High-throughput, subpixel precision analysis of bacterial morphogenesis and intracellular spatio-temporal dynamics.
Oleksii Sliusarenko,Jennifer Heinritz,Thierry Emonet,Christine Jacobs-Wagner,Christine Jacobs-Wagner +4 more
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TLDR
Using MicrobeTracker, a versatile and high‐throughput image analysis program that outlines and segments cells with subpixel precision, even in crowded images and mini‐colonies, enabling cell lineage tracking, it is discovered that the dynamics of the extensively studied Escherichia coli Min oscillator depends on Min protein concentration.Abstract:
Bacteria display various shapes and rely on complex spatial organization of their intracellular components for many cellular processes. This organization changes in response to internal and external cues. Quantitative, unbiased study of these spatio-temporal dynamics requires automated image analysis of large microscopy datasets. We have therefore developed MicrobeTracker, a versatile and high-throughput image analysis program that outlines and segments cells with subpixel precision, even in crowded images and mini-colonies, enabling cell lineage tracking. MicrobeTracker comes with an integrated accessory tool, SpotFinder, which precisely tracks foci of fluorescently labelled molecules inside cells. Using MicrobeTracker, we discover that the dynamics of the extensively studied Escherichia coli Min oscillator depends on Min protein concentration, unveiling critical limitations in robustness within the oscillator. We also find that the fraction of MinD proteins oscillating increases with cell length, indicating that the oscillator has evolved to be most effective when cells attain an appropriate length. MicrobeTracker was also used to uncover novel aspects of morphogenesis and cell cycle regulation in Caulobacter crescentus. By tracking filamentous cells, we show that the chromosomal origin at the old-pole is responsible for most replication/separation events while the others remain largely silent despite contiguous cytoplasm. This surprising position-dependent silencing is regulated by division.read more
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MicrobeJ, a tool for high throughput bacterial cell detection and quantitative analysis
TL;DR: MicrobeJ, a plug-in for the open-source platform ImageJ1, provides a comprehensive framework to process images derived from a wide variety of microscopy experiments with special emphasis on large image sets, and provides a robust way to verify the accuracy and veracity of the data.
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The Bacterial Cytoplasm Has Glass-like Properties and Is Fluidized by Metabolic Activity
Bradley R. Parry,Ivan V. Surovtsev,Ivan V. Surovtsev,Matthew T. Cabeen,Corey S. O'Hern,Eric R. Dufresne,Christine Jacobs-Wagner,Christine Jacobs-Wagner +7 more
TL;DR: This work finds that the bacterial cytoplasm displays properties that are characteristic of glass-forming liquids and changes from liquid-like to solid-like in a component size-dependent fashion, which provides insight into bacterial dormancy and has broad implications for understanding of bacterial physiology.
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Coupled, Circumferential Motions of the Cell Wall Synthesis Machinery and MreB Filaments in B. subtilis
Ethan C. Garner,Remi Bernard,Wenqin Wang,Xiaowei Zhuang,Xiaowei Zhuang,David Z. Rudner,Timothy J. Mitchison +6 more
TL;DR: Bacteria elongate by the uncoordinated, circumferential movements of synthetic complexes that insert radial hoops of new peptidoglycan during their transit, possibly driving the motion of the underlying MreB filaments.
Journal ArticleDOI
Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments.
David Van Valen,Takamasa Kudo,Keara Michelle Lane,Derek N. Macklin,Nicolas Quach,Mialy M. DeFelice,Inbal Maayan,Yu Tanouchi,Euan A. Ashley,Markus W. Covert +9 more
TL;DR: Deep convolutional neural networks are an accurate method that require less curation time, are generalizable to a multiplicity of cell types, from bacteria to mammalian cells, and expand live-cell imaging capabilities to include multi-cell type systems.
Journal ArticleDOI
A Constant Size Extension Drives Bacterial Cell Size Homeostasis
Manuel Campos,Manuel Campos,Ivan V. Surovtsev,Ivan V. Surovtsev,Setsu Kato,Ahmad Paintdakhi,Ahmad Paintdakhi,Bruno Beltran,Bruno Beltran,Sarah Ebmeier,Christine Jacobs-Wagner +10 more
TL;DR: This work shows through single-cell microscopy and modeling that the evolutionarily distant bacteria Escherichia coli and Caulobacter crescentus achieve cell size homeostasis by growing, on average, the same amount between divisions, irrespective of cell length at birth.
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