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Epigenetics most often denotes changes in a chromosome that affect gene activity and expression, but can also be used to describe any heritable phenotypic change that does not derive from a modification of the genome, such as prions.

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When Waddington coined the term, the physical nature of genes and their role in heredity was not known; he used it as a conceptual model of how genes might interact with their surroundings to produce a phenotype; he used the phrase "epigenetic landscape" as a metaphor for biological development.Epigenetic changes modify the activation of certain genes, but not the genetic code sequence of DNA.The microstructure (not code) of DNA itself or the associated chromatin proteins may be modified, causing activation or silencing.This view encompasses all of the possible developing factors on an organism and how they not only influence the organism and each other, but how the organism also influences its own development.The developmental psychologist Erik Erikson wrote of an epigenetic principle in his book Identity: Youth and Crisis (1968), encompassing the notion that we develop through an unfolding of our personality in predetermined stages, and that our environment and surrounding culture influence how we progress through these stages.A radical epigenetic view (physiological epigenesis) was developed by Paul Wintrebert.

Another variation, probabilistic epigenesis, was presented by Gilbert Gottlieb in 2003.

Such redefinitions however are not universally accepted and are still subject to dispute.

The NIH "Roadmap Epigenomics Project", ongoing as of 2016, uses the following definition: "For purposes of this program, epigenetics refers to both heritable changes in gene activity and expression (in the progeny of cells or of individuals) and also stable, long-term alterations in the transcriptional potential of a cell that are not necessarily heritable." In 2008, a consensus definition of the epigenetic trait, "stably heritable phenotype resulting from changes in a chromosome without alterations in the DNA sequence", was made at a Cold Spring Harbor meeting.

These epigenetic changes may last through cell divisions for the duration of the cell's life, and may also last for multiple generations even though they do not involve changes in the underlying DNA sequence of the organism; One example of an epigenetic change in eukaryotic biology is the process of cellular differentiation.

During morphogenesis, totipotent stem cells become the various pluripotent cell lines of the embryo, which in turn become fully differentiated cells.

The phrase "genetic code" has also been adapted—the "epigenetic code" has been used to describe the set of epigenetic features that create different phenotypes in different cells.