达分析

为鉴定和分析苏尼特羊肌肉不同发育时期lncRNA的差异表达,利用RNA-seq技术对120d苏尼特羊胎儿和5月龄羔羊肌肉组织进行了lncRNA比较分析,筛选出差异表达的lncRNA及其靶基因,并对预测的mRNA进行了GO和KEGG分析,同时对随机筛选的差异表达lncRNA进行qRT-PCR验证。结果显示,120d和5月龄羔羊肌肉之间差异表达的lncRNA数共为626个,共靶向1 273个mRNA编码基因。GO和KEGG分析表明,这些差异基因主要涉及代谢过程的调控,生物合成,基因表达,蛋白结合以及mTOR信号通路、FoxO信号通路、胰岛素信号、肌动蛋白细胞骨架的调节、Wnt信号通路和间隙连接等信号通路。qRT-PCR验证证明,随机选取的8个lncRNA在肌肉组织中的表达量与RNA-seq结果一致。综上,本研究利用RNA-Seq技术分析了苏尼特羊120d胎儿和5月龄羔羊的差异表达lncRNA及其靶基因,发现其参与了不同生长时期苏尼特羊的肌肉发育和生长过程,为从lncRNA的角度更好地理解苏尼特羊肌肉生长发育的遗传调控机制提供了理论基础,也为绵羊分子辅助育种提供参考。     

Control of local protein synthesis and initial events in myelination by action potentials

Formation of myelin, the electrical insulation on axons produced by oligodendrocytes, is controlled by complex cell-cell signaling that regulates oligodendrocyte development and myelin formation on appropriate axons. If electrical activity could stimulate myelin induction, then neurodevelopment and the speed of information transmission through circuits could be modified by neural activity. We find that release of glutamate from synaptic vesicles along axons of mouse dorsal root ganglion neurons in culture promotes myelin induction by stimulating formation of cholesterol-rich signaling domains between oligodendrocytes and axons, and increasing local synthesis of the major protein in the myelin sheath, myelin basic protein, through Fyn kinase-dependent signaling. This axon-oligodendrocyte signaling would promote myelination of electrically active axons to regulate neural development and function according to environmental experience.     

针叶树G ID1同源基因分离鉴定与功能预测

GID1作为赤霉素(GA)受体蛋白,是GA信号通路的重要组成部分,其编码基因GID1在被子植物中已经被广泛克隆,但在针叶树种中的研究十分滞后。为了分离针叶树GA受体GID1基因并推测其功能,本研究以拟南芥GID1s序列为探针,在油松高质量参考转录组内筛选并鉴别出了油松GID1直系同源基因;基于该基因序列同源克隆了樟子松、白皮松、赤松GID1基因,通过BLAST获得了日本落叶松、火炬松、白云杉与挪威云杉的GID1-like基因;对针叶树GID1基因进行序列保守性、蛋白结构和组织表达活性分析。结果表明:针叶树种很可能只含有一个GID1基因,该基因在针叶树中具有很高的保守性;虽然与被子植物GID1之间的序列一致性较低,但其保持GA亲和活性所必需的氨基酸残基十分保守,与其下游DELLA蛋白相互作用的功能域与结构同样十分保守,推测其在针叶树GA信号转导中具有受体功能;表达分析显示GID1在挪威云杉不同组织和油松雌雄球花不同发育阶段间表达较为稳定,表明GID1可能广泛参与这些组织的发育过程,针叶树GA信号调控通路中GA受体的转录调控可能并不是核心调控机制。研究结果为GID1基因在针叶树生长发育过程中的分子调控机制研究奠定了基础。      

拟南芥和大白菜YABBY蛋白家族的生物信息学分析

YABBY基因家族是一类含有C2C2锌指结构域和YABBY结构域的转录因子,在植物叶器官发育过程中起到重要的调控作用。本研究利用生物信息学的方法对拟南芥和大白菜YABBY基因家族的结构、系统进化、序列保守性以及顺式反应元件进行了分析。主要结果如下:YABBY基因在拟南芥和大白菜染色体上呈不均匀分布;基因的结构以含有6个内含子为主要形式;所有拟南芥和大白菜YABBY基因都具有保守的C2C2锌指结构域和YABBY结构域;YABBY蛋白家族在进化上可分为4个不同的亚组;YABBY基因的启动子序列中存在多个能够响应不同激素和逆境信号的顺式反应元件。本文为进一步研究YABBY基因在大白菜叶球发育中的调控作用和逆境响应中的功能奠定了基础。     

杨树磷酸肌醇特异性磷脂酶C基因家族鉴定与分析

为了对已测序杨树Populus trichocarpa Torr.Gray中磷酸肌醇特异性磷脂酶C(phosphoinositidespecific phospholipase C,PI-PLC)家族基因进行系统分析,利用杨树基因组数据库,通过生物信息学手段,鉴定杨树PI-PLC家族基因的基因结构、染色体定位和编码蛋白,通过蛋白序列比对进行进化和分类分析。结果表明,杨树中含有7个PI-PLC家族基因,含有8~10个外显子,分布于杨树的4条染色体上。MEME和Pfam保守结构域分析显示,杨树PI-PLC蛋白均含有4个保守的EF、X、Y和C2结构域。蛋白质进化树分析结果表明PI-PLC可分为2个亚家族。     

Progression of vertebrate limb development through SHH-mediated counteraction of GLI3

Distal limb development and specification of digit identities in tetrapods are under the control of a mesenchymal organizer called the polarizing region. Sonic Hedgehog (SHH) is the morphogenetic signal produced by the polarizing region in the posterior limb bud. Ectopic anterior SHH signaling induces digit duplications and has been suspected as a major cause underlying congenital malformations that result in digit polydactyly. Here, we report that the polydactyly of Gli3-deficient mice arises independently of SHH signaling. Disruption of one or both Gli3 alleles in mouse embryos lacking Shh progressively restores limb distal development and digit formation. Our genetic analysis indicates that SHH signaling counteracts GLI3-mediated repression of key regulator genes, cell survival, and distal progression of limb bud development.