scholarly journals Mathematical modelling of SigE regulatory network reveals new insights into bistability of mycobacterial stress response

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Irene Zorzan ◽  
Simone Del Favero ◽  
Alberto Giaretta ◽  
Riccardo Manganelli ◽  
Barbara Di Camillo ◽  
...  

Abstract Background The ability to rapidly adapt to adverse environmental conditions represents the key of success of many pathogens and, in particular, of Mycobacterium tuberculosis. Upon exposition to heat shock, antibiotics or other sources of stress, appropriate responses in terms of genes transcription and proteins activity are activated leading part of a genetically identical bacterial population to express a different phenotype, namely to develop persistence. When the stress response network is mathematically described by an ordinary differential equations model, development of persistence in the bacterial population is associated with bistability of the model, since different emerging phenotypes are represented by different stable steady states. Results In this work, we develop a mathematical model of SigE stress response network that incorporates interactions not considered in mathematical models currently available in the literature. We provide, through involved analytical computations, accurate approximations of the system’s nullclines, and exploit the obtained expressions to determine, in a reliable though computationally efficient way, the number of equilibrium points of the system. Conclusions Theoretical analysis and perturbation experiments point out the crucial role played by the degradation pathway involving RseA, the anti-sigma factor of SigE, for coexistence of two stable equilibria and the emergence of bistability. Our results also indicate that a fine control on RseA concentration is a necessary requirement in order for the system to exhibit bistability.

2020 ◽  
Vol 17 (04) ◽  
pp. 2050062 ◽  
Author(s):  
Chunsheng Feng ◽  
Qiujian Huang ◽  
Yongjian Liu

Little seems to be known about the study of the chaotic system with only Lyapunov stable equilibria from the perspective of differential geometry. Therefore, this paper presents Jacobi analysis of an unusual three-dimensional (3D) autonomous chaotic system. Under certain parameter conditions, this system has positive Lyapunov exponents and only two linear stable equilibrium points, which means that chaotic attractor and Lyapunov stable equilibria coexist. The dynamical behavior of the deviation vector near the whole trajectories (including all equilibrium points) is analyzed in detail. The results show that the value of the deviation curvature tensor at equilibrium points is only related to parameters; the two equilibrium points of the system are Jacobi stable if the parameters satisfy certain conditions. Particularly, for a specific set of parameters, the linear stable equilibrium points of the system are always Jacobi unstable. A periodic orbit that is Lyapunov stable is also proven to be always Jacobi unstable. Next, Jacobi-stable regions of the Lorenz system, the Chen system and the system under study are compared for specific parameters. It can be found that although these three chaotic systems are very similar, their regions of Jacobi stable parameters are much different. Finally, by comparing Jacobi stability with Lyapunov stability, the obtained results demonstrate that the Jacobi stable parameter region is basically symmetric with the Lyapunov stable parameter region.


2019 ◽  
Author(s):  
David R. Amici ◽  
Jasen M. Jackson ◽  
Kyle A. Metz ◽  
Daniel J. Ansel ◽  
Roger S. Smith ◽  
...  

SummaryThe interrelated programs essential for cellular fitness in the face of stress are critical to understanding tumorigenesis, neurodegeneration, and aging. However, modelling the combinatorial landscape of stresses experienced by diseased cells is challenging, leaving functional relationships within the global stress response network incompletely understood. Here, we leverage genome-scale fitness screening data from 625 cancer cell lines, each representing a unique biological context, to build a network of “coessential” gene relationships centered around master regulators of the response to proteotoxic, oxidative, hypoxic, and genotoxic stress. This approach organizes the stress response into functional modules, identifies genes connecting distinct modules, and reveals mechanisms underlying cellular dependence on individual modules. As an example of the power of this approach, we discover that the previously unannotated HAPSTR (C16orf72) promotes resilience to diverse stressors as a stress-inducible regulator of the E3 ligase HUWE1. Altogether, we present a broadly applicable framework and interactive tool (http://fireworks.mendillolab.org/) to interrogate biological networks using unbiased genetic screens.


Author(s):  
Andrew F. Roberts ◽  
Elizabeth C. Hunke ◽  
Richard Allard ◽  
David A. Bailey ◽  
Anthony P. Craig ◽  
...  

A new collaborative organization for sea-ice model development, the CICE Consortium, has devised quality control procedures to maintain the integrity of its numerical codes' physical representations, enabling broad participation from the scientific community in the Consortium's open software development environment. Using output from five coupled and uncoupled configurations of the Los Alamos Sea Ice Model, CICE, we formulate quality control methods that exploit common statistical properties of sea-ice thickness, and test for significant changes in model results in a computationally efficient manner. New additions and changes to CICE are graded into four categories, ranging from bit-for-bit amendments to significant, answer-changing upgrades. These modifications are assessed using criteria that account for the high level of autocorrelation in sea-ice time series, along with a quadratic skill metric that searches for hemispheric changes in model answers across an array of different CICE configurations. These metrics also provide objective guidance for assessing new physical representations and code functionality. This article is part of the theme issue ‘Modelling of sea-ice phenomena’.


2014 ◽  
Vol 42 (2) ◽  
pp. 485-490 ◽  
Author(s):  
Charanpreet Kaur ◽  
Ajit Ghosh ◽  
Ashwani Pareek ◽  
Sudhir K. Sopory ◽  
Sneh L. Singla-Pareek

The glyoxalase pathway is required for detoxification of cytotoxic metabolite MG (methylglyoxal) that would otherwise increase to lethal concentrations under adverse environmental conditions. Since its discovery 100 years ago, several roles have been assigned to glyoxalases, but, in plants, their involvement in stress response and tolerance is the most widely accepted role. The plant glyoxalases have emerged as multigene family and this expansion is considered to be important from the perspective of maintaining a robust defence machinery in these sessile species. Glyoxalases are known to be differentially regulated under stress conditions and their overexpression in plants confers tolerance to multiple abiotic stresses. In the present article, we review the importance of glyoxalases in plants, discussing possible roles with emphasis on involvement of the glyoxalase pathway in plant stress tolerance.


2016 ◽  
Vol 4 (4) ◽  
Author(s):  
Rupa Iyer ◽  
Ashish Damania

Exiguobacterium sp. KKBO11, isolated near a wastewater treatment plant in Houston, Texas, USA, possesses a large number of genes involved in stress response and transport critical to survival in adverse environmental conditions. An unusually high copy number of RNA genes also possibly contributes to this microorganism’s versatility by promoting nutrient uptake.


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