高粱GRF基因家族鉴定及在非生物胁迫下的表达分析

生长调控因子（growth regulation factor,GRF）是植物中特有的一类转录因子,在植物激素调控、生长发育以及胁迫应答等多个领域扮演重要角色。对高粱GRF基因家族成员进行筛选鉴定,得到8个家族基因,分析了这些基因的理化性质、保守蛋白序列、基因功能及其共线性,分析了这些基因在非生物胁迫下转录组表达差异。结果表明,GRF基因家族结构较为保守,启动子元件含有干旱、低温、茉莉酸等响应元件,推测该家族基因参与生物及非生物胁迫应答响应。通过盐胁迫和烯效唑处理下的转录组数据分析,得到一个与耐盐相关的基因（SORBI_3002G297800）和一个与激素相关的基因（SORBI_3006G203400）,为进一步探究这些基因在高粱应对非生物胁迫中的作用提供了重要参考。     

潘那利番茄GRF基因家族全基因组鉴定分析

【目的】分析研究潘那利番茄GRF基因家族全基因组鉴定分析。【方法】研究基于生物信息学方法对潘那利GRF基因家族成员进行全基因组鉴定和分析,并对其起源及进化进行了追溯。【结果】潘那利番茄中共鉴定了10个SpGRF成员,不均匀分布在7条染色体上,预测了SpGRFs蛋白的分子量、等电点、亲水性总均值等理化性质。SpGRFs基因可分为6个亚家族。所有SpGRF基因N端都含有1个QLQ和1个WRC结构域,C端则为多种保守基序。共线性结果显示基因组内有3对6个旁系同源基因,全部为片段复制,SpGRFs受自然选择压力下,有共同起源祖先,与拟南芥亲缘关系更近。【结论】鉴定了潘那利番茄中GRF基因家族的基本信息。     

Noise propagation in gene networks

Accurately predicting noise propagation in gene networks is crucial for understanding signal fidelity in natural networks and designing noise-tolerant gene circuits. To quantify how noise propagates through gene networks, we measured expression correlations between genes in single cells. We found that noise in a gene was determined by its intrinsic fluctuations, transmitted noise from upstream genes, and global noise affecting all genes. A model was developed that explains the complex behavior exhibited by the correlations and reveals the dominant noise sources. The model successfully predicts the correlations as the network is systematically perturbed. This approach provides a step toward understanding and manipulating noise propagation in more complex gene networks.     

水稻种子蛋白质含量遗传研究进展

水稻(Oryza sativa L.)种子中的蛋白质含量是决定稻米营养品质的一个关键因素,增加稻米中的蛋白质含量对其品质改良具有十分重要的意义.文章综述了水稻种子蛋白质的组成、蛋白质含量的数量性状位点(Quantitative trait locus,QTL)定位、相关基因分离克隆及其基因表达调控等方面的研究进展,针对目前对水稻种子蛋白质含量相关基因功能和遗传调控规律尚不清楚的问题,提出采用基因聚合或利用分子标记辅助选择育种提高水稻种子蛋白质含量的策略,为水稻和其他重要作物品质的遗传改良提供参考和借鉴.     

An ultrasensitive bacterial motor revealed by monitoring signaling proteins in single cells

Understanding biology at the single-cell level requires simultaneous measurements of biochemical parameters and behavioral characteristics in individual cells. Here, the output of individual flagellar motors in Escherichia coli was measured as a function of the intracellular concentration of the chemotactic signaling protein. The concentration of this molecule, fused to green fluorescent protein, was monitored with fluorescence correlation spectroscopy. Motors from different bacteria exhibited an identical steep input-output relation, suggesting that they actively contribute to signal amplification in chemotaxis. This experimental approach can be extended to quantitative in vivo studies of other biochemical networks.     

Tunability and noise dependence in differentiation dynamics

The dynamic process of differentiation depends on the architecture, quantitative parameters, and noise of underlying genetic circuits. However, it remains unclear how these elements combine to control cellular behavior. We analyzed the probabilistic and transient differentiation of Bacillus subtilis cells into the state of competence. A few key parameters independently tuned the frequency of initiation and the duration of competence episodes and allowed the circuit to access different dynamic regimes, including oscillation. Altering circuit architecture showed that the duration of competence events can be made more precise. We used an experimental method to reduce global cellular noise and showed that noise levels are correlated with frequency of differentiation events. Together, the data reveal a noise-dependent circuit that is remarkably resilient and tunable in terms of its dynamic behavior.     

Identification of Hedgehog pathway components by RNAi in Drosophila cultured cells

Classical genetic screens can be limited by the selectivity of mutational targeting, the complexities of anatomically based phenotypic analysis, or difficulties in subsequent gene identification. Focusing on signaling response to the secreted morphogen Hedgehog (Hh), we used RNA interference (RNAi) and a quantitative cultured cell assay to systematically screen functional roles of all kinases and phosphatases, and subsequently 43% of predicted Drosophila genes. Two gene products reported to function in Wingless (Wg) signaling were identified as Hh pathway components: a cell surface protein (Dally-like protein) required for Hh signal reception, and casein kinase 1alpha, a candidate tumor suppressor that regulates basal activities of both Hh and Wg pathways. This type of cultured cell-based functional genomics approach may be useful in the systematic analysis of other biological processes.     

植物耐盐基因工程研究进展

盐害是农作物减产的主要因素,提高作物的耐盐性是提高全球粮食产量的基础。文章较系统地概述了植物盐胁迫信号传导通路研究现状,植物耐盐基因的挖掘,包括基于EST数据库的基因挖掘、通过转录谱确定胁迫响应基因以及应用转基因手段确定基因在胁迫耐受机制中的功能。同时系统阐述了各类耐盐基因的应用,包括渗透调节物质合成酶基因、氧胁迫相关基因、离子转运相关基因、编码转录因子的调节基因、感应和传导胁迫信号的蛋白激酶基因和其他调控序列。文章还对植物耐盐基因工程研究的现状进行了分析和提出建议,对进行植物基因工程研究工作具有参考价值和指导意义。     

Using gene expression noise to understand gene regulation

Phenotypic variation is ubiquitous in biology and is often traceable to underlying genetic and environmental variation. However, even genetically identical cells in identical environments display variable phenotypes. Stochastic gene expression, or gene expression "noise," has been suggested as a major source of this variability, and its physiological consequences have been topics of intense research for the last decade. Several recent studies have measured variability in protein and messenger RNA levels, and they have discovered strong connections between noise and gene regulation mechanisms. When integrated with discrete stochastic models, measurements of cell-to-cell variability provide a sensitive "fingerprint" with which to explore fundamental questions of gene regulation. In this review, we highlight several studies that used gene expression variability to develop a quantitative understanding of the mechanisms and dynamics of gene regulation.     

Genes and social behavior

What genes and regulatory sequences contribute to the organization and functioning of neural circuits and molecular pathways in the brain that support social behavior? How does social experience interact with information in the genome to modulate brain activity? Here, we address these questions by highlighting progress that has been made in identifying and understanding two key "vectors of influence" that link genes, the brain, and social behavior: (i) Social information alters gene expression in the brain to influence behavior, and (ii) genetic variation influences brain function and social behavior. We also discuss how evolutionary changes in genomic elements influence social behavior and outline prospects for a systems biology of social behavior.     

作物耐旱基因的表达特性及遗传工程研究

干旱会限制作物生长及产量形成,并引起作物体内一系列生理生化反应。作物耐旱性是多基因控制的复杂数量性状,为了应对水分缺失,作物体内形成多条信号途径,并在形态、生理和分子水平上适应干旱。受到干旱胁迫后,作物通过激活相关转录因子来调控相应下游基因的表达,并且通过转录后调控和渗透调节来适应干旱,维持正常的生理活动和代谢活动,减少干旱胁迫对植物的伤害。逆境也会诱导小RNA的产生,其通过诱导目的基因mRNA的降解以及阻止翻译过程去调控靶基因,达到耐胁迫逆境的作用。耐旱相关基因的遗传工程对作物在非生物逆境下的正常生长非常重要,总结了干旱响应机制所涉及的基因的功能及利用情况,以期为耐旱育种提供参考依据。     

Synchrony dynamics during initiation, failure, and rescue of the segmentation clock

The "segmentation clock" is thought to coordinate sequential segmentation of the body axis in vertebrate embryos. This clock comprises a multicellular genetic network of synchronized oscillators, coupled by intercellular Delta-Notch signaling. How this synchrony is established and how its loss determines the position of segmentation defects in Delta and Notch mutants are unknown. We analyzed the clock's synchrony dynamics by varying strength and timing of Notch coupling in zebra-fish embryos with techniques for quantitative perturbation of gene function. We developed a physical theory based on coupled phase oscillators explaining the observed onset and rescue of segmentation defects, the clock's robustness against developmental noise, and a critical point beyond which synchrony decays. We conclude that synchrony among these genetic oscillators can be established by simultaneous initiation and self-organization and that the segmentation defect position is determined by the difference between coupling strength and noise.     

小麦籽粒多酚氧化酶活性的遗传分析

为了揭示小麦籽粒多酚氧化酶活性的遗传特点,应用植物数量性状主基因+多基因混合遗传模型对杂交组合IDO580×宁麦13号、鄂恩1号×IDO580的两套P1、F1、P2、B1、B2和F2的6个世代群体的籽粒多酚氧化酶活性进行了多世代联合分析。结果表明:两组合籽粒多酚氧化酶活性均受2对加性-显性-上位性主基因+加性-显性-上位性多基因(E-0)混合遗传的控制;在两对主基因的一阶遗传参数中,加性效应大于显性效应,但以上位性效应所占比例为最大;在二阶遗传参数中,主基因遗传率远大于多基因遗传率,以主基因遗传为主。在B1、B2和F2的3个分离世代中,以F2世代的主基因遗传率为最高,其在这两个组合中的主基因遗传率分别为80.49%和82.24%。     

Spongiform degeneration in mahoganoid mutant mice

mahoganoid is a mouse coat-color mutation whose pigmentary phenotype and genetic interactions resemble those of Attractin (Atrn). Atrn mutations also cause spongiform neurodegeneration. Here, we show that a null mutation for mahoganoid causes a similar age-dependent neuropathology that includes many features of prion diseases but without accumulation of protease-resistant prion protein. The gene mutated in mahoganoid encodes a RING-containing protein with E3 ubiquitin ligase activity in vitro. Similarities in phenotype, expression, and genetic interactions suggest that mahoganoid and Atrn genes are part of a conserved pathway for regulated protein turnover whose function is essential for neuronal viability.     

种猪场内个体性能测定技术

种猪选育是指通过性能测定,选择表现优异的种猪个体进入核心群,配种后产生后代,并将优秀的遗传品质传给下一代的过程。选育的性状包括质量性状和数量性状。质量性状比较稳定,不易受环境条件的影响;它在群体内的分布是不连续的,杂交后代的个体可以进行明确分组,从而可以计算杂交子代各组个体的比率。数量性状易受环境的影响,在群体内的分布是连续的,它受微效多基因影响,也可能其中有主（效）基因。研究选择的性状大多属于具有经济价值的数量性状,品种选育就是一个加性效应的积累和促使对经济性状有利的基因纯合的过程。本文将从种猪性能测定的重要性出发,介绍种猪场内个体性能测定的技术,以期为种猪选育提供参考。     

Scaling up digital circuit computation with DNA strand displacement cascades

To construct sophisticated biochemical circuits from scratch, one needs to understand how simple the building blocks can be and how robustly such circuits can scale up. Using a simple DNA reaction mechanism based on a reversible strand displacement process, we experimentally demonstrated several digital logic circuits, culminating in a four-bit square-root circuit that comprises 130 DNA strands. These multilayer circuits include thresholding and catalysis within every logical operation to perform digital signal restoration, which enables fast and reliable function in large circuits with roughly constant switching time and linear signal propagation delays. The design naturally incorporates other crucial elements for large-scale circuitry, such as general debugging tools, parallel circuit preparation, and an abstraction hierarchy supported by an automated circuit compiler.     

过表达ZmIBH1-1提高玉米苗期抗旱性

【目的】干旱是严重影响玉米生长发育进程的一个重要因素。挖掘玉米抗旱相关基因,通过转基因功能验证和转录组分析,解析关键基因在响应干旱胁迫过程中的分子调控机制,为抗旱分子育种和遗传改良提供理论依据。【方法】以玉米自交系B104（WT）为背景材料,利用农杆菌介导方法构建过表达ZmIBH1-1转基因株系（ZmIBH1-1-OE）;通过对转基因植株进行草铵膦抗性筛选、标记基因和目的基因PCR检测,以及运用实时荧光定量PCR检测目的基因的表达情况,鉴定阳性植株和株系;以WT和ZmIBH1-1-OE转基因株系为材料,通过干旱处理（20% PEG6000）,进行表型鉴定和耐旱生理生化指标测定,验证ZmIBH1-1的抗旱功能;通过对干旱胁迫下玉米4叶期转录组的比较分析,鉴定出差异表达的基因（differentially expressed genes,DEGs）;结合DAP-seq（DNA affinity purification sequencing）分析,初步确定ZmIBH1-1蛋白直接调控与抗旱相关的下游靶基因,利用基因组可视化软件IGV（integrative genomics viewer）分析ZmIBH1-1蛋白结合候选靶基因的位置,然后通过Dual-Luciferase试验验证ZmIBH1-1蛋白与靶基因的调控关系。【结果】通过玉米遗传转化获得12个转化事件;T₃代中,能同时检测到标记基因Bar和目的基因ZmIBH1-1的植株有458个,实时荧光定量PCR检测结果表明,ZmIBH1-1-OE中ZmIBH1-1的表达量显著高于WT,株系3和株系8表达量最高,将其自交获得T₄代转基因株系用于后续试验。在干旱胁迫条件下,ZmIBH1-1-OE株系存活率、叶片相对含水量、叶绿素含量、可溶性蛋白含量及其生理生化指标（超氧化物歧化酶、过氧化物酶、过氧化氢酶活性）均显著高于WT,说明玉米中过量表达ZmIBH1-1赋予玉米更高的耐旱性。转录组分析结果表明,WT与ZmIBH1-1-OE株系在干旱胁迫下有1 214个差异表达基因;Gene Ontology（GO）功能富集分析结果表明,差异表达基因主要涉及生物过程、细胞组分和分子功能,如在生物过程中主要涉及到光合作用、应激响应、脱水响应等;KEGG富集分析表明,差异表达基因主要参与植物激素信号传导、新陈代谢等过程。结合转录组显著差异表达基因和DAP-Seq分析所得到ZmIBH1-1蛋白的靶基因,初步确定ZmIBH1-1蛋白直接调控与抗旱相关的11个候选靶基因,包括2个钙信号相关基因、3个半胱氨酸代谢相关基因、1个bHLH转录因子、1个应激响应蛋白、1个谷胱甘肽转移酶、1个氧化还原过程蛋白和2个乙烯响应因子;基因组可视化结果显示ZmIBH1-1蛋白可以结合靶基因启动子区;随后通过Dual-Luciferase试验进一步表明,ZmIBH1-1蛋白可以直接作用于11个候选靶基因,其中,ZmIBH1-1蛋白可以促进ZmCa-M、ZmSYCO、ZmbHLH54、ZmGlu-r1、ZmCLPB3和ZmP450-99A2的表达,抑制ZmAGD12、ZmCYS、ZmCYSB、ZmERF-107和ZmEIN3的表达。此外,在干旱胁迫下NAC、WRKY、MYB等转录因子在ZmIBH1-1-OE和WT株系中也存在差异表达。【结论】ZmIBH1-1的过表达可以增强玉米苗期的耐旱性;ZmIBH1-1蛋白通过直接调控乙烯信号通路中的ZmERF-107和ZmEIN3的表达提高玉米的耐旱性;ZmIBH1-1蛋白通过直接调控钙信号相关基因ZmCa-M和ZmAGD12增强玉米的耐旱性;ZmIBH1-1蛋白可能通过间接调控NAC、WRKY、MYB等转录因子响应干旱胁迫。