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| Open AccessPositive feedback induces switch between distributive and processive phosphorylation of Hog1
How cells shape signalling dynamics in MAPK cascades remains unclear. Here the authors combine mathematical modelling with in vivo validation to uncover a novel feedback mechanism that increases processivity and robustness of the yeast Hog1 module.
- Maximilian Mosbacher
- , Sung Sik Lee
- & Manfred Claassen
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Article
| Open AccessRobustness and innovation in synthetic genotype networks
Genotype networks are sets of genotypes connected by small mutational changes that share the same phenotype. Here the authors combine construction of over 20 synthetic gene regulatory networks with mathematical modeling to exemplify how gene regulatory networks provide robustness in face of mutations while enabling transitions to innovative phenotypes.
- Javier Santos-Moreno
- , Eve Tasiudi
- & Yolanda Schaerli
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Article
| Open AccessBenchmarking tools for detecting longitudinal differential expression in proteomics data allows establishing a robust reproducibility optimization regression approach
Longitudinal proteomics holds great promise for biomarker discovery, but the data interpretation has remained a challenge. Here, the authors evaluate several tools to detect longitudinal differential expression in proteomics data and introduce RolDE, a robust reproducibility optimization approach.
- Tommi Välikangas
- , Tomi Suomi
- & Laura L. Elo
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Article
| Open AccessCoupling of growth rate and developmental tempo reduces body size heterogeneity in C. elegans
Animals must reach the correct size during development, despite stochastic differences in their growth rate. Here, Stojanovski et al. show that a coupling of growth and development by an oscillatory timer buffers fluctuations in the growth of the nematode C. elegans to ensure its correct size.
- Klement Stojanovski
- , Helge Großhans
- & Benjamin D. Towbin
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Article
| Open AccessRobustness and lethality in multilayer biological molecular networks
Robustness is a prominent feature of most biological systems, but most of the current efforts have been focused on studying homogeneous molecular networks. Here the authors propose a comprehensive framework for understanding how the interactions between genes, proteins, and metabolites contribute to the determinants of robustness.
- Xueming Liu
- , Enrico Maiorino
- & Amitabh Sharma
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Article
| Open AccessAn endoribonuclease-based feedforward controller for decoupling resource-limited genetic modules in mammalian cells
Accurately predicting the behaviour of a genetic circuit remains difficult due to the lack of modularity. Here the authors quantify the effects of resource loading in mammalian systems and develop an endoribonuclease-based feedfoward controller to adapt gene expression to the effects of resource loading.
- Ross D. Jones
- , Yili Qian
- & Domitilla Del Vecchio
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Article
| Open AccessAsymmetric division events promote variability in cell cycle duration in animal cells and Escherichia coli
We know that variations in cell cycle duration between cells naturally occur but the mechanisms are largely unknown. Here, using lineage tracking, hierarchical clustering and Monte Carlo methods, the authors show that large differences in granddaughter cell cycle duration are driven by asymmetric divisions.
- Ulrich Berge
- , Daria Bochenek
- & Ruth Kroschewski
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Article
| Open AccessOcean acidification conditions increase resilience of marine diatoms
Diatoms account for 40% of marine primary production and their sensitivity to ocean acidification could have ecosystem-wide consequences. Here, the authors developed and applied a stress test, demonstrating that resilience of diatoms increases significantly in ocean acidification conditions.
- Jacob J. Valenzuela
- , Adrián López García de Lomana
- & Nitin S. Baliga
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Article
| Open AccessThe topological requirements for robust perfect adaptation in networks of any size
Robust perfect adaptation (RPA), the ability of a system to return to its pre-stimulus state in the presence of a new signal, enables organisms to respond to further changes in stimuli. Here, the authors identify the modular structure of the full set of network topologies that can confer RPA on complex networks.
- Robyn P. Araujo
- & Lance A. Liotta
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Article
| Open AccessControl of primary metabolism by a virulence regulatory network promotes robustness in a plant pathogen
How pathogens maintain phenotypic robustness during infection is poorly understood. Here the authors couple the virulence regulatory network (VRN) of the pathogen R. solanacearum to a model of its metabolic network, and find that the VRN activates functionally redundant primary metabolism genes to promote phenotypic robustness during infection.
- Rémi Peyraud
- , Ludovic Cottret
- & Stéphane Genin
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Article
| Open AccessThe interdependent network of gene regulation and metabolism is robust where it needs to be
Although networks of interacting genes and metabolic reactions are interdependent, they have largely been treated as separate systems. Here the authors apply a statistical framework for interdependent networks to E. coli, and show that it is sensitive to gene and protein perturbations but robust against metabolic changes.
- David F. Klosik
- , Anne Grimbs
- & Marc-Thorsten Hütt