Browse
Submit Data
Databases
API
Help

Dataset Information

33 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Spontaneous symmetry breaking in genome evolution.

ABSTRACT: The quest for evolutionary mechanisms providing separation between the coding (exons) and noncoding (introns) parts of genomic DNA remains an important focus of genetics. This work combines an analysis of the most recent achievements of genomics and fundamental concepts of random processes to provide a novel point of view on genome evolution. Exon sizes in sequenced genomes show a lognormal distribution typical of a random Kolmogoroff fractioning process. This implies that the process of intron incretion may be independent of exon size, and therefore could be dependent on intron-exon boundaries. All genomes examined have two distinctive classes of exons, each with different evolutionary histories. In the framework proposed in this article, these two classes of exons can be derived from a hypothetical ancestral genome by (spontaneous) symmetry breaking. We note that one of these exon classes comprises mostly alternatively spliced exons.

SUBMITTER: Ryabov Y

PROVIDER: S-EPMC2377439 | biostudies-literature | 2008 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Spontaneous symmetry breaking in genome evolution.

Ryabov Yaroslav Y Gribskov Michael M

Nucleic acids research 20080326 8

The quest for evolutionary mechanisms providing separation between the coding (exons) and noncoding (introns) parts of genomic DNA remains an important focus of genetics. This work combines an analysis of the most recent achievements of genomics and fundamental concepts of random processes to provide a novel point of view on genome evolution. Exon sizes in sequenced genomes show a lognormal distribution typical of a random Kolmogoroff fractioning process. This implies that the process of intron ...[more]

PMID: 18367477

Similar Datasets

The origin of a primordial genome through spontaneous symmetry breaking.

Project description:The heredity of a cell is provided by a small number of non-catalytic templates-the genome. How did genomes originate? Here, we demonstrate the possibility that genome-like molecules arise from symmetry breaking between complementary strands of self-replicating molecules. Our model assumes a population of protocells, each containing a population of self-replicating catalytic molecules. The protocells evolve towards maximising the catalytic activities of the molecules to increase their growth rates. Conversely, the molecules evolve towards minimising their catalytic activities to increase their intracellular relative fitness. These conflicting tendencies induce the symmetry breaking, whereby one strand of the molecules remains catalytic and increases its copy number (enzyme-like molecules), whereas the other becomes non-catalytic and decreases its copy number (genome-like molecules). This asymmetry increases the equilibrium cellular fitness by decreasing mutation pressure and increasing intracellular genetic drift. These results implicate conflicting multilevel evolution as a key cause of the origin of genetic complexity.Early molecules of life likely served both as templates and catalysts, raising the question of how functionally distinct genomes and enzymes arose. Here, the authors show that conflict between evolution at the molecular and cellular levels can drive functional differentiation of the two strands of self-replicating molecules and lead to copy number differences between the two.

| S-EPMC5557888 | biostudies-literature

Spontaneous symmetry breaking in polar fluids.

Project description:Spontaneous symmetry breaking and emergent polar order are each of fundamental importance to a range of scientific disciplines, as well as generating rich phase behaviour in liquid crystals (LCs). Here, we show the union of these phenomena to lead to two previously undiscovered polar liquid states of matter. Both phases have a lamellar structure with an inherent polar ordering of their constituent molecules. The first of these phases is characterised by polar order and a local tilted structure; the tilt direction processes about a helix orthogonal to the layer normal, the period of which is such that we observe selective reflection of light. The second new phase type is anti-ferroelectric, with the constituent molecules aligning orthogonally to the layer normal. This has led us to term the phases the SmCPH and SmAAF phases, respectively. Further to this, we obtain room temperature ferroelectric nematic (NF) and SmCPH phases via binary mixture formulation of the novel materials described here with a standard NF compound (DIO), with the resultant materials having melting points (and/or glass transitions) which are significantly below ambient temperature. The new soft matter phase types discovered herein can be considered as electrical analogues of topological structures of magnetic spins in hard matter.

| S-EPMC11239904 | biostudies-literature

Spontaneous symmetry breaking in interdependent networked game.

Project description:Spatial evolution game has traditionally assumed that players interact with direct neighbors on a single network, which is isolated and not influenced by other systems. However, this is not fully consistent with recent research identification that interactions between networks play a crucial rule for the outcome of evolutionary games taking place on them. In this work, we introduce the simple game model into the interdependent networks composed of two networks. By means of imitation dynamics, we display that when the interdependent factor α is smaller than a threshold value α(C), the symmetry of cooperation can be guaranteed. Interestingly, as interdependent factor exceeds α(C), spontaneous symmetry breaking of fraction of cooperators presents itself between different networks. With respect to the breakage of symmetry, it is induced by asynchronous expansion between heterogeneous strategy couples of both networks, which further enriches the content of spatial reciprocity. Moreover, our results can be well predicted by the strategy-couple pair approximation method.

| S-EPMC3924213 | biostudies-literature

Forced and spontaneous symmetry breaking in cell polarization.

Project description:How does breaking the symmetry of an equation alter the symmetry of its solutions? Here, we systematically examine how reducing underlying symmetries from spherical to axisymmetric influences the dynamics of an archetypal model of cell polarization, a key process of biological spatial self-organization. Cell polarization is characterized by nonlinear and non-local dynamics, but we overcome the theory challenges these traits pose by introducing a broadly applicable numerical scheme allowing us to efficiently study continuum models in a wide range of geometries. Guided by numerical results, we discover a dynamical hierarchy of timescales that allows us to reduce relaxation to a purely geometric problem of area-preserving geodesic curvature flow. Through application of variational results, we analytically construct steady states on a number of biologically relevant shapes. In doing so, we reveal non-trivial solutions for symmetry breaking.

| S-EPMC10260237 | biostudies-literature

Spontaneous time-reversal symmetry breaking in twisted double bilayer graphene.

Project description:Twisted double bilayer graphene (tDBG) comprises two Bernal-stacked bilayer graphene sheets with a twist between them. Gate voltages applied to top and back gates of a tDBG device tune both the flatness and topology of the electronic bands, enabling an unusual level of experimental control. Metallic states with broken spin and valley symmetries have been observed in tDBG devices with twist angles in the range 1.2-1.3°, but the topologies and order parameters of these states have remained unclear. We report the observation of an anomalous Hall effect in the correlated metal state of tDBG, with hysteresis loops spanning hundreds of mT in out-of-plane magnetic field (B⊥) that demonstrate spontaneously broken time-reversal symmetry. The B⊥ hysteresis persists for in-plane fields up to several Tesla, suggesting valley (orbital) ferromagnetism. At the same time, the resistivity is strongly affected by even mT-scale values of in-plane magnetic field, pointing to spin-valley coupling or to a direct orbital coupling between in-plane field and the valley degree of freedom.

| S-EPMC9617879 | biostudies-literature

Spontaneous chiral symmetry breaking in a random driven chemical system.

Project description:Living systems have evolved to efficiently consume available energy sources using an elaborate circuitry of chemical reactions which, puzzlingly, bear a strict restriction to asymmetric chiral configurations. While autocatalysis is known to promote such chiral symmetry breaking, whether a similar phenomenon may also be induced in a more general class of configurable chemical systems-via energy exploitation-is a sensible yet underappreciated possibility. This work examines this question within a model of randomly generated complex chemical networks. We show that chiral symmetry breaking may occur spontaneously and generically by harnessing energy sources from external environmental drives. Key to this transition are intrinsic fluctuations of achiral-to-chiral reactions and tight matching of system configurations to the environmental drives, which together amplify and sustain diverged enantiomer distributions. These asymmetric states emerge through steep energetic transitions from the corresponding symmetric states and sharply cluster as highly-dissipating states. The results thus demonstrate a generic mechanism in which energetic drives may give rise to homochirality in an otherwise totally symmetrical environment, and from an early-life perspective, might emerge as a competitive, energy-harvesting advantage.

| S-EPMC9042824 | biostudies-literature

Spontaneous mirror symmetry breaking in heterocatalytically coupled enantioselective replicators.

Project description:Chiral hypercycle replicators (first-order autocatalysis together with mutual cross-catalysis) formed from achiral or racemizing resources may lead to spontaneous mirror symmetry breaking (SMSB) without the need for additional heterochiral inhibition reactions, such as those of the Frank-like models, which are an obstacle for the emergence of evolutionary selection properties. The results indicate that the chemical models for the emergence of primordial autocatalytic self-reproducing systems, of and by themselves, can also explain naturally the emergence of biological homochirality.

| S-EPMC5299794 | biostudies-other

Spontaneous breaking of time-reversal symmetry in topological superconductors.

Project description:We study the behavior of spinless fermions in superconducting state, in which the phases of the superconducting order parameter depend on the direction of the link. We find that the energy of the superconductor depends on the phase differences of the superconducting order parameter. The solutions for the phases corresponding to the energy minimuma, lead to a topological superconducting state with the nontrivial Chern numbers. We focus our quantitative analysis on the properties of topological states of superconductors with different crystalline symmetry and show that the phase transition in the topological superconducting state is result of spontaneous breaking of time-reversal symmetry in the superconducting state. The peculiarities in the chiral gapless edge modes behavior are studied, the Chern numbers are calculated.

| S-EPMC5539255 | biostudies-other

Ultrafast imaging of spontaneous symmetry breaking in a photoionized molecular system.

Project description:The Jahn-Teller effect is an essential mechanism of spontaneous symmetry breaking in molecular and solid state systems, and has far-reaching consequences in many fields. Up to now, to directly image the onset of Jahn-Teller symmetry breaking remains unreached. Here we employ ultrafast ion-coincidence Coulomb explosion imaging with sub-10 fs resolution and unambiguously image the ultrafast dynamics of Jahn-Teller deformations of [Formula: see text] cation in symmetry space. It is unraveled that the Jahn-Teller deformation from C3v to C2v geometries takes a characteristic time of 20 ± 7 fs for this system. Classical and quantum molecular dynamics simulations agree well with the measurement, and reveal dynamics for the build-up of the C2v structure involving complex revival process of multiple vibrational pathways of the [Formula: see text] cation.

| S-EPMC8270947 | biostudies-literature

Spontaneous rotational symmetry breaking in KTaO<sub>3</sub> heterointerface superconductors.

Project description:Broken symmetries play a fundamental role in superconductivity and influence many of its properties in a profound way. Understanding these symmetry breaking states is essential to elucidate the various exotic quantum behaviors in non-trivial superconductors. Here, we report an experimental observation of spontaneous rotational symmetry breaking of superconductivity at the heterointerface of amorphous (a)-YAlO3/KTaO3(111) with a superconducting transition temperature of 1.86 K. Both the magnetoresistance and superconducting critical field in an in-plane field manifest striking twofold symmetric oscillations deep inside the superconducting state, whereas the anisotropy vanishes in the normal state, demonstrating that it is an intrinsic property of the superconducting phase. We attribute this behavior to the mixed-parity superconducting state, which is an admixture of s-wave and p-wave pairing components induced by strong spin-orbit coupling inherent to inversion symmetry breaking at the heterointerface of a-YAlO3/KTaO3. Our work suggests an unconventional nature of the underlying pairing interaction in the KTaO3 heterointerface superconductors, and brings a new broad of perspective on understanding non-trivial superconducting properties at the artificial heterointerfaces.

| S-EPMC10220087 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data