Predictive biology: modelling, understanding and harnessing microbial complexity

AJ Lopatkin, JJ Collins - Nature Reviews Microbiology, 2020 - nature.com
Predictive biology is the next great chapter in synthetic and systems biology, particularly for
microorganisms. Tasks that once seemed infeasible are increasingly being realized such as …

Sizing up the bacterial cell cycle

L Willis, KC Huang - Nature Reviews Microbiology, 2017 - nature.com
It is remarkable how robustly a bacterial species can maintain its preferred size. This
capacity is intimately related to control of the cell cycle: cell size and growth rate determine …

Deep learning automates the quantitative analysis of individual cells in live-cell imaging experiments

DA Van Valen, T Kudo, KM Lane… - PLoS computational …, 2016 - journals.plos.org
Live-cell imaging has opened an exciting window into the role cellular heterogeneity plays
in dynamic, living systems. A major critical challenge for this class of experiments is the …

[HTML][HTML] Mechanistic origin of cell-size control and homeostasis in bacteria

F Si, G Le Treut, JT Sauls, S Vadia, PA Levin, S Jun - Current Biology, 2019 - cell.com
Evolutionarily divergent bacteria share a common phenomenological strategy for cell-size
homeostasis under steady-state conditions. In the presence of inherent physiological …

Simultaneous cross-evaluation of heterogeneous E. coli datasets via mechanistic simulation

DN Macklin, TA Ahn-Horst, H Choi, NA Ruggero… - Science, 2020 - science.org
INTRODUCTION The generation of biological data is presenting us with one of the most
demanding analysis challenges the world has ever faced, not only in terms of storage and …

Relative rates of surface and volume synthesis set bacterial cell size

LK Harris, JA Theriot - Cell, 2016 - cell.com
Many studies have focused on the mechanisms underlying length and width determination
in rod-shaped bacteria. Here, we focus instead on cell surface area to volume ratio (SA/V) …

Homeostasis of protein and mRNA concentrations in growing cells

J Lin, A Amir - Nature communications, 2018 - nature.com
Many experiments show that the numbers of mRNA and protein are proportional to the cell
volume in growing cells. However, models of stochastic gene expression often assume …

Robust, linear correlations between growth rates and β-lactam–mediated lysis rates

AJ Lee, S Wang, HR Meredith, B Zhuang, Z Dai… - Proceedings of the …, 2018 - pnas.org
It is widely acknowledged that faster-growing bacteria are killed faster by β-lactam
antibiotics. This notion serves as the foundation for the concept of bacterial persistence …

Cell size and growth regulation in the Arabidopsis thaliana apical stem cell niche

L Willis, Y Refahi, R Wightman, B Landrein… - Proceedings of the …, 2016 - pnas.org
Cell size and growth kinetics are fundamental cellular properties with important
physiological implications. Classical studies on yeast, and recently on bacteria, have …

Size-dependent increase in RNA polymerase II initiation rates mediates gene expression scaling with cell size

XM Sun, A Bowman, M Priestman, F Bertaux… - Current Biology, 2020 - cell.com
Cell size varies during the cell cycle and in response to external stimuli. This requires the
tight coordination, or" scaling," of mRNA and protein quantities with the cell volume in order …