| Markerless Gene Editing in the Hyperthermophilic Archaeon Thermococcus kodakarensis
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Author:
Date:
2017-11-20
[Abstract] The advent of single cell genomics and the continued use of metagenomic profiling in diverse environments has exponentially increased the known diversity of life. The recovered and assembled genomes predict physiology, consortium interactions and gene function, but experimental validation of metabolisms and molecular pathways requires more directed approaches. Gene function–and the correlation between phenotype and genotype is most obviously studied with genetics, and it is therefore critical to develop techniques permitting rapid and facile strain construction. Many new and candidate archaeal lineages have recently been discovered, but experimental, genetic access to archaeal genomes is currently limited to a few model organisms. The results obtained from manipulating the genomes of ...
[摘要] 单细胞基因组学的出现以及在不同环境中宏基因组分析的持续使用已经成倍地增加了已知的生命多样性。恢复和组装的基因组预测生理，财团相互作用和基因功能，但代谢和分子途径的实验验证需要更直接的方法。基因功能 - 表型和基因型之间的相关性用遗传学得到最明显的研究，因此开发允许快速和容易地构建应变的技术是至关重要的。最近已经发现了许多新的和候选的古细菌谱系，但是对古细菌基因组的实验性，遗传途径目前仅限于一些模式生物。操纵这些基因可获得的生物的基因组所获得的结果已经对我们对古菌生理和信息处理系统的理解产生了深远的影响，这些持续的研究也有助于解决生命树的系统发育重建。超嗜热，浮游，海洋异养古细菌Thermococcus kodakarensis已经成为理想的遗传系统，其具有一系列可用于增加或减少编码活性的技术或修饰基因在体内的表达 。我们在这里概述一些技术，可以快速，无标记地删除单个，或者重复删除几个连续的从 T的序列。 kodakarensis 基因组。我们的程序包括构建转化所必需的质粒DNA的细节，所述质粒DNA通过同源重组指导整合到基因组中，鉴定已经整合了质粒序列的菌株（称为中间菌株）和确认质粒切除，导致最终菌株中的目标基因。可以使用几乎相同的程序来修饰而不是删除基因组基因座。
【背景】古细菌常常在看起来荒凉和迅速变化的环境中繁衍生息。古菌基因组的分析揭示了大量的代谢策略，预测了复杂和高度相互依赖的基因表达的调控网络，并揭示了许多基因，其蛋白质和日益稳定的RNA产物缺乏确定的功能。通过遗传操作挑战现有的和定义新的途径的能力已经辅助了古细菌生理学和信息处理系统的去卷积，并且最近开放了古细菌物种到合成和系统级的方法来定义细胞内和细胞间网络。 ...
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| Evaluation of Nodulation Speed by Sinorhizobium Strains
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Author:
Date:
2015-08-05
[Abstract] Rhizobia interact symbiotically with legumes to form root nodules, where by rhizobia fix atmospheric dinitrogen into ammonia in exchange for carbon produced via photosynthesis. The symbiotic interaction is agriculturally important by reducing the need for fertilizer containing nitrogen. The root and stem nodule bacteria commonly include bacteria in the genera Rhizobium, Mesorhizobium, Sinorhizobium (Ensifer), and Bradyrhizobium, although other genera of bacteria have now been shown to form root nodule symbioses with several legume species (Weir, 2012). Different rhizobial strains form different numbers of nodules on specific legume plant varieties (or cultivars), and the nitrogen fixing effectiveness of each rhizobial strain, its ability to fix ...
[摘要] 根瘤菌与豆科植物共生相互作用形成根瘤，其中根瘤菌将大气氮固定为氨，以交换通过光合作用产生的碳。共生相互作用在农业上是重要的，通过减少对含氮肥的需要。根和茎结节细菌通常包括根瘤菌属，中生根瘤菌，中华根瘤菌属（ Ensifer ）和 Bradyrhizobium >，虽然其他属的细菌现在已经显示形成根瘤与多种豆科物种的共生（Weir，2012）。不同的根瘤菌菌株在特定豆科植物品种（或品种）上形成不同数目的结节，并且每种根瘤菌菌株的氮固定效率，其固定氮并将其转移到植物的能力也是高度可变的（Toro，1996）。一些天然根瘤菌在固氮但在所生长的植物中形成大多数结节方面无效。这被称为结瘤问题的竞争（Triplett和Sadowsky，1992）。当评估大量不同的天然菌株时，竞争研究是不可行的。然而，单个菌株的结瘤速度与总体竞争性良好相关，并且可用于鉴定克服竞争问题的天然菌株（De Oliveira和Graham，1990; Bhuvaneswari等人，1980）。
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| Quantitative Evaluation of Competitive Nodulation among Different Sinorhizobium Strains
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Author:
Date:
2015-08-05
[Abstract] Legumes play a vital role in global food supply because they are uniquely capable of fixing atmospheric nitrogen (N) through symbioses with root and stem nodule bacteria, collectively called the rhizobia. These commonly include bacteria in the genera Rhizobium, Mesorhizobium, Sinorhizobium (Ensifer), and Bradyrhizobium, although other genera of bacteria have now been shown to form root nodule symbioses with several legume species (Weir, 2012). The symbiotic interaction is important for agricultural productivity, especially in less developed countries where nitrogen fertilizer is expensive. However, nodulation ability and competitiveness have practical importance in agricultural production, because the inoculation of efficient rhizobia is often ...
[摘要] 豆类在全球食物供应中起着至关重要的作用，因为它们独特地能够通过与根和茎结节细菌的共生固定大气氮（N），统称为根瘤菌。这些通常包括根瘤菌属，中生根瘤菌属，中华根瘤菌属（ Ensifer ）和 Bradyrhizobium 属中的细菌，的细菌现已显示与几种豆科物种形成根瘤共生（Weir，2012）。共生相互作用对于农业生产力是重要的，特别是在其中氮肥昂贵的欠发达国家中。然而，结瘤能力和竞争力在农业生产中具有实际重要性，因为高效根瘤菌的接种通常不成功，这主要是由于土壤中存在无效的土着根瘤菌的竞争性群体（Toro，1996; Triplett和Sadowsky， 。该协议允许我们定量评价中华根瘤菌菌株的相对结瘤竞争性。
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