PASIV: A Pooled Approach-Based Workflow to Overcome Toxicity-Induced Design of Experiments Failures and Inefficiencies.
PASIV: A Pooled Approach-Based Workflow to Overcome Toxicity-Induced Design of Experiments Failures and Inefficiencies.
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DOI：
10.1021/acssynbio.1c00562
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发表时间：
2022-03-18
影响因子：
4.7
通讯作者：
Kitney R
中科院分区：
文献类型：
--
作者：
Casas A;Bultelle M;Motraghi C;Kitney R
我们在这里提出了一个新开发的工作流程-我们称之为PASIV-旨在提供一个解决方案的实验设计（DoE）方法的实际问题：即，如果DoE周期的范围界定阶段受到负担和毒性问题（由代谢物或中间体引起）的严重阻碍，使其不可靠或不可能进入筛选阶段，该怎么办？PASIV-代表汇集的方法，筛选，识别和可视化-被设计为使（可行的）感兴趣的区域可以通过生物学和软件之间的相互作用而出现。这是通过合并方法（一锅反应）中的多重构建与活力测定和一系列生物信息学工具（包括新型构建体匹配工具）相结合来实现的。PASIV在番茄红素途径的样本上进行了测试-在压力组成型表达下-产生了具有相对较强生产者的感兴趣区域。
We present here a newly developed workflow—which we have called PASIV—designed to provide a solution to a practical problem with design of experiments (DoE) methodology: i.e., what can be done if the scoping phase of the DoE cycle is severely hampered by burden and toxicity issues (caused by either the metabolite or an intermediary), making it unreliable or impossible to proceed to the screening phase? PASIV—standing for pooled approach, screening, identification, and visualization—was designed so the (viable) region of interest can be made to appear through an interplay between biology and software. This was achieved by combining multiplex construction in a pooled approach (one-pot reaction) with a viability assay and with a range of bioinformatics tools (including a novel construct matching tool). PASIV was tested on the exemplar of the lycopene pathway—under stressful constitutive expression—yielding a region of interest with comparatively stronger producers.
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