Novel methods for analysing bacterial tracks reveal persistence in Rhodobacter sphaeroides.
Novel methods for analysing bacterial tracks reveal persistence in Rhodobacter sphaeroides.
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DOI：
10.1371/journal.pcbi.1003276
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发表时间：
2013-10
影响因子：
4.3
通讯作者：
Baker RE
中科院分区：
文献类型：
--
作者：
Rosser G;Fletcher AG;Wilkinson DA;de Beyer JA;Yates CA;Armitage JP;Maini PK;Baker RE
使用视频显微镜跟踪细菌是一种强大的实验方法来探测它们的运动行为。所获得的轨迹包含了许多与细菌运动的复杂模式有关的信息。然而，对这些数据进行定量分析的方法是有限的。大多数游动细菌以近似直线的方式移动，其间穿插着随机的重新定向阶段。因此，有必要将观察到的轨迹分割成游泳和重定向阶段，以提取有用的统计数据。我们提出了新的强大的分析工具来辨别这两个阶段的轨道。我们的方法包括一个简单而有效的协议，用于从跟踪数据集中删除虚假的轨道，然后基于两状态隐马尔可夫模型进行分析，利用表现出仅游泳或仅重新定向运动的突变株的可用性来生成经验先验分布。使用不同水平的附加噪声的模拟轨道，我们验证我们的方法，并与现有的启发式方法进行比较。据我们所知，这是系统评估这一领域分析方法的第一个例子。新方法对噪声的鲁棒性大大提高，并且比启发式方法引入更少的系统偏差。我们应用我们的方法，从细菌物种Rhodobacter sphaeroides和大肠杆菌获得的轨道。结果表明，R. sphaeroides在翻滚事件过程中表现出持续性，这是一个新的结果，在该物种和类似物种的研究中具有重要意义。许多种类的浮游细菌能够通过使用一个或多个螺旋鞭毛来推动它们自己通过液体介质。通常，所观察到的运动行为由一系列近似直线的运动组成，其间穿插着随机的、近似静止的重定向事件。这种现象是目前的兴趣，因为它是已知的重要的细菌过程，如致病性和生物膜形成。在近似本土条件下研究细菌运动性的公认实验方法是使用显微镜跟踪细胞。然而，目前没有有效的方法来分析这种跟踪数据。特别是，识别的重定向阶段，这是复杂的各种来源的噪音的数据，仍然是一个开放的挑战。在本文中，我们提出了分析大型细菌跟踪数据集的新方法。我们评估我们的新方法使用计算模拟的性能，并表明它们比以前公布的方法更可靠。我们继续分析以前未发表的轨道从细菌物种球形红杆菌，一个新兴的模式生物在该领域的细菌运动，和大肠杆菌，一个研究良好的模式细菌。分析证明了R. sphaeroides在重定向事件的过程中表现出定向持久性。
Tracking bacteria using video microscopy is a powerful experimental approach to probe their motile behaviour. The trajectories obtained contain much information relating to the complex patterns of bacterial motility. However, methods for the quantitative analysis of such data are limited. Most swimming bacteria move in approximately straight lines, interspersed with random reorientation phases. It is therefore necessary to segment observed tracks into swimming and reorientation phases to extract useful statistics. We present novel robust analysis tools to discern these two phases in tracks. Our methods comprise a simple and effective protocol for removing spurious tracks from tracking datasets, followed by analysis based on a two-state hidden Markov model, taking advantage of the availability of mutant strains that exhibit swimming-only or reorientating-only motion to generate an empirical prior distribution. Using simulated tracks with varying levels of added noise, we validate our methods and compare them with an existing heuristic method. To our knowledge this is the first example of a systematic assessment of analysis methods in this field. The new methods are substantially more robust to noise and introduce less systematic bias than the heuristic method. We apply our methods to tracks obtained from the bacterial species Rhodobacter sphaeroides and Escherichia coli. Our results demonstrate that R. sphaeroides exhibits persistence over the course of a tumbling event, which is a novel result with important implications in the study of this and similar species. Many species of planktonic bacteria are able to propel themselves through a liquid medium by the use of one or more helical flagella. Commonly, the observed motile behaviour consists of a series of approximately straight-line movements, interspersed with random, approximately stationary, reorientation events. This phenomenon is of current interest as it is known to be linked to important bacterial processes such as pathogenicity and biofilm formation. An accepted experimental approach for studying bacterial motility in approximately indigenous conditions is the tracking of cells using a microscope. However, there are currently no validated methods for the analysis of such tracking data. In particular, the identification of reorientation phases, which is complicated by various sources of noise in the data, remains an open challenge. In this paper we present novel methods for analysing large bacterial tracking datasets. We assess the performance of our new methods using computational simulations, and show that they are more reliable than a previously published method. We proceed to analyse previously unpublished tracks from the bacterial species Rhodobacter sphaeroides, an emerging model organism in the field of bacterial motility, and Escherichia coli, a well-studied model bacterium. The analysis demonstrates the novel result that R. sphaeroides exhibits directional persistence over the course of a reorientation event.
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影响因子：
2
作者：
Hill, NA;Hader, DP
通讯作者：
Hader, DP
影响因子：
2.9
作者：
Amsler, CD
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Amsler, CD
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BERG, HC
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Lauga, E;DiLuzio, WR;Stone, HA
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Stone, HA
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通讯作者：
Schmitt, R