Gene-environment interaction in yeast gene expression
April 14, 2008The nature vs. nurture debate is familiar to most people, and modern conclusions usually predict a balance between the two. A new paper published this week in the open-access journal PLoS Biology shows that there is a similar balance between the genes we inherit nature and the environment nurture in determining thousands of traits in yeast.
As we approach the age of personal genomics, in which each of us knows something about the genetic variations we carry, it is important to understand how genes and the environment interact in order to draw medically sound conclusions from the information available e.g. whether exercise can reduce risks that are increased because of a genetic predisposition towards a certain illness.
The phenomenon of gene/environment interaction has been documented before, that the environment affects the ways it genes are expressed so that genes that are on in one condition may be downregulated or switched off in other environments. What the new research, by Leonid Kruglyak and Erin Smith, of Princeton University, adds is the ability to study thousands of gene expression patterns simultaneously, to understand the general properties of these previously poorly understood interactions.
In this research, the individuals are yeast one from the lab and one from the vineyard, which differed genetically and the environment varied between two energy sources: glucose and ethanol. The experiment, then, is to measure how the genetic and the environmental differences interact to alter the gene expression of the yeast cells.
The expression of many genes is under the control of other genes. This paper shows that the environment often has a bigger effect on these regulated genes than on ones that are switched on and off by other, more direct mechanisms. Intriguingly, sometimes a control gene that positively affects another gene in one environment may have the opposite effect in another environment.
Citation: Smith EN, Kruglyak L (2008) Gene environment interaction in yeast gene expression. PLoS Biol 6(4): e83. doi:10.1371/journal.pbio.0060083
Source: Public Library of Science
Nov 19, 2009 |
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Culture Is Biology, It Imprints Genetics, Drives Evolution
Darwinism Corrected To Tomorrow's Comprehension.
Darwinians, It Is Culture That Drives Evolution!
March 16 2008
http://www.physfo...ic=14988&st=165&#entry323376
"By plain common sense it is therefore culture, the ubiqitous biological entity, that drives earth life evolution."
March 1 2008
"Culture Is Biology, It Imprints Genetics"
http://forum.phys...ic=14988&st=165&#entry316631
I. Quotes from "Chimp and human communication trace to same brain region"
http://www.eureka...2108.php
" An area of the brain involved in the planning and production of spoken and signed language in humans plays a similar role in chimpanzee communication.
This might be interpreted in one of two ways:
One interpretation of our results is that chimpanzees have, in essence, a %u2018language-ready brain'. By this, we are suggesting that apes are born with and use the brain areas identified here when producing signals that are part of their communicative repertoire.
Alternatively, one might argue that, because our apes were captive-born and producing communicative signals not seen often in the wild, the specific learning and use of these signals %u2018induced%u2019 the pattern of brain activation we saw. This would suggest that there is tremendous plasticity in the chimpanzee brain, as there is in the human brain, and that the development of certain kinds of communicative signals might directly influence the structure and function of the brain."
II. Quotes from earlier postings in this thread:
Culture Is Biology, It Affects Genetics
The Common Mistake: Genetic Changes Have NOT Made Us Human; Human Culture Has Been Changing Our Genetics.
A. http://www.eureka...0607.php
Are humans evolving faster?
Findings suggest we are becoming more different, not alike.
B. http://www.eureka...0507.php
Genome study places modern humans in the evolutionary fast lane.
C. http://blog.360.y...Q--?cq=1]http://blog.360.y...Q--?cq=1[/url]]http://blog.360.y...Q--?cq=1[/url]&p=207
From my postings way back in 2005, which cites genetic evidence/demonstration of the workings of human cultural evolution:
- From Science, 2 Sept 2005: "Page's team compared human and chimp Ys to see whether either lineage has lost functional genes since they split.
The researchers found that the chimp had indeed suffered the slings and arrows of evolutionary fortune. Of the 16 functional genes in this part of the human Y, chimps had lost the function of five due to mutations. In contrast, humans had all 11 functional genes also seen on the chimp Y. "The human Y chromosome hasn't lost a gene in 6 million years," says Page. "It seems like the demise of the hypothesis of the demise of the Y," says geneticist Andrew Clark of Cornell University in Ithaca, New York.
Chimp's genome has been continuing survival by physiologically adapting to changing environments.
- But look at this: From Science, Vol 309, 16 Sept 2005, Evolving Sequence and Expression:"An analysis of the evolution of both gene sequences and expression patterns in humans and chimpanzees...shows that...surprisingly, genes expressed in the brain have changed more on the human lineage than on the chimpanzee lineage, not only in terms of gene expression but also in terms of amino acid sequences".
Surprisingly...???
Human's genome continued survival mainly by modifying-controling its environment.
- And I suggest that detailed study of other creatures that, like humans, underwent radical change of living circumstances, for example ocean-dwelling mammals, might bring to light unique effects of culture-evolution processes and features of evolutionary implications parallel to those of humans.
D. Chapter II, Life, Tomorrow's Comprehension:
http://blog.360.y...Q--?cq=1]http://blog.360.y...Q--?cq=1[/url]]http://blog.360.y...Q--?cq=1[/url]&p=372
Natural Selection Is A Two Level Interdependent Affair
1) Evolution ensues from genome/genes modifications ("mutations"), inherently ever more of them as new functional options arise for the organism.
2) Modifications of genome's functional capabilities can be explained by the second-stratum organism's culture-life-experience feedbacks to its genome, its prime/base organism. The route-modification selection of a replicating gene, when it is at its alternative-splicing-steps junctions, is biased by the feedback gained by the genome, the parent organism, from the culture-life-experience of its progeny big organism. THIS IS HOW EVOLUTION COMES ABOUT.
3) The challenge now is to figure out the detailed seperate steps involved in introducing and impressing the big organism's experiences (culture) feedbacks on its founding parents' genome's genes, followed by the detailed seperate steps involved in biasing-directing the genes to prefer-select the biased-favored splicing.
4) I find it astonishing that only very few persons, non-professional as well as professional biologists-evolutionists, have the clear conception that selection for survival occurs on two interdependent levels - (a) during the life of the second-stratum progeny organism in its environment, and (b) during the life of its genome, which is also an organism. Most, if not all, persons think - incorrectly - that evolution is about randomly occurring genes-genome modifications ("mutations") followed with selection by survival of the progeny organism in its environment. Whereas actually evolution is the interdependent , interactive and interenhencing selection at both the two above levels.
E. Eventually
Eventually it will be comprehended that things don't just "happen", "mutate", randomly in the base-prime organism, genome, constitution; the capability of the base-prime organisms to "happen" and "mutate" is indeed innate, but things "happen" and "mutate" not randomly but in biased directions, affected by the culture-experience feedback of the second level multi-cell organisms (or the mono-cell communities).
Dov Henis
http://blog.360.y...Q--?cq=1]http://blog.360.y...Q--?cq=1[/url]]http://blog.360.y...Q--?cq=1[/url]