scholarly journals Maximization of information transmission influences selection of native phosphorelay architectures

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11558
Author(s):  
Rui Alves ◽  
Baldiri Salvadó ◽  
Ron Milo ◽  
Ester Vilaprinyo ◽  
Albert Sorribas
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Signal Transduction ◽  
Bacillus Subtilis ◽  
Mathematical Models ◽  
Information Transmission ◽  
Environmental Changes ◽  
Design Principles ◽  
Biological Design ◽  
Parameter Values ◽  
Selection Of

Phosphorelays are signal transduction circuits that sense environmental changes and adjust cellular metabolism. Five different circuit architectures account for 99% of all phosphorelay operons annotated in over 9,000 fully sequenced genomes. Here we asked what biological design principles, if any, could explain selection among those architectures in nature. We began by studying kinetically well characterized phosphorelays (Spo0 of Bacillus subtilis and Sln1 of Saccharomyces cerevisiae). We find that natural circuit architecture maximizes information transmission in both cases. We use mathematical models to compare information transmission among the architectures for a realistic range of concentration and parameter values. Mapping experimentally determined phosphorelay protein concentrations onto that range reveals that the native architecture maximizes information transmission in sixteen out of seventeen analyzed phosphorelays. These results suggest that maximization of information transmission is important in the selection of native phosphorelay architectures, parameter values and protein concentrations.

scholarly journals What influences selection of native phosphorelay architectures?

2020 ◽  
Author(s):  
Rui Alves ◽  
Baldiri Salvado ◽  
Ron Milo ◽  
Ester Vilaprinyo ◽  
Albert Sorribas
Keyword(s):  
Information Transmission ◽  
Clustering Analysis ◽  
Environmental Changes ◽  
Metabolic Cost ◽  
Data Driven ◽  
Protein Abundance ◽  
Biological Design ◽  
Natural Architecture ◽  
Parameter Values ◽  
Selection Of

AbstractPhosphorelays are signal transduction circuits that combine four different phosphorylatable protein domains for sensing environmental changes and use that information to adjust cellular metabolism to the new conditions in the milieu. Five alternative circuit architectures account for more than 99% of all phosphorelay operons annotated in over 9000 fully sequenced genomes, with one of those architectures accounting for more than 72% of all cases.Here we asked if there are biological design principles that explain the selection of preferred phosphorelay architectures in nature and what might those principles be. We created several types of data-driven mathematical models for the alternative phosphorelay architectures, exploring the dynamic behavior of the circuits in concentration and parameter space, both analytically and through over 108 numerical simulations. We compared the behavior of architectures with respect to signal amplification, speed and robustness of the response, noise in the response, and transmission of environmental information to the cell.Clustering analysis of massive Monte Carlo simulations suggests that either information transmission or metabolic cost could be important in selecting the architecture of the phosphorelay. A more detailed study using models of kinetically well characterized phosphorelays (Spo0 of Bacillus subtilis and Sln1-Ypd1-Ssk1-Skn7 of Saccharomyces cerevisiae) shows that information transmission is maximized by the natural architecture of the phosphorelay. In view of this we analyze seventeen additional phosphorelays, for which protein abundance is available but kinetic parameters are not. The architectures of 16 of these are also consistent with maximization of information transmission.Our results highlight the complexity of the genotype (architecture, parameter values, and protein abundance) to phenotype (physiological output of the circuit) mapping in phosphorelays. The results also suggest that maximizing information transmission through the circuit is important in the selection of natural circuit genotypes.

scholarly journals Real-Time 3D Imaging at the Single Molecule Level of Signal Transduction in Saccharomyces CerevisiÆ Responding to Environmental Changes

2016 ◽  
Vol 110 (3) ◽  
pp. 145a
Author(s):  
Erik G. Hedlund ◽  
Sviatlana Shashkova ◽  
Adam J.M. Wollman ◽  
Stefan Hohmann ◽  
Mark C. Leake
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Signal Transduction ◽  
Real Time ◽  
Single Molecule ◽  
3D Imaging ◽  
Environmental Changes ◽  
Single Molecule Level

scholarly journals Mechanistic Modeling of Biochemical Systems Without A Priori Parameter Values Using the Design Space Toolbox v.3.0

2020 ◽  
Author(s):  
Miguel Á. Valderrama-Gómez ◽  
Jason G. Lomnitz ◽  
Rick A. Fasani ◽  
Michael A. Savageau
Keyword(s):  
Design Space ◽  
A Priori ◽  
Design Principles ◽  
Mechanistic Modeling ◽  
Design And Optimization ◽  
Biological Design ◽  
Biological Phenomena ◽  
Biochemical Systems ◽  
Space Formalism ◽  
Parameter Values

SummaryMechanistic models of biochemical systems provide a rigorous kinetics-based description of various biological phenomena. They are indispensable to elucidate biological design principles and to devise and engineer systems with novel functionalities. To date, mathematical analysis and characterization of these models remain a challenging endeavor, the main difficulty being the lack of information for most system parameters. Here, we introduce the Design Space Toolbox v.3.0 (DST3), a software implementation of the Design Space formalism that enables mechanistic modeling of complex biological processes without requiring previous knowledge of the parameter values involved. This is achieved by making use of a phenotype-centric modeling approach, in which the system is first decomposed into a series of biochemical phenotypes. Parameter values realizing phenotypes of interest are predicted in a second step. DST3 represents the most generally applicable implementation of the Design Space formalism to date and offers unique advantages over earlier versions. By expanding the capabilities of the Design Space formalism and streamlining its distribution, DST3 represents a valuable tool for elucidating biological design principles and guiding the design and optimization of novel synthetic circuits.

The Study of Bacillus Subtils Antimicrobial Activity on Some of the Pathological Isolates

2019 ◽  
Vol 9 (02) ◽  
Author(s):  
Hussein A Kadhum ◽  
Thualfakar H Hasan2
Keyword(s):  
Staphylococcus Aureus ◽  
Pseudomonas Aeruginosa ◽  
Antimicrobial Activity ◽  
Bacillus Subtilis ◽  
Bacterial Growth ◽  
Broad Spectrum ◽  
Inhibitory Activity ◽  
Bacterial Pathogens ◽  
Inhibitory Ability ◽  
Selection Of

The study involved the selection of two isolates from Bacillus subtilis to investigate their inhibitory activity against some bacterial pathogens. B sub-bacteria were found to have a broad spectrum against test bacteria such as Staphylococcus aureus and Pseudomonas aeruginosa. They were about 23-30 mm and less against Klebsiella sp. The sensitivity of some antibodies was tested on the test samples. The results showed that the inhibitory ability of bacterial growth in the test samples using B. subtilis extract was more effective than the antibiotics used.

Studying noise immunity of radio information transmission systems with noise-like phase-shift keyed signals and synchronization delay errors

2019 ◽  
pp. 105-113
Author(s):  
G. N. Maltsev ◽  
A. V. Evteev
Keyword(s):  
Phase Shift ◽  
Information Transmission ◽  
Noise Immunity ◽  
Tracking System ◽  
Tracking Error ◽  
Information Symbol ◽  
Transmission Systems ◽  
Synchronization System ◽  
Correlation Receiver ◽  
Selection Of

Introduction: Radio information transmission systems with noise-like phase-shift keyed signals based on pseudo-random sequences have potential noise immunity provided by accurately tracking the delay of the received signal in the correlation receiver. When working with moving objects, the delay of the received signal varies continuously, and the reception quality for noise-like phase-shifted signals highly depends on the synchronization system operation and on the accuracy of estimating the received signal delay by the tracking system. To ensure the required signal reception quality, it is necessary to provide an informed choice of tracking system parameters, taking into account their effects, which are the random and systematic components of the delay tracking error, on the selected noise immunity indicator.Purpose: Analyzing how the errors in tracking the delay of a received phase-shift keyed signal based on a pseudorandom sequence by the synchronization system of a radio information transmission system can affect the probability of erroneous reception of an information symbol.Results: The calculation method was used to obtain families of dependencies of the probability of erroneous reception of an information symbol on the signal-noise ratio (SNR), and the values of the random and systematic components of the delay tracking error which are normalized to the capture band of the correlation receiver. It has been shown that at a fixed SNR, the values of the random and systematic components of the delay tracking error are critical for the erroneous reception probability. In all the cases discussed, all the dependencies are characterized by a slow change of the erroneous reception probability while the synchronization errors within the area of small SNR have fixed values. As the SNR value grows, the erroneous reception probability rapidly drops. To ensure the specified signal reception quality and the reliability of the selection of information symbols and messages in a radio information transmission system with noise-like phase-manipulated signals, its synchronization system requires a joint selection of the tracking system parameters, taking into account the limitations imposed by the operating conditions and technical implementation features.Practical relevance: The obtained results can be used in noise immunity analysis of radio information transmission systems with noise-like phase-shift keyed signals in a wide range of communication conditions, and in providing technical solutions for synchronization systems ensuring the required quality of signal reception.

Evolution and Selection of Quantitative Traits

2018 ◽  
Author(s):  
Bruce Walsh ◽  
Michael Lynch
Keyword(s):  
Mathematical Models ◽  
Quantitative Genetics ◽  
Complex Traits ◽  
Evolutionary Biology ◽  
Quantitative Traits ◽  
Specific Gene ◽  
Real World Data ◽  
Holistic Treatment ◽  
Genetics And Genomics ◽  
Selection Of

Quantitative traits—be they morphological or physiological characters, aspects of behavior, or genome-level features such as the amount of RNA or protein expression for a specific gene—usually show considerable variation within and among populations. Quantitative genetics, also referred to as the genetics of complex traits, is the study of such characters and is based on mathematical models of evolution in which many genes influence the trait and in which non-genetic factors may also be important. Evolution and Selection of Quantitative Traits presents a holistic treatment of the subject, showing the interplay between theory and data with extensive discussions on statistical issues relating to the estimation of the biologically relevant parameters for these models. Quantitative genetics is viewed as the bridge between complex mathematical models of trait evolution and real-world data, and the authors have clearly framed their treatment as such. This is the second volume in a planned trilogy that summarizes the modern field of quantitative genetics, informed by empirical observations from wide-ranging fields (agriculture, evolution, ecology, and human biology) as well as population genetics, statistical theory, mathematical modeling, genetics, and genomics. Whilst volume 1 (1998) dealt with the genetics of such traits, the main focus of volume 2 is on their evolution, with a special emphasis on detecting selection (ranging from the use of genomic and historical data through to ecological field data) and examining its consequences. This extensive work of reference is suitable for graduate level students as well as professional researchers (both empiricists and theoreticians) in the fields of evolutionary biology, genetics, and genomics. It will also be of particular relevance and use to plant and animal breeders, human geneticists, and statisticians.

Sign in / Sign up

Export Citation Format

Share Document