A simple regulatory network coordinates a bacterial stress response in space and time DOI Creative Commons
Divya Choudhary, Kevin R. Foster, Stephan Uphoff

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: March 12, 2024

Abstract Bacteria employ diverse gene regulatory networks to protect themselves from stressful environments. While transcriptomics and proteomics show that the expression of different genes can shift strongly in response stress, underlying logic large is difficult understand bulk measurements performed at discrete time points. As a result, it remains challenging predict how these function system level. Here we use time-resolved single-cell imaging explore functioning key bacterial stress response: The Escherichia coli oxidative stress. Our work reveals striking diversity dynamics network, with differences timing, magnitude, direction changes. Nevertheless, find patterns have simple logic. Firstly, all exhibit transient increase their protein levels simply due slowing down cell growth under Controlling for this effect three classes regulation driven by transcription factor OxyR. Downregulated drop level, while upregulated either pulsatile decays rapidly or gradual induction, dependent upon binding dynamics. These appear serve distinct functional roles populations. Pulsatile are stress-sensitive activate transiently few cells, which provides an initial protection groups. Gradually less sensitive induce more evenly generating lasting involves larger number cells. study shows populations principles coordinate space time.

Language: Английский

The Nonlinear Cysteine Redox Dynamics in the i-Space: A Proteoform-centric Theory of Redox Regulation DOI Creative Commons
James N. Cobley, Panagiotis N. Chatzinikolaou, Cameron A. Schmidt

et al.

Redox Biology, Journal Year: 2025, Volume and Issue: 81, P. 103523 - 103523

Published: Feb. 5, 2025

The post-translational redox regulation of protein function by cysteine oxidation controls diverse biological processes, from cell division to death. However, most current site-centric paradigms fail capture the nonlinear and emergent nature in proteins with multiple cysteines. Here, we present a proteoform-centric theory grounded i-space. i-space encapsulates theoretical landscape all possible proteoforms. Using computational approaches, quantify vast size abstract i-space, revealing its scale-free architecture-elucidating disproportionate influence cysteine-rich proteins. We define mathematical rules governing proteoform dynamics. Their dynamics are inherently nonlinear, context-dependent, fundamentally constrained copy numbers. Monte Carlo simulations human PTP1B reveal extensive sampling beyond models, supporting "oxiform conjecture". This conjecture posits that highly oxidised proteoforms, molecules bearing cysteines, central regulation. In support, even 90%-reduced proteomes can house numbers unique, potentially functioanlly diverse, oxiforms. framework offers transformative lens for understanding biology

Language: Английский

Citations

1
Robust Chaos in a Totally Symmetric Network of Four Phase Oscillators DOI
Efrosiniia Karatetskaia, Alexey Kazakov, Klim Safonov

et al.

Physical Review Letters, Journal Year: 2025, Volume and Issue: 134(16)

Published: April 21, 2025

The Kuramoto model and its generalizations are universal models of collective behavior in oscillatory networks. We provide conditions on the coupling function such that system with four globally coupled identical oscillators has chaotic attractors: a pair Lorenz attractors or four-winged analog attractor. emerge near triple instability threshold splay-phase synchronization state oscillators. theoretical arguments verify numerically, based pseudohyperbolicity test, dynamics robust respect to small, e.g., time-dependent, perturbations system. chaoticity should also be inherited by any network weakly interacting systems attractors.

Language: Английский

Citations

1
Microbial Biotic Associations Dominated Adaptability Differences of Dioecious Poplar Under Salt Stress DOI Open Access
Kun Yan,

Shuqi Ma,

Qiliang Zhu

et al.

Plant Cell & Environment, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 2, 2025

How different stress responses by male and female plants are influenced interactions with rhizosphere microbes remains unclear. In this study, we employed poplar as a dioecious model plant quantified biotic associations between microorganisms to explore the relationship microbial adaptation. We propose health index (HI) comprehensively characterize physiological characteristics adaptive capacity of under stress. It was found that poplars demonstrated higher salt tolerance than females, root-secreted citric acid significantly in rhizospheres poplars. Positive association among bacteria increased HI stress, while fungal cross-domain (bacteria-fungi) did not. further identified keystone bacterial taxon regulating association, ASV_22706, which itself regulated positively correlated host HI. The abundance taxa negatively Compared poplars, enriched more prebiotics probiotics This work primarily reveals adaptation differences plants, suggests approach improve adaptability conditions.

Language: Английский

Citations

0
CRISPR-Cas-mediated adaptation of Thermus thermophilus HB8 to environmental stress conditions DOI

Abbas Karimi-Fard,

Abbas Saidi, Masoud Tohidfar

et al.

Archives of Microbiology, Journal Year: 2025, Volume and Issue: 207(2)

Published: Jan. 23, 2025

Language: Английский

Citations

0
Chaos Anticontrol and Switching Frequency Impact on MOSFET Junction Temperature and Lifetime DOI Creative Commons
Cristina Morel,

Jean-Yves Morel

Actuators, Journal Year: 2025, Volume and Issue: 14(5), P. 203 - 203

Published: April 23, 2025

Generating chaos from originally non-chaotic systems is a promising issue. Indeed, has been successfully applied in many fields to improve system performance. In this work, Buck converter chaotified using combination of the switching piecewise-constant characteristic and anticontrol feedback. For electromagnetic compatibility compliance reasons, feedback control method able, at same time, achieve low spectral emissions maintain small ripple output voltage inductance current. This new implies fast non-linear action MOSFET on period ramp generator. Thus, it essential analyze its thermal why we propose an original analysis influence frequency variation junction temperature: investigate correlation between lifetime power electronic component stress due addition chaos. It appeared that reduction current did not degrade performance, despite MOSFET. Furthermore, degradation was indicated for chaotic behavior versus periodic behavior. leads conclusion produces accumulated fatigue effect semiconductor.

Language: Английский

Citations

0
The master regulator OxyR orchestrates bacterial oxidative stress response genes in space and time DOI Creative Commons
Divya Choudhary, Kevin R. Foster, Stephan Uphoff

et al.

Cell Systems, Journal Year: 2024, Volume and Issue: 15(11), P. 1033 - 1045.e6

Published: Nov. 1, 2024

Bacteria employ diverse gene regulatory networks to survive stress, but deciphering the underlying logic of these complex has proved challenging. Here, we use time-resolved single-cell imaging explore functioning E. coli response oxidative stress. We observe expression dynamics within network. However, by controlling for stress-induced growth-rate changes, show that patterns involve just three classes regulation: downregulated genes, upregulated pulsatile and gradually genes. The two are distinguished differences in binding transcription factor, OxyR, appear play distinct roles during stress protection. Pulsatile genes activate transiently a few cells initial protection group cells, whereas induce evenly, generating lasting involving many cells. Our study shows how bacterial populations simple principles coordinate responses space time. A record this paper's transparent peer review process is included supplemental information.

Language: Английский

Citations

3
Viewing cancer as a chaotic ‘information processing system’ DOI
Mesut Tez

Systems Research and Behavioral Science, Journal Year: 2024, Volume and Issue: unknown

Published: June 14, 2024

Abstract The effort to define life encompasses a wide range of disciplines, from biology and physics spirituality. Traditionally, replies were restricted specialized specialties, resulting in disjointed solutions. Cancer research has mostly concentrated on genetic cellular factors. This essay aims reframe the way we think about cancer by looking at it through perspective information processing. It investigates cybernetic component life, perceiving as unified system processing all scales. Stem cell reveals their complex heterogeneity flexibility, which are critical for tissue repair development. Initially thought be harmful, chaotic gene expression is now acknowledged provide flexibility. Using chaos improve adaptation contrasts with unpredictability evolution, showcasing system's ability learn adapt. Creativity, disorder interact, opening up new avenues ideas. viewpoint opposes gene‐centric view highlights importance understanding biological processes beyond reductionism. finishes pushing paradigm change towards seeing an informational process rather than just hereditary disease encouraging better knowledge capabilities life.

Language: Английский

Citations

1
Combining multiple stressors blocks bacterial migration and growth DOI

Anuradha Sharma,

Alexander M. Shuppara, Gilberto C. Padron

et al.

Current Biology, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 1, 2024

Language: Английский

Citations

1
Combining multiple stressors unexpectedly blocks bacterial migration and growth DOI Creative Commons

Anuradha Sharma,

Alexander M. Shuppara, Gilberto C. Padron

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 27, 2024

In nature, organisms experience combinations of stressors. However, laboratory studies typically simplify reality and focus on the effects an individual stressor. Here, we use a microfluidic approach to simultaneously provide physical stressor (shear flow) chemical (H

Language: Английский

Citations

0
A simple regulatory network coordinates a bacterial stress response in space and time DOI Creative Commons
Divya Choudhary, Kevin R. Foster, Stephan Uphoff

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: March 12, 2024

Abstract Bacteria employ diverse gene regulatory networks to protect themselves from stressful environments. While transcriptomics and proteomics show that the expression of different genes can shift strongly in response stress, underlying logic large is difficult understand bulk measurements performed at discrete time points. As a result, it remains challenging predict how these function system level. Here we use time-resolved single-cell imaging explore functioning key bacterial stress response: The Escherichia coli oxidative stress. Our work reveals striking diversity dynamics network, with differences timing, magnitude, direction changes. Nevertheless, find patterns have simple logic. Firstly, all exhibit transient increase their protein levels simply due slowing down cell growth under Controlling for this effect three classes regulation driven by transcription factor OxyR. Downregulated drop level, while upregulated either pulsatile decays rapidly or gradual induction, dependent upon binding dynamics. These appear serve distinct functional roles populations. Pulsatile are stress-sensitive activate transiently few cells, which provides an initial protection groups. Gradually less sensitive induce more evenly generating lasting involves larger number cells. study shows populations principles coordinate space time.

Language: Английский

Citations

0