BACKGROUND & AIMS: :The exocyst is a eukaryotic tethering complex necessary for the fusion of exocytic vesicles with the plasma membrane. Its function in vivo is tightly regulated by interactions with multiple small GTPases. Exo70, one of the eight subunits of the exocyst, is important for the localization of the exocyst to the plasma membrane. It interacts with TC10 and Rho3 GTPases in mammals and yeast, respectively, and has been shown recently to bind to the actin-polymerization complex Arp2/3. Here, we present the crystal structure of Mus musculus Exo70 at 2.25 A resolution. Exo70 is composed of alpha-helices in a series of right-handed helix-turn-helix motifs organized into a long rod of length 170 A and width 35 A. Although the alpha-helical organization of this molecule is similar to that in Saccharomyces cerevisiae Exo70, major structural differences are observed on the surface of the molecule, at the domain boundaries, and in various loop structures. In particular, the C-terminal domain of M. musculus Exo70 adopts a new orientation relative to the N-terminal half not seen in S. cerevisiae Exo70 structures. Given the low level of sequence conservation within Exo70, this structure provides new insights into our understanding of many species-specific functions of the exocyst.

背景与目标： : 胞外囊是一种真核系留复合物，是胞外囊泡与质膜融合所必需的。其在体内的功能受到与多个小gtp酶相互作用的严格调节。Exo70是胞外囊的八个亚基之一，对于胞外囊在质膜上的定位很重要。它分别与哺乳动物和酵母中的TC10和Rho3 gtp酶相互作用，最近已显示出与肌动蛋白聚合复合物Arp2/3结合。在这里，我们以2.25 A的分辨率介绍小家鼠Exo70的晶体结构。Exo70由一系列右旋螺旋-转弯-螺旋基序中的 α-螺旋组成，这些基序被组织成长170 a、宽35 a的长杆。尽管该分子的 α-螺旋组织与酿酒酵母Exo70中的组织相似，但在分子表面，结构域边界和各种环结构中观察到主要的结构差异。特别是，M. musculus Exo70的C末端结构域相对于N末端的一半采用了新的方向。酿酒酵母Exo70结构。鉴于Exo70内的序列保守性较低，该结构为我们对胞外囊的许多物种特异性功能的理解提供了新的见解。

BACKGROUND & AIMS: :When females mate promiscuously, sperm from rival males compete within the female reproductive tract to fertilize ova. Sperm competition is a powerful selective force that has shaped sexual behavior, sperm production, and sperm morphology. However, nothing is known about the influence of sperm competition on fertilization-related processes, because it has been assumed that sperm competition only involves a race to reach the site of fertilization. We compared four closely related rodent species with different levels of sperm competition to examine whether there are differences in the proportion of spermatozoa that become ready to interact with the ovum ("capacitated") and in the proportion of spermatozoa that experience the acrosome reaction in response to a natural stimulant. Our results show that differences between species in levels of sperm competition were associated with the proportion of spermatozoa that undergo capacitation and with the proportion of spermatozoa that respond to progesterone, an ovum-associated signal. Sperm competition thus favors a larger population of spermatozoa that are competent to fertilize, and spermatozoa that are more sensitive to the signals emitted by the ovum and that may penetrate the ova vestments more rapidly. These results suggest that, contrary to previous assumptions, competition between spermatozoa from rival males continues at the site of fertilization. These findings may have further evolutionary implications because the enhanced competitiveness of spermatozoa during fertilization may increase the risk of polyspermy to females. This could lead to antagonistic coevolution between the sexes and may contribute to the explanation of the rapid divergence observed in fertilization-related traits.

背景与目标： : 当雌性混杂交配时，来自敌对雄性的精子在雌性生殖道内竞争以使卵子受精。精子竞争是一种强大的选择力量，它塑造了性行为，精子产生和精子形态。但是，对于精子竞争对受精相关过程的影响一无所知，因为人们认为精子竞争仅涉及到达受精地点的竞赛。我们比较了四种具有不同精子竞争水平的密切相关的啮齿动物，以检查准备与卵子相互作用的精子比例 (“有能力”) 和经历顶体反应的精子比例是否存在差异。对自然兴奋剂的反应。我们的结果表明，物种之间的精子竞争水平差异与接受获能的精子比例以及对孕酮 (卵子相关信号) 做出反应的精子比例有关。因此，精子竞争有利于更多的能够受精的精子，以及对卵子发出的信号更敏感并可能更快地穿透卵子的精子。这些结果表明，与先前的假设相反，在受精地点，来自敌对雄性的精子之间的竞争仍在继续。这些发现可能具有进一步的进化意义，因为受精过程中精子的竞争力增强可能会增加雌性多精子的风险。这可能导致两性之间的拮抗性共同进化，并可能有助于解释受精相关性状中观察到的快速差异。

BACKGROUND & AIMS: :A novel murine gene, designated ayk1, which encodes a putative serine/threonine kinase has been cloned and characterized. The predicted catalytic domain of the protein is highly similar to that of Drosophila aurora (62.9% identity), and to that of Saccharomyces Ipl1 (49.4% identity). All three proteins also have very basic calculated isoelectric points (higher than 10). aurora has been recently shown to be crucial for centrosome separation and chromosome segregation, while Ipl1 is essential for yeast viability and accurate chromosome segregation. The results of Northern analysis and in situ RNA localization support a similar role for ayk1. The gene is specifically expressed in meiotically active cells, and during spermatogenesis, ayk1 transcripts accumulate just before the first meiotic division. Much lower levels are found in mitotically active cells. We propose that Ayk1, aurora and Ipl1 belong to a distinct new subfamily of kinases. These results suggest that the pathways controlling chromosome segregation are evolutionary conserved, and that similar control mechanisms operate in mitosis and meiosis.

背景与目标： : 已克隆并鉴定了一种新的鼠基因ayk1，该基因编码假定的丝氨酸/苏氨酸激酶。该蛋白质的预测催化结构域与果蝇aurora的催化结构域 (62.9% 身份) 和酵母ipp1的催化结构域 (49.4% 身份) 高度相似。这三种蛋白质也都有非常基本的计算等电点 (高于10)。aurora最近被证明对于中心体分离和染色体分离至关重要，而Ipl1对于酵母活力和准确的染色体分离至关重要。Northern分析和原位RNA定位的结果支持ayk1的类似作用。该基因在减数活性细胞中特异性表达，在精子发生过程中，ayk1转录本在第一次减数分裂分裂之前就积累了。在有丝分裂活性的细胞中发现的水平要低得多。我们建议Ayk1，aurora和ipp1属于一个独特的新激酶亚科。这些结果表明，控制染色体分离的途径是进化保守的，并且类似的控制机制在有丝分裂和减数分裂中起作用。

BACKGROUND & AIMS: BACKGROUND:Currently, there is little data available regarding the role of gender-specific gene expression on synonymous codon usage (translational selection) in most organisms, and particularly plants. Using gender-specific EST libraries (with > 4000 ESTs) from Zea mays and Triticum aestivum, we assessed whether gender-specific gene expression per se and gender-specific gene expression level are associated with selection on codon usage. RESULTS:We found clear evidence of a greater bias in codon usage for genes expressed in female than in male organs and gametes, based on the variation in GC content at third codon positions and the frequency of species-preferred codons. This finding holds true for both highly and for lowly expressed genes. In addition, we found that highly expressed genes have greater codon bias than lowly expressed genes for both female- and male-specific genes. Moreover, in both species, genes with female-specific expression show a greater usage of species-specific preferred codons for each of the 18 amino acids having synonymous codons. A supplemental analysis of Brassica napus suggests that bias in codon usage could also be higher in genes expressed in male gametophytic tissues than in heterogeneous (flower) tissues. CONCLUSION:This study reports gender-specific bias in codon usage in plants. The findings reported here, based on the analysis of 1,497,876 codons, are not caused either by differences in the biological functions of the genes or by differences in protein lengths, nor are they likely attributable to mutational bias. The data are best explained by gender-specific translational selection. Plausible explanations for these findings and the relevance to these and other organisms are discussed.

背景与目标：

BACKGROUND & AIMS: :The amplified fragment length polymorphism (AFLP) technique is being increasingly used in phylogenetic studies, especially in groups of rapidly radiating taxa. One of the key issues in the phylogenetic suitability of this technique is whether the DNA fragments generated via the AFLP method are homologous within and among the taxa being studied. We used a bioinformatics approach to assess homology based on both chromosomal location and sequence similarity of AFLP fragments. The AFLP technique was electronically simulated on genomes from eight organisms that represented a range of genome sizes. The results demonstrated that within a genome, the number of fragments is positively associated with genome size, and the degree of homology decreases with increasing numbers of fragments generated. The average homology of fragments was 89% for small genomes (< 400 Mb) but decreased to 59% for large genomes (> 2 Gb). Fragment homology for large genomes can be increased by excluding smaller fragments, although there is no clear upper limit for the size of fragments to exclude. A second approach is to increase the number of selective nucleotides in the final selective amplification step. For strains of the same organism, homology based on chromosome location and sequence similarity of fragments was 100%. Fragment homology for more distantly related taxa, however, decreased with greater time since divergence. We conclude that AFLP data are best suited for examining phylogeographic patterns within species and among very recently diverged species.

背景与目标： : 扩增片段长度多态性 (AFLP) 技术越来越多地用于系统发育研究，尤其是在快速辐射的类群中。该技术的系统发育适用性的关键问题之一是，通过AFLP方法产生的DNA片段在所研究的分类单元内部和之间是否同源。我们使用生物信息学方法根据AFLP片段的染色体位置和序列相似性来评估同源性。AFLP技术是在代表一系列基因组大小的八种生物的基因组上进行电子模拟的。结果表明，在基因组中，片段的数量与基因组大小呈正相关，并且同源性程度随着生成片段数量的增加而降低。对于小基因组 (< 400 Mb)，片段的平均同源性89%，但是对于大基因组 (> 2 gb)，片段的平均同源性降低到59%。可以通过排除较小的片段来增加大基因组的片段同源性，尽管没有明确的上限来排除片段的大小。第二种方法是在最终的选择性扩增步骤中增加选择性核苷酸的数量。对于同一生物体的菌株，基于片段的染色体位置和序列相似性100% 了同源性。然而，自发散以来，远缘类群的片段同源性随时间的延长而降低。我们得出的结论是，AFLP数据最适合检查物种内部和最近分歧物种之间的系统地理模式。

BACKGROUND & AIMS: :During lung development, proper epithelial cell arrangements are critical for the formation of an arborized network of tubes. Each tube requires a lumen, the diameter of which must be tightly regulated to enable optimal lung function. Lung branching and lumen morphogenesis require close epithelial cell-cell contacts that are maintained as a result of adherens junctions, tight junctions and by intact apical-basal (A/B) polarity. However, the molecular mechanisms that maintain epithelial cohesion and lumen diameter in the mammalian lung are unknown. Here we show that Scribble, a protein implicated in planar cell polarity (PCP) signalling, is necessary for normal lung morphogenesis. Lungs of the Scrib mouse mutant Circletail (Crc) are abnormally shaped with fewer airways, and these airways often lack a visible, 'open' lumen. Mechanistically we show that Scrib genetically interacts with the core PCP gene Vangl2 in the developing lung and that the distribution of PCP pathway proteins and Rho mediated cytoskeletal modification is perturbed in Scrib(Crc/Crc) lungs. However A/B polarity, which is disrupted in Drosophila Scrib mutants, is largely unaffected. Notably, we find that Scrib mediates functions not attributed to other PCP proteins in the lung. Specifically, Scrib localises to both adherens and tight junctions of lung epithelia and knockdown of Scrib in lung explants and organotypic cultures leads to reduced cohesion of lung epithelial cells. Live imaging of Scrib knockdown lungs shows that Scrib does not affect bud bifurcation, as previously shown for the PCP protein Celsr1, but is required to maintain epithelial cohesion. To understand the mechanism leading to reduced cell-cell association, we show that Scrib associates with β-catenin in embryonic lung and the sub-cellular distribution of adherens and tight junction proteins is perturbed in mutant lung epithelia. Our data reveal that Scrib is required for normal lung epithelial organisation and lumen morphogenesis by maintaining cell-cell contacts. Thus we reveal novel and important roles for Scrib in lung development operating via the PCP pathway, and in regulating junctional complexes and cell cohesion.

背景与目标： : 在肺发育过程中，适当的上皮细胞排列对于管的树状网络的形成至关重要。每个管都需要一个管腔，必须严格调节其直径以实现最佳的肺功能。肺分支和管腔形态发生需要紧密的上皮细胞-细胞接触，这些接触是粘附连接，紧密连接和完整的顶基 (a/B) 极性的结果。然而，维持哺乳动物肺上皮内聚和管腔直径的分子机制尚不清楚。在这里，我们显示Scribble (一种与平面细胞极性 (PCP) 信号有关的蛋白质) 对于正常的肺形态发生是必需的。Scrib小鼠突变体Circletail (Crc) 的肺形状异常，气道较少，并且这些气道通常缺乏可见的 “开放” 腔。从机制上讲，我们表明Scrib与发育中的肺中的核心PCP基因Vangl2发生遗传相互作用，并且在Scrib(Crc/Crc) 肺中PCP途径蛋白和Rho介导的细胞骨架修饰的分布受到干扰。然而，在果蝇Scrib突变体中被破坏的A/B极性在很大程度上不受影响。值得注意的是，我们发现Scrib介导的功能不归因于肺中的其他PCP蛋白。具体来说，Scrib定位于肺上皮的粘附和紧密连接以及肺外植体和器官型培养物中Scrib的敲除导致肺上皮细胞的凝聚力降低。Scrib敲低肺的实时成像表明，Scrib不影响芽分叉，如先前对PCP蛋白Celsr1所示，但是维持上皮凝聚力所必需的。为了了解导致细胞-细胞关联减少的机制，我们显示Scrib与胚胎肺中的 β-catenin缔合，并且粘附和紧密连接蛋白的亚细胞分布在突变的肺上皮中受到干扰。我们的数据表明，通过维持细胞与细胞的接触，正常的肺上皮组织和管腔形态发生需要Scrib。因此，我们揭示了Scrib在通过PCP途径运作的肺发育中以及在调节连接复合物和细胞凝聚力方面的新的重要作用。

BACKGROUND & AIMS: :Middle East and North Africa (MENA) encompass very unique populations, with a rich history and encompasses characteristic ethnic, linguistic and genetic diversity. The genetic diversity of MENA region has been largely unknown. The recent availability of whole-exome and whole-genome sequences from the region has made it possible to collect population-specific allele frequencies. The integration of data sets from this region would provide insights into the landscape of genetic variants in this region. We integrated genetic variants from multiple data sets systematically, available from this region to create a compendium of over 26 million genetic variations. The variants were systematically annotated and their allele frequencies in the data sets were computed and available as a web interface which enables quick query. As a proof of principle for application of the compendium for genetic epidemiology, we analyzed the allele frequencies for variants in transglutaminase 1 (TGM1) gene, associated with autosomal recessive lamellar ichthyosis. Our analysis revealed that the carrier frequency of selected variants differed widely with significant interethnic differences. To the best of our knowledge, al mena is the first and most comprehensive repertoire of genetic variations from the Arab, Middle Eastern and North African region. We hope al mena would accelerate Precision Medicine in the region.

背景与目标： : 中东和北非 (MENA) 涵盖了非常独特的人口，具有丰富的历史，并包含了独特的种族，语言和遗传多样性。MENA地区的遗传多样性在很大程度上是未知的。该地区最近获得的全外显子组和全基因组序列使收集特定人群的等位基因频率成为可能。来自该地区的数据集的整合将提供对该地区遗传变异景观的见解。我们系统地整合了来自该地区的多个数据集的遗传变异，以创建超过2600万个遗传变异的汇编。对变体进行了系统注释，并计算了它们在数据集中的等位基因频率，并可以作为web界面使用，从而可以快速查询。作为遗传流行病学学纲要应用原理的证明，我们分析了转谷氨酰胺酶1 (TGM1) 基因变异的等位基因频率，与常染色体隐性层状鱼鳞病有关。我们的分析表明，所选变体的载波频率差异很大，种族间差异很大。据我们所知，al mena是来自阿拉伯，中东和北非地区的第一个也是最全面的遗传变异库。我们希望al mena能够加快该地区的精准医学。

BACKGROUND & AIMS: :Sexual eukaryotes reproduce via the meiotic cell division, where ploidy is halved and homologous chromosomes undergo reciprocal genetic exchange, termed crossover (CO). CO frequency has a profound effect on patterns of genetic variation and species evolution. Relative CO rates vary extensively both within and between plant genomes. Plant genome size varies by over 1000-fold, largely due to differential expansion of repetitive sequences, and increased genome size is associated with reduced CO frequency. Gene versus repeat sequences associate with distinct chromatin modifications, and evidence from plant genomes indicates that this epigenetic information influences CO patterns. This is consistent with data from diverse eukaryotes that demonstrate the importance of chromatin structure for control of meiotic recombination. In this review I will discuss CO frequency patterns in plant genomes and recent advances in understanding recombination distributions.

背景与目标： : 有性真核生物通过减数分裂细胞分裂繁殖，倍性减半，同源染色体经历相互的遗传交换，称为交叉 (CO)。CO频率对遗传变异和物种进化的模式有深远的影响。植物基因组内部和之间的相对CO速率差异很大。植物基因组大小变化超过1000倍，这主要是由于重复序列的差异扩展，并且增加的基因组大小与减少的CO频率相关。基因与重复序列与明显的染色质修饰相关，来自植物基因组的证据表明，这种表观遗传信息会影响CO模式。这与来自各种真核生物的数据一致，这些数据证明了染色质结构对控制减数分裂重组的重要性。在这篇综述中，我将讨论植物基因组中的CO频率模式以及理解重组分布的最新进展。

BACKGROUND & AIMS: -2

背景与目标： -2

BACKGROUND & AIMS: :The hallmark of a virus is its capsid, which harbors the viral genome and is formed from protein subunits, which assemble following precise geometric rules. dsRNA viruses use an unusual protein multiplicity (120 copies) to form their closed capsids. We have determined the atomic structure of the capsid protein (P1) from the dsRNA cystovirus Φ8. In the crystal P1 forms pentamers, very similar in shape to facets of empty procapsids, suggesting an unexpected assembly pathway that proceeds via a pentameric intermediate. Unlike the elongated proteins used by dsRNA mammalian reoviruses, P1 has a compact trapezoid-like shape and a distinct arrangement in the shell, with two near-identical conformers in nonequivalent structural environments. Nevertheless, structural similarity with the analogous protein from the mammalian viruses suggests a common ancestor. The unusual shape of the molecule may facilitate dramatic capsid expansion during phage maturation, allowing P1 to switch interaction interfaces to provide capsid plasticity.

背景与目标： 病毒的标志是它的衣壳，它藏有病毒基因组，由蛋白质亚基形成，这些亚基按照精确的几何规则组装。dsRNA病毒使用一种不寻常的蛋白质多样性 (120个拷贝) 来形成它们的封闭衣壳类。我们已经确定了dsRNA囊病毒 Φ8的衣壳蛋白 (P1) 的原子结构。在晶体中，P1形成五聚体，其形状与空的前五胞体的小面非常相似，这表明通过五聚体中间体进行的意外组装途径。与dsRNA哺乳动物reoviruses使用的细长蛋白不同，P1具有紧凑的梯形形状和在壳中的独特排列，在非等效结构环境中具有两个几乎相同的构象体。尽管如此，与哺乳动物病毒类似蛋白的结构相似，表明有共同的祖先。分子的异常形状可能会在噬菌体成熟过程中促进衣壳的急剧膨胀，从而允许P1切换相互作用界面以提供衣壳可塑性。

BACKGROUND & AIMS: :Highly ordered degradation of cell proteins by the ubiquitin-proteasome system, a sophisticated cellular proteolytic machinery, has been identified as a key regulatory mechanism in many eukaryotic cells. Accumulating evidence reveals that the ubiquitin-proteasome system is involved in the regulation of fundamental processes in mammalian stem and progenitor cells of embryonic, neural, hematopoietic, and mesenchymal origin. Such processes, including development, survival, differentiation, lineage commitment, migration, and homing, are directly controlled by the ubiquitin-proteasome system, either via proteolytic degradation of key regulatory proteins of signaling and gene expression pathways or via nonproteolytic mechanisms involving the proteasome itself or posttranslational modifications of target proteins by ubiquitin or other ubiquitin-like modifiers. Future characterization of the precise roles and functions of the ubiquitin-proteasome system in mammalian stem and early progenitor cells will improve our understanding of stem cell biology and may provide an experimental basis for the development of novel therapeutic strategies in regenerative medicine. Disclosure of potential conflicts of interest is found at the end of this article.

背景与目标： : 泛素-蛋白酶体系统 (一种复杂的细胞蛋白水解机制) 对细胞蛋白的高度有序降解已被确定为许多真核细胞中的关键调节机制。越来越多的证据表明，泛素-蛋白酶体系统参与了胚胎，神经，造血和间充质来源的哺乳动物干细胞和祖细胞的基本过程的调节。这些过程，包括发展，生存，分化，谱系承诺，迁移和归巢，直接由泛素-蛋白酶体系统控制，通过信号和基因表达途径的关键调节蛋白的蛋白水解降解，或通过涉及蛋白酶体本身的非蛋白水解机制或泛素或其他泛素样修饰剂对靶蛋白的翻译后修饰。未来对泛素-蛋白酶体系统在哺乳动物干细胞和早期祖细胞中的精确作用和功能的表征将提高我们对干细胞生物学的理解，并可能为再生医学中新的治疗策略的开发提供实验基础。在本文的末尾找到了潜在利益冲突的披露。

BACKGROUND & AIMS: :Cell behavior is controlled through spatio-temporally localized protein activity. Despite unique and often contradictory roles played by Src-family-kinases (SFKs) in regulating cell physiology, activity patterns of individual SFKs have remained elusive. Here, we report a biosensor for specifically visualizing active conformation of SFK-Fyn in live cells. We deployed combinatorial library screening to isolate a binding-protein (F29) targeting activated Fyn. Nuclear-magnetic-resonance (NMR) analysis provides the structural basis of F29 specificity for Fyn over homologous SFKs. Using F29, we engineered a sensitive, minimally-perturbing fluorescence-resonance-energy-transfer (FRET) biosensor (FynSensor) that reveals cellular Fyn activity to be spatially localized, pulsatile and sensitive to adhesion/integrin signaling. Strikingly, growth factor stimulation further enhanced Fyn activity in pre-activated intracellular zones. However, inhibition of focal-adhesion-kinase activity not only attenuates Fyn activity, but abolishes growth-factor modulation. FynSensor imaging uncovers spatially organized, sensitized signaling clusters, direct crosstalk between integrin and growth-factor-signaling, and clarifies how compartmentalized Src-kinase activity may drive cell fate.

背景与目标： : 细胞行为是通过时空定位的蛋白质活性来控制的。尽管Src家族激酶 (sfk) 在调节细胞生理中起着独特且经常相互矛盾的作用，但单个sfk的活动模式仍然难以捉摸。在这里，我们报告了一种生物传感器，用于特异性可视化活细胞中SFK-Fyn的活性构象。我们部署了组合文库筛选，以分离靶向活化Fyn的结合蛋白 (F29)。核磁共振 (NMR) 分析为Fyn对同源sfk的F29特异性提供了结构基础。使用F29，我们设计了一种灵敏的，最小扰动的荧光共振能量转移 (FRET) 生物传感器 (FynSensor)，该传感器揭示了细胞Fyn活性在空间上是局部的，脉动的并且对粘附/整联蛋白信号敏感。引人注目的是，生长因子刺激进一步增强了预激活细胞内区域的Fyn活性。然而，对粘着斑激酶活性的抑制不仅减弱了Fyn活性，而且消除了生长因子的调节。FynSensor成像揭示了空间组织的，敏化的信号簇，整联蛋白和生长因子信号之间的直接串扰，并阐明了分隔的Src激酶活性如何驱动细胞命运。

BACKGROUND & AIMS: :Changes or innovations in gene regulatory networks for the developmental program in the ancestral chordate genome appear to be a major component in the evolutionary process in which tadpole-type larvae, a unique characteristic of chordates, arose. These alterations may include new genetic interactions as well as the acquisition of new regulatory genes. Previous analyses of the Ciona genome revealed that many genes may have emerged after the divergence of the tunicate and vertebrate lineages. In this paper, we examined this possibility by examining a second non-vertebrate chordate genome. We conclude from this analysis that the ancient chordate included almost the same repertory of regulatory genes, but less redundancy than extant vertebrates, and that approximately 10% of vertebrate regulatory genes were innovated after the emergence of vertebrates. Thus, refined regulatory networks arose during vertebrate evolution mainly as preexisting regulatory genes multiplied rather than by generating new regulatory genes. The inferred regulatory gene sets of the ancestral chordate would be an important foundation for understanding how tadpole-type larvae, a unique characteristic of chordates, evolved.

背景与目标： : 祖先脊索动物基因组发育程序的基因调控网络的变化或创新似乎是进化过程中的主要组成部分，在进化过程中，the型幼虫是脊索动物的独特特征。这些改变可能包括新的遗传相互作用以及新调控基因的获取。先前对Ciona基因组的分析表明，在被膜和脊椎动物谱系分化之后，可能出现了许多基因。在本文中，我们通过检查第二个非脊椎动物脊索动物基因组来研究这种可能性。我们从该分析得出的结论是，古代脊索动物包含几乎相同的调控基因库，但比现存的脊椎动物少冗余，并且大约10% 的脊椎动物调控基因在脊椎动物出现后被创新。因此，在脊椎动物进化过程中出现了完善的调控网络，主要是由于先前存在的调控基因成倍增加，而不是通过产生新的调控基因。推断出的祖先脊索动物的调控基因集将是了解The型幼虫 (脊索动物的独特特征) 如何进化的重要基础。

BACKGROUND & AIMS: :Here, we describe an extension of our original transformation-associated recombination (TAR) cloning protocol, enabling selective isolation of DNA segments from microbial genomes. The technique is based on the previously described TAR cloning procedure developed for isolation of a desirable region from mammalian genomes that are enriched in autonomously replicating sequence (ARS)-like sequences, elements that function as the origin of replication in yeast. Such sequences are not common in microbial genomes. In this Protocol Extension, an ARS is inserted into the TAR vector along with a counter-selectable marker, allowing for selection of cloning events against vector circularization. Pre-treatment of microbial DNA with CRISPR-Cas9 to generate double-stranded breaks near the targeted sequences greatly increases the yield of region-positive colonies. In comparison to other available methods, this Protocol Extension allows selective isolation of any region from microbial genomes as well as from environmental DNA samples. The entire procedure can be completed in 10 d.

背景与目标： : 在这里，我们描述了我们原始的转化相关重组 (TAR) 克隆方案的扩展，从而可以从微生物基因组中选择性隔离DNA片段。该技术基于先前描述的TAR克隆程序，该程序开发用于从富含自主复制序列 (ARS) 样序列的哺乳动物基因组隔离所需区域，这些元素在酵母中起复制起点的作用。这种序列在微生物基因组中并不常见。在此协议扩展中，将ARS与反选择标记一起插入TAR载体中，从而可以针对载体循环化选择克隆事件。用CRISPR-Cas9预处理微生物DNA以在目标序列附近产生双链断裂，大大提高了区域阳性菌落的产量。与其他可用方法相比，此协议扩展允许从微生物基因组以及环境DNA样品中选择性隔离任何区域。整个过程可以在10天内完成。

BACKGROUND & AIMS: :Euphorbiaceae plants are important as suppliers of biodiesel. In the current study, the codon usage patterns and sources of variance in chloroplast genome sequences of six different Euphorbiaceae plant species have been systematically analyzed. Our results revealed that the chloroplast genomes of six Euphorbiaceae plant species were biased towards A/T bases and A/T-ending codons, followed by detection of 17 identical high-frequency codons including GCT, TGT, GAT, GAA, TTT, GGA, CAT, AAA, TTA, AAT, CCT, CAA, AGA, TCT, ACT, TAT and TAA. It was found that mutation pressure was a minor factor affecting the variation of codon usage, however, natural selection played a significant role. Comparative analysis of codon usage frequencies of six Euphorbiaceae plant species with four model organisms reflected that Arabidopsis thaliana, Populus trichocarpa, and Saccharomyces cerevisiae should be considered as suitable exogenous expression receptor systems for chloroplast genes of six Euphorbiaceae plant species. Furthermore, it is optimal to choose Saccharomyces cerevisiae as the exogenous expression receptor. The outcome of the present study might provide important reference information for further understanding the codon usage patterns of chloroplast genomes in other plant species.

背景与目标： : 大戟科植物作为生物柴油的供应商很重要。在当前的研究中，已经对六种不同大戟科植物物种的叶绿体基因组序列的密码子使用模式和变异来源进行了系统分析。我们的结果表明，六个大戟科植物的叶绿体基因组偏向A/T碱基和A/T结尾密码子，随后检测到17个相同的高频密码子，包括GCT，TGT，GAT，GAA，TTT，GGA，CAT，AAA，TTA，AAT，CCT，CAA、AGA、TCT、ACT、TAT和TAA。发现突变压力是影响密码子使用变化的次要因素，但是自然选择起着重要作用。6种大戟科植物与4种模式生物密码子使用频率的比较分析表明，拟南芥，毛白杨和酿酒酵母应被视为六种大戟科植物叶绿体基因的合适外源表达受体系统。此外，选择酿酒酵母作为外源表达受体是最佳的。本研究的结果可能为进一步了解其他植物物种中叶绿体基因组的密码子使用模式提供重要的参考信息。