scholarly journals Characterization of fundamental networks

2019 ◽  
Vol 150 (1) ◽  
pp. 453-474
Author(s):  
Manuela A. D. Aguiar ◽  
Ana P. S. Dias ◽  
Pedro Soares
Keyword(s):  
Network Architecture ◽  
Cell System ◽  
Hidden Symmetries ◽  
Network Construction ◽  
Cell Systems ◽  
Cell Network ◽  
A Cell ◽  
Network Synchrony ◽  
Coupled Cell Systems

AbstractIn the framework of coupled cell systems, a coupled cell network describes graphically the dynamical dependencies between individual dynamical systems, the cells. The fundamental network of a network reveals the hidden symmetries of that network. Subspaces defined by equalities of coordinates which are flow-invariant for any coupled cell system consistent with a network structure are called the network synchrony subspaces. Moreover, for every synchrony subspace, each network admissible system restricted to that subspace is a dynamical system consistent with a smaller network called a quotient network. We characterize networks such that: the network is a subnetwork of its fundamental network, and the network is a fundamental network. Moreover, we prove that the fundamental network construction preserves the quotient relation and it transforms the subnetwork relation into the quotient relation. The size of cycles in a network and the distance of a cell to a cycle are two important properties concerning the description of the network architecture. In this paper, we relate these two architectural properties in a network and its fundamental network.

scholarly journals The lattice of balanced equivalence relations of a coupled cell network

2007 ◽  
Vol 143 (1) ◽  
pp. 165-183 ◽  
Author(s):  
IAN STEWART
Keyword(s):  
Network Architecture ◽  
Linear Chain ◽  
Cell System ◽  
Equivalence Relations ◽  
Locally Finite ◽  
Cell Network ◽  
Equality Relation ◽  
Coupled Cell Systems ◽  
Infinite Networks

AbstractA coupled cell system is a collection of dynamical systems, or ‘cells’, that are coupled together. The associated coupled cell network is a labelled directed graph that indicates how the cells are coupled, and which cells are equivalent. Golubitsky, Stewart, Pivato and Török have presented a framework for coupled cell systems that permits a classification of robust synchrony in terms of the concept of a ‘balanced equivalence relation’, which depends solely on the network architecture. In their approach the network is assumed to be finite. We prove that the set of all balanced equivalence relations on a network forms a lattice, in the sense of a partially ordered set in which any two elements have a meet and a join. The partial order is defined by refinement. Some aspects of the theory make use of infinite networks, so we work in the category of networks of ‘finite type’, a class that includes all locally finite networks. This context requires some modifications to the standard framework. As partial compensation, the lattice of balanced equivalence relations can then be proved complete. However, the intersection of two balanced equivalence relations need not be balanced, as we show by a simple example, so this lattice is not a sublattice of the lattice of all equivalence relations with its usual operations of meet and join. We discuss the structure of this lattice and computational issues associated with it. In particular, we describe how to determine whether the lattice contains more than the equality relation. As an example, we derive the form of the lattice for a linear chain of identical cells with feedback.

Proteomic Characterization of Protein-Protein Interactions

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Veenstra TD ◽  
Keyword(s):  
Protein Interactions ◽  
Disease Diagnosis ◽  
Cell System ◽  
Protein Protein Interactions ◽  
Novel Technologies ◽  
Cell Functions ◽  
Single Protein ◽  
A Cell ◽  
Molecular Components

Identifying all the molecular components within a living cell is the first step into understanding how it functions. To further understand how a cell functions requires identifying the interactions that occur between these components. This fact is especially relevant for proteins. No protein within a human cell functions on its own without interacting with another biomolecule - usually another protein. While Protein-Protein Interactions (PPI) have historically been determined by examining a single protein per study, novel technologies developed over the past couple of decades are enabling high-throughput methods that aim to describe entire protein networks within cells. In this review, some of the technologies that have led to these developments are described along with applications of these techniques. Ultimately the goal of these technologies is to map out the entire circuitry of PPI within human cells to be able to predict the global consequences of perturbations to the cell system. This predictive capability will have major impacts on the future of both disease diagnosis and treatment.

scholarly journals Metabolic characterization of cell systems used in in vitro toxicology testing: Lung cell system BEAS-2B as a working example

2013 ◽  
Vol 27 (6) ◽  
pp. 1719-1727 ◽  
Author(s):  
Carolina Garcia-Canton ◽  
Emmanuel Minet ◽  
Arturo Anadon ◽  
Clive Meredith
Keyword(s):  
Cell System ◽  
In Vitro Toxicology ◽  
Cell Systems

Characterization of the Murine Platelet IIb Gene and Encoded cDNA

Blood ◽  
1999 ◽  
Vol 94 (11) ◽  
pp. 3947-3950 ◽  
Author(s):  
Michael A. Thornton ◽  
Mortimer Poncz
Keyword(s):  
Amino Acids ◽  
Comparative Analysis ◽  
Platelet Aggregation ◽  
Ligand Binding ◽  
Human Gene ◽  
Cell System ◽  
Biological Studies ◽  
A Cell

Abstract The IIb/β3 receptor is central to platelet aggregation. Biological studies of this receptor have been limited by the inability to reproduce IIb/β3 function in a cell system. Increasingly, efforts are being directed at studies of this receptor in mice models. The structure of murine (m) β3 has been reported. We now have sequenced the mIIb gene and found that it has the same size and organization as the human gene. The exon/intron borders are reported here, as are the distances between exons. mIIb protein is 1,033 amino acids (aa), 7 and 5 aa shorter than human (h) and rodent (r) IIb, respectively, with 79% and 90% homology, respectively. As part of the comparative analysis of the 3 known IIb chains included in this report, we found that a particular region of the IIb N-terminal β-propeller is highly conserved and speculate that it directly participates in ligand binding.

scholarly journals Collective Oscillations in Coupled-Cell Systems

2021 ◽  
Vol 83 (6) ◽  
Author(s):  
Kuan-Wei Chen ◽  
Chih-Wen Shih
Keyword(s):  
Hopf Bifurcation ◽  
Single Cell ◽  
Single Cells ◽  
System Modeling ◽  
Average Frequency ◽  
Cell System ◽  
Coupled Systems ◽  
Cell Systems ◽  
Coupled Cell Systems ◽  
The One

AbstractWe investigate oscillations in coupled systems. The methodology is based on the Hopf bifurcation theorem and a condition extended from the Routh–Hurwitz criterion. Such a condition leads to locating the bifurcation values of the parameters. With such an approach, we analyze a single-cell system modeling the minimal genetic negative feedback loop and the coupled-cell system composed by these single-cell systems. We study the oscillatory properties for these systems and compare these properties between the model with Hill-type repression and the one with protein-sequestration-based repression. As the parameters move from the Hopf bifurcation value for single cells to the one for coupled cells, we compute the eigenvalues of the linearized systems to obtain the magnitude of the collective frequency when the periodic solution of the coupled-cell system is generated. Extending from this information on the parameter values, we further compute and compare the collective frequency for the coupled-cell system and the average frequency of the decoupled individual cells. To compare these scenarios with other biological oscillators, we perform parallel analysis and computations on a segmentation clock model.

Characterization of the Murine Platelet IIb Gene and Encoded cDNA

Blood ◽  
1999 ◽  
Vol 94 (11) ◽  
pp. 3947-3950
Author(s):  
Michael A. Thornton ◽  
Mortimer Poncz
Keyword(s):  
Amino Acids ◽  
Comparative Analysis ◽  
Platelet Aggregation ◽  
Ligand Binding ◽  
Human Gene ◽  
Cell System ◽  
Biological Studies ◽  
A Cell

The IIb/β3 receptor is central to platelet aggregation. Biological studies of this receptor have been limited by the inability to reproduce IIb/β3 function in a cell system. Increasingly, efforts are being directed at studies of this receptor in mice models. The structure of murine (m) β3 has been reported. We now have sequenced the mIIb gene and found that it has the same size and organization as the human gene. The exon/intron borders are reported here, as are the distances between exons. mIIb protein is 1,033 amino acids (aa), 7 and 5 aa shorter than human (h) and rodent (r) IIb, respectively, with 79% and 90% homology, respectively. As part of the comparative analysis of the 3 known IIb chains included in this report, we found that a particular region of the IIb N-terminal β-propeller is highly conserved and speculate that it directly participates in ligand binding.

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