scholarly journals Physics takes another stab at biological design principles

2005 ◽  
Vol 1 (1) ◽  
Author(s):  
Daniil Zhuravel ◽  
Mads Kærn
Keyword(s):  
Design Principles ◽  
Biological Design

Biological Design Principles of Complex Feedback Modules in the E. coli Ammonia Assimilation System

2011 ◽  
Vol 18 (1) ◽  
pp. 53-90 ◽  
Author(s):  
Koichi Masaki ◽  
Kazuhiro Maeda ◽  
Hiroyuki Kurata
Keyword(s):  
Feedback Control ◽  
Design Principles ◽  
Cellular Systems ◽  
Fine Tuning ◽  
Ammonia Assimilation ◽  
Control Module ◽  
E Coli ◽  
Biological Design ◽  
Modular Structures ◽  
Assimilation System

To synthesize natural or artificial life, it is critically important to understand the design principles of how biochemical networks generate particular cellular functions and evolve complex systems in comparison with engineering systems. Cellular systems maintain their robustness in the face of perturbations arising from environmental and genetic variations. In analogy to control engineering architectures, the complexity of modular structures within a cell can be attributed to the necessity of achieving robustness. To reveal such biological design, the E. coli ammonia assimilation system is analyzed, which consists of complex but highly structured modules: the glutamine synthetase (GS) activity feedback control module with bifunctional enzyme cascades for catalyzing reversible reactions, and the GS synthesis feedback control module with positive and negative feedback loops. We develop a full-scale dynamic model that unifies the two modules, and we analyze its robustness and fine tuning with respect to internal and external perturbations. The GS activity control is added to the GS synthesis module to improve its transient response to ammonia depletion, compensating the tradeoffs of each module, but its robustness to internal perturbations is lost. These findings suggest some design principles necessary for the synthesis of life.

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.

Special issue on biological design principles

2011 ◽  
Vol 231 (1) ◽  
pp. 1-2 ◽  
Author(s):  
Rui Alves ◽  
Albert Sorribas
Keyword(s):  
Design Principles ◽  
Special Issue ◽  
Biological Design

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.

Phenotype-centric modeling for elucidation of biological design principles

2018 ◽  
Vol 455 ◽  
pp. 281-292 ◽  
Author(s):  
Miguel A. Valderrama-Gómez ◽  
Rebecca E. Parales ◽  
Michael A. Savageau
Keyword(s):  
Design Principles ◽  
Biological Design

Systematic Reverse Engineering of Biological Systems

2007 ◽  
Author(s):  
Jamal O. Wilson ◽  
David Rosen
Keyword(s):  
Reverse Engineering ◽  
Biological Systems ◽  
Variable Stiffness ◽  
Design Principles ◽  
Efficient Solutions ◽  
Engineering Systems ◽  
Biological Design ◽  
Engineering Problems ◽  
Airplane Wing ◽  
Current Engineering

The duality between biological systems and engineering systems exists in the pursuit of economical and efficient solutions. By adapting biological design principles, nature’s technology can be harnessed. In this paper, we present a systematic method for reverse engineering biological systems to assist the designer in searching for solutions in nature to current engineering problems. Specifically, we present methods for decomposing the physical and functional biological architectures, representing dynamic functions, and abstracting biological design principles to guide conceptual design. We illustrate this method with an example of the design of a variable stiffness skin for a morphable airplane wing based on the mutable connective tissue of the sea cucumber.

scholarly journals Bio-based Wrinkled Surfaces Harnessed from Biological Design Principles of Wood and Peroxidase Activity

ChemSusChem ◽  
2015 ◽  
Vol 8 (22) ◽  
pp. 3892-3896 ◽  
Author(s):  
Hironori Izawa ◽  
Noriko Okuda ◽  
Shinsuke Ifuku ◽  
Minoru Morimoto ◽  
Hiroyuki Saimoto ◽  
...  
Keyword(s):  
Peroxidase Activity ◽  
Design Principles ◽  
Biological Design

scholarly journals Synthetic Biology: Integrated Gene Circuits

Science ◽  
2011 ◽  
Vol 333 (6047) ◽  
pp. 1244-1248 ◽  
Author(s):  
Nagarajan Nandagopal ◽  
Michael B. Elowitz
Keyword(s):  
Synthetic Biology ◽  
Biological Systems ◽  
Design Principles ◽  
Genetic Circuits ◽  
Major Goal ◽  
Gene Circuits ◽  
Biological Design ◽  
Cellular Processes ◽  
Regulatory Architecture ◽  
New Generation

A major goal of synthetic biology is to develop a deeper understanding of biological design principles from the bottom up, by building circuits and studying their behavior in cells. Investigators initially sought to design circuits “from scratch” that functioned as independently as possible from the underlying cellular system. More recently, researchers have begun to develop a new generation of synthetic circuits that integrate more closely with endogenous cellular processes. These approaches are providing fundamental insights into the regulatory architecture, dynamics, and evolution of genetic circuits and enabling new levels of control across diverse biological systems.

scholarly journals Systems Analysis for Peptide Systems Chemistry

Life ◽  
2019 ◽  
Vol 9 (3) ◽  
pp. 55
Author(s):  
Martha A. Grover ◽  
Ming-Chien Hsieh ◽  
David G. Lynn
Keyword(s):  
Model Simulation ◽  
Reaction Network ◽  
Design Principles ◽  
Chemistry Curriculum ◽  
Biological Design ◽  
Rate Limiting Step ◽  
Systems Chemistry ◽  
Assembly Kinetics ◽  
Construction Model ◽  
Rate Limiting

Living systems employ both covalent chemistry and physical assembly to achieve complex behaviors. The emerging field of systems chemistry, inspired by these biological systems, attempts to construct and analyze systems that are simpler than biology, while still embodying biological design principles. Due to the multiple phenomena at play, it can be difficult to predict which phenomena will dominate and when. Conversely, there may be no single rate-limiting step, but rather a reaction network that is difficult to intuit from a purely experimental approach. Mathematical modeling can help to sort out these issues, although it can be challenging to build such models, especially for assembly kinetics. Numerical and statistical methods can play an important role to facilitate the synergistic and iterative use of modeling and experiment, and should be part of a systems chemistry curriculum. Three case studies are presented here, from our work in peptide-based systems, to illustrate some of the tools available for model construction, model simulation, and experimental design. Examples are provided in which these tools help to evaluate hypotheses, uncover design principles, and design new experiments.

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