Data for: Direct measurement of dynamic attractant gradients reveals breakdown of the Patlak-Keller-Segel chemotaxis model

Chemotactic bacteria not only navigate chemical gradients but also shape their environments by consuming and secreting attractants. Investigating how these processes influence the dynamics of bacterial populations has been challenging because of a lack of experimental methods for measuring spatial profiles of chemoattractants in real-time. Here, we use a fluorescent sensor for aspartate to directly measure bacterially generated chemoattractant gradients during collective migration. Our measurements show that the standard Patlak-Keller-Segel model for collective chemotactic bacterial migration breaks down at high cell densities. To address this, we propose modifications to the model that consider the impact of cell density on bacterial chemotaxis and attractant consumption. With these changes, the model explains our experimental data across all cell densities, offering new insight into chemotactic dynamics. Our findings highlight the significance of considering cell density effects on ba..., See Methods in the paper for details. These are density measurements of E. coli cells migrating as a band along a straight microfluidics channel as they consume and chase aspartate. Both the cell density and the concentration of aspartate are measured using fluorescent microscopy. The data was analyzed using MATLAB. Raw data, processed data and codes used to process the data are provided. See the Methods section of the paper and README file located with the data., MATLAB is required. , ## Data for: Direct measurement of dynamic attractant gradients reveals breakdown of the Patlak-Keller-Segel chemotaxis model

## Data for the paper:

### Direct measurement of dynamic attractant gradients reveals breakdown of the Patlak-Keller-Segel chemotaxis model

### Authors

Trung V. Phan, Henry H. Mattingly, Lam Vo, Jonathan S. Marvin, Loren L. Looger, Thierry Emonet

### Abstract

Chemotactic bacteria not only navigate chemical gradients but also shape their environments by consuming and secreting attractants. Investigating how these processes influence the dynamics of bacterial populations has been challenging because of a lack of experimental methods for measuring spatial profiles of chemoattractants in real-time. Here, we use a fluorescent sensor for aspartate to directly measure bacterially generated chemoattractant gradients during collective migration. Our measurements show that the standard Patlak-Keller-Segel model for collective chemotactic bacterial migration breaks do...

趋化细菌不仅能够沿化学梯度定向运动，还可通过消耗与分泌趋化引诱剂塑造自身微环境。此前由于缺乏实时测量趋化引诱剂空间分布的实验手段，探究此类过程对细菌种群动态的影响始终存在难点。本研究采用天冬氨酸荧光传感器，直接原位测量了集体迁移过程中细菌产生的趋化引诱剂梯度。实验结果显示，用于描述细菌集体趋化迁移的经典Patlak-Keller-Segel模型（Patlak-Keller-Segel model）在高细胞密度下不再成立。为此，我们提出改进模型，将细胞密度对细菌趋化行为与引诱剂消耗的影响纳入考量。经修正后的模型可解释所有细胞密度下的实验数据，为趋化动力学研究提供了全新视角。本研究结果凸显了考虑细胞密度对细菌趋化行为影响的重要性……详见论文方法部分。
本数据集为大肠杆菌（E. coli）沿直线微流控通道以条带形式集体迁移、同时消耗并追踪天冬氨酸的密度测量数据。通过荧光显微镜同步采集细胞密度与天冬氨酸浓度数据，采用MATLAB完成数据分析。本数据集包含原始数据、处理后数据及数据分析所用代码，详见论文方法部分与数据附带的README文件。实验需使用MATLAB软件。

## 数据集对应论文：《Direct measurement of dynamic attractant gradients reveals breakdown of the Patlak-Keller-Segel chemotaxis model》
## 论文数据：
### Direct measurement of dynamic attractant gradients reveals breakdown of the Patlak-Keller-Segel chemotaxis model
### 作者
Trung V. Phan, Henry H. Mattingly, Lam Vo, Jonathan S. Marvin, Loren L. Looger, Thierry Emonet
### 摘要
趋化细菌不仅能够沿化学梯度定向运动，还可通过消耗与分泌趋化引诱剂塑造自身微环境。此前由于缺乏实时测量趋化引诱剂空间分布的实验手段，探究此类过程对细菌种群动态的影响始终存在难点。本研究采用天冬氨酸荧光传感器，直接原位测量了集体迁移过程中细菌产生的趋化引诱剂梯度。实验结果显示，用于描述细菌集体趋化迁移的经典Patlak-Keller-Segel模型在高细胞密度下不再成立。为此，我们提出改进模型，将细胞密度对细菌趋化行为与引诱剂消耗的影响纳入考量。经修正后的模型可解释所有细胞密度下的实验数据，为趋化动力学研究提供了全新视角。本研究结果凸显了考虑细胞密度对细菌趋化行为影响的重要性……