Gene networks

Колчанов, Н. А.; Ananko, E. A.; Kolpakov, Fedor A.; Podkolodnaya, O. A.; Игнатьева, Е. В.; Goryachkovskaya, T. N.; Степаненко, И. Л.

doi:10.1007/bf02759554

Cited by 23 publications

(14 citation statements)

References 40 publications

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“…The significance of the function of each gene critically depends on the rest of the genes in the network and, specially, on how they are globally connected. Thus, the topology of the genetic networks, and not just their constituent genes, are critical for understanding how development works (Waddington, '57;Kolchanov et al, 2000;Wilkins, 2001;Hall, 2003;Rast, 2003;Boldogkoi, 2004;Fraser and Marcotte, 2004;Silver and Rebay, 2005). Thus the morphological changes produced by a new allele would change depending on the rest of the alleles existing in the other genes of the network.…”

Section: Relationship Between the Genotype And Phenotype In Current Dmentioning

confidence: 96%

Developmental constraints vs. variational properties: how pattern formation can help to understand evolution and development

Salazar‐Ciudad

2005

J Exp Zool Pt B

109

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This article suggests that apparent disagreements between the concept of developmental constraints and neo-Darwinian views on morphological evolution can disappear by using a different conceptualization of the interplay between development and selection. A theoretical framework based on current evolutionary and developmental biology and the concepts of variational properties, developmental patterns and developmental mechanisms is presented. In contrast with existing paradigms, the approach in this article is specifically developed to compare developmental mechanisms by the morphological variation they produce and the way in which their functioning can change due to genetic variation. A developmental mechanism is a gene network, which is able to produce patterns in space though the regulation of some cell behaviour (like signalling, mitosis, apoptosis, adhesion, etc.). The variational properties of a developmental mechanism are all the pattern transformations produced under different initial and environmental conditions or IS-mutations. IS-mutations are DNA changes that affect how two genes in a network interact, while T-mutations are mutations that affect the topology of the network itself. This article explains how this new framework allows predictions not only about how pattern formation affects variation, and thus phenotypic evolution, but also about how development evolves by replacement between pattern formation mechanisms. This article presents testable inferences about the evolution of the structure of development and the phenotype under different selective pressures. That is what kind of pattern formation mechanisms, in which relative temporal order, and which kind of phenotypic changes, are expected to be found in development.

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Section: Relationship Between the Genotype And Phenotype In Current Dmentioning

confidence: 96%

Developmental constraints vs. variational properties: how pattern formation can help to understand evolution and development

Salazar‐Ciudad

2005

J Exp Zool Pt B

109

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“…1 The major components of a gene network are the biopolymers DNA, RNA, and proteins; their coordinated synthesis and degradation form the basis for the cell function as a self-reproducing system. In this perspective, the cell can be regarded as a set of individual gene networks controlling particular individual processes.…”

Section: Introductionmentioning

confidence: 99%

On the Chaos in Gene Networks

Лихошвай

Fadeev

Kogai

et al. 2013

J. Bioinform. Comput. Biol.

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The methods for constructing "chaotic" nonlinear systems of differential equations modeling gene networks of arbitrary structure and dimensionality with various types of symmetry are considered. It has been shown that an increase in modality of the functions describing the control of gene expression efficiency allows for a decrease in the dimensionality of these systems with retention of their chaotic dynamics. Three-dimensional "chaotic" cyclic systems are considered. Symmetrical and asymmetrical attractors with "narrow" chaos having a Moebius-like structure have been detected in such systems. As has been demonstrated, a complete symmetry of the systems with respect to permutation of variables does not prevent the emergence of their chaotic dynamics.

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“…The key element of gene network controlling the processes of cell differentiation is an external factor for nuclear genome signal, which activates these groups of interactively expressing genes (Kolchanov et al, 2000). We suggest that the processes of cell ageing, differentiation and division are regulated by cytoplasmic factors.…”

Section: Need For a Self-replicating Controllermentioning

confidence: 87%

Potential role of centrioles in determining the morphogenetic status of animal somatic cells

Tkemaladze¹,

Chichinadze²

2005

Cell Biology International

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Irreversible differentiation (change of morphogenetic status) and programmed death (apoptosis) are observed only in somatic cells. Cell division is the only way by which the morphogenetic status of the offspring cells may be modified. It is known that there is a fixed limit to the number of possible cell divisions, the so-called 'Hayflick limit'. Existing links between cell division, differentiation and apoptosis make it possible to conclude that all these processes could be controlled by a single self-reproducing structure. Potential candidates for this replicable structure in a somatic cell are chromosomes, mitochondria (both contain DNA), and centrioles. Centrioles (diplosome) are the most likely unit that can fully regulate the processes of irreversible differentiation, determination and modification of the morphogenetic status. It may contain differently encoded RNA molecules stacked in a definite order. During mitosis, these RNA molecules are released one by one into the cytoplasm. In the presence of reverse transcriptase and endonuclease, RNA can be embedded in nuclear DNA. This process presumably changes the status of repressed and potentially active genes and, subsequently, the morphogenetic status of a cell.

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Gene networks

Cited by 23 publications

References 40 publications

Developmental constraints vs. variational properties: how pattern formation can help to understand evolution and development

Developmental constraints vs. variational properties: how pattern formation can help to understand evolution and development

On the Chaos in Gene Networks

Potential role of centrioles in determining the morphogenetic status of animal somatic cells

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