PHENOS: a high-throughput and flexible tool for microorganism growth phenotyping on solid media.
PHENOS: a high-throughput and flexible tool for microorganism growth phenotyping on solid media.
复制标题
现象：用于固体培养基上微生物生长表型的高通量和灵活工具。
DOI：
10.1186/s12866-017-1143-y
复制
发表时间：
2018-01-24
期刊：
影响因子：
4.2
通讯作者：
Foster SS
中科院分区：
文献类型：
--
作者：
Barton DBH;Georghiou D;Dave N;Alghamdi M;Walsh TA;Louis EJ;Foster SS
微生物阵列在一个平板上以机器人的精度打印出大量不同的菌株，为越来越多的遗传和基因组方法奠定了基础。这些技术包括合成遗传阵列分析、高通量数量性状基因座(QTL)分析和双杂交技术。测量这些阵列内单个菌落的生长是许多这些技术的重要组成部分，但对任何阵列工作都很有用。测量通常是使用输入复杂图像分析软件的间歇性图像进行的，这种图像不是特别准确，而且很难有效使用。我们已经开发出一种简单快速的替代技术，它使用钉扎机器人和普通的微型平板阅读器来连续测量固体琼脂上生长的菌落厚度，并辅之以一种技术，以使最初打印到阵列每个点的细胞数量标准化。我们已经开发了软件来自动化合并多套读数、减去琼脂吸光度以及以多种信息方式可视化菌落厚度变化的过程。针对酵母菌优化的“PHENOS”流水线(固体介质上的表型)产生了高度可重复性的生长曲线，对低水平的生长特别敏感。我们已经根据经验确定了从吸光度测量中估计菌落细胞计数的公式，并表明这与从液体中测量的估计值相当。我们还通过复制早期用传统液体表型进行的QTL研究的结果来验证这项技术，并发现PHENOS的敏感性要高得多。“PHENOS”是一种经济有效且可靠的高通量技术，用于量化酵母阵列的生长，并可能对一系列其他类型的微生物阵列同样非常有用。Https://github.com/gact/phenos.上的安装文件中提供了管道和软件的详细指南本文的在线版本(10.1186/s12866-0171143-y)包含向授权用户提供的补充材料。
Microbial arrays, with a large number of different strains on a single plate printed with robotic precision, underpin an increasing number of genetic and genomic approaches. These include Synthetic Genetic Array analysis, high-throughput Quantitative Trait Loci (QTL) analysis and 2-hybrid techniques. Measuring the growth of individual colonies within these arrays is an essential part of many of these techniques but is useful for any work with arrays. Measurement is typically done using intermittent imagery fed into complex image analysis software, which is not especially accurate and is challenging to use effectively. We have developed a simple and fast alternative technique that uses a pinning robot and a commonplace microplate reader to continuously measure the thickness of colonies growing on solid agar, complemented by a technique for normalizing the amount of cells initially printed to each spot of the array in the first place. We have developed software to automate the process of combining multiple sets of readings, subtracting agar absorbance, and visualizing colony thickness changes in a number of informative ways. The “PHENOS” pipeline (PHENotyping On Solid media), optimized for Saccharomyces yeasts, produces highly reproducible growth curves and is particularly sensitive to low-level growth. We have empirically determined a formula to estimate colony cell count from an absorbance measurement, and shown this to be comparable with estimates from measurements in liquid. We have also validated the technique by reproducing the results of an earlier QTL study done with conventional liquid phenotyping, and found PHENOS to be considerably more sensitive. “PHENOS” is a cost effective and reliable high-throughput technique for quantifying growth of yeast arrays, and is likely to be equally very useful for a range of other types of microbial arrays. A detailed guide to the pipeline and software is provided with the installation files at https://github.com/gact/phenos. The online version of this article (10.1186/s12866-017-1143-y) contains supplementary material, which is available to authorized users.
登录
查看更多内容
酵母进化遗传学的令人敬畏的力量：Saccharomyces sensu stricto属的新基因组序列和应变资源。
DOI：
10.1534/g3.111.000273
发表时间：
2011-06
期刊：
G3 (Bethesda, Md.)
影响因子：
--
作者：
Scannell DR;Zill OA;Rokas A;Payen C;Dunham MJ;Eisen MB;Rine J;Johnston M;Hittinger CT
通讯作者：
Hittinger CT
影响因子：
46.9
作者：
Harrington, JJ;Sherf, B;Ducar, M
通讯作者：
Ducar, M
影响因子：
4.4
作者：
Meersman, Esther;Steensels, Jan;Verstrepen, Kevin J.
通讯作者：
Verstrepen, Kevin J.
通过延时成像和琼脂酵母培养阵列的自动化图像分析对细胞增殖动力学的准确，精确的建模。
影响因子：
--
作者：
Shah, Najaf A;Laws, Richard J;Wardman, Bradley;Zhao, Lue Ping;Hartman, John L 4th
通讯作者：
Hartman, John L 4th
影响因子：
3.7
作者：
Jung PP;Christian N;Kay DP;Skupin A;Linster CL
通讯作者：
Linster CL