Epigenetics- exploring

[Michaelangelica]

I thought it would be nice to have a thread where we could discuss this emerging field and refine our knowledge to it and post new developments (which seem to be happening weekly!).

I have a young friend, of my daughter's, finishing a PhD in it. She is very excited by it all.

 

I was not sure where to put the thread medicine/ law? ecology, agriculture, space exploration, evolution? economics, ethics, chemistry,history, archeology, physics- as the concept will fundamentally change our understanding of life and will reverberate though all these areas INMHO

 

Something to start the ball rolling (also some good links in "Darwin re-visited)

How epigenetics is changing our fight with disease › Science Features (ABC Science)

In Depth › Science Features

How epigenetics is changing our fight with disease

Sequencing the human genome was supposed to answer our questions about the genetic origins of disease but the burgeoning science of epigenetics is telling us it's a whole lot more complicated.

 

By Jane McCredie

 

 

 

Epigenetics is the science that describes all modifications to genes other than changes to the DNA sequence itself

 

* Audio: Epigenetics - The Science Show (The Science Show)

* Royal jelly triggers queen genes, Science Online, 14 Mar 2008

* Multiple sclerosis research, The Health Report, 22 Jun 2009

* Lamarck's evolution, Ockham's Razor, 04 Jan 2009

 

Decoding the human genome was supposed to answer all our questions about the genetic origins of disease.

 

But six years after the complete genome was sequenced, more evidence than ever suggests it's not just our genes that affect our susceptibility to disease but also our environment. In our battle against disease could we be fighting the wrong adversary?

 

Epigenetics is the science that describes all modifications to genes other than changes to the DNA sequence itself. Epigenetic marks can switch particular genes 'on' or 'off', and this process can have major implications for health.

 

Although epigenetics is a normal part of human development, things can go badly wrong when the marks switch off genes that we need to remain healthy, such as those that fight cancer or regulate our metabolism.

 

While we don't yet fully understand how or why most of the marks operate, scientists believe they are often a response to environmental factors, particularly those we were exposed to in the womb, such as our mother's diet or her exposure to toxins or diseases.

 

With research suggesting a . . .

[Turtle]

i first heard the term last week when i chanced on this program. i'm not yet well enough versed to offer anything other than this link.

 

program page:NOVA | Ghost in Your Genes | PBS

 

transcript: NOVA | Transcripts | Ghost in Your Genes | PBS

MARK MEHLER (Albert Einstein College of Medicine): We're in the midst of probably the biggest revolution in biology that is going to forever transform the way we understand genetics, environment, the way the two interact, what causes disease. It's another level of biology, which, for the first time, really, is up to the task of explaining the biological complexity of life. ...

[lemit]

Epigenetics fascinates me. The intertwining of heredity and environment instead of their mutual exclusivity means to me that the world works the way it should.

 

I'm really excited about this thread. I wish I knew enough to provide information. Right now I'm just going to try to sponge it up. Who knows, maybe something I read here will change me in a genetic way. (Maybe that's stretching it a little. But then, if something is stretched far enough . . . )

 

--lemit

[freeztar]

Epigenetics might not be so new after all.

 

Early 20th Century Evolutionist May Have Discovered Epigenetics

 

A new study into the research of the renowned Lamarckian experimentalist Paul Kammerer may help to end the controversy which has engulfed his research for almost a century. The study, published in The Journal of Experimental Zoology, suggests that far from being a fraud Kammerer may have discovered the field of epigenetics, placing him decades ahead of his contemporaries.

[Turtle]

Epigenetics might not be so new after all.

 

Early 20th Century Evolutionist May Have Discovered Epigenetics

 

summations from my reading of your article:

perhaps he observed some of the effects, but he had no clue as to the chemical nature or workings of these effects. seems that tho his observations were later confirmed, there was fraud in his lab over the genetic experiments and he killed himself over it. :) science daily looooooves their headlines!!

[Michaelangelica]

Epigenetics fascinates me.. . .

Who knows, maybe something I read here will change me in a genetic way. (Maybe that's stretching it a little. But then, if something is stretched far enough . . . )

 

--lemit

LOL :)

 

Epigenetics might not be so new after all.

yes some see it as Lamark's revenge!

In his most controversial experiment, Kammerer forced midwife toads, a species that lives and mates on land, to live in water. Their offspring preferred to live and mate in water and by the third generation he noted that they began to develop black nuptial pads on their forelimbs, a feature common to water dwelling species.

 

In 1926 Kammerer fell into disgrace when it was found that his only remaining fixed specimen had been injected with India ink to produce the appearance of the black nuptial pads. Kammerer's own role in the alleged fraud has never been proven. . .

. . .

Kammerer reported hybrid crosses of treated and untreated toads in which 'parent-of-origin effects' can be observed, a recurrent phenomenon in epigenetics.

Intersting link freeztar, never heard of the guy.

There are a few good links on that page too

Rethinking The Genetic Theory Of Inheritance: Heritability May Not Be Limited To DNA

 

ScienceDaily (Jan. 20, 2009) — Scientists at the Centre for Addiction and Mental Health (CAMH) have detected evidence that DNA may not be the only carrier of heritable information; a secondary molecular mechanism called epigenetics may also account for some inherited traits and diseases. These findings challenge the fundamental principles of genetics and inheritance, and potentially provide a new insight into the primary causes of human diseases.

http://www.sciencedaily.com/releases/2009/01/090118200632.htm

 

Germ cells carry the epigenetic benefits of grandmother's diet

Craig A. Cooney*

Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205

 

 

Environmental influences on epigenetics are important for understanding the mechanisms and inheritance of biological variation. Some of the best models for mammalian epigenetics are the yellow alleles of agouti in mice. Alleles such as Avy produce readily distinguished agouti, yellow, and mottled coat-color epigenetic phenotypes. Dietary and genetic variations during development affect the epigenetic phenotypes of offspring (1, 2). Little is known regarding the gestational timing of dietary treatments to affect epigenetics. Although the epigenetic phenotype is partially maternally, and grandmaternally, inherited (1, 3, 4), transgenerational effects of grandmaternal diets have not been reported. In this issue of PNAS, Cropley et al. (5) report the effects of specific timing of maternal dietary methyl supplementation on the coat color of offspring. Surprisingly, they find that maternal supplementation only during midgestation substantially affects offspring coat color. Importantly, they also find that this effect is inherited by the next generation, presumably through germ-line modifications during grandmaternal supplementation.

 

. . .

 

. . .Lots of technical biology)

 

DNA methylation

 

There is also a grandmaternal effect on inheritance. That is, when mother and grandmother are fully agouti, a higher proportion of offspring have fully agouti coats than when the grandmother has a mottled or yellow phenotype (4). However, the effect of grandmaternal methyl supplementation was unknown. To answer this question,. . .

 

. . . These results demonstrate a transgenerational effect of maternal diet on the F2 generation, and they suggest a mechanism, namely modification of the F1 germ line. The degree of change in offspring phenotype was similar in the F1 and F2 generations, indicating that germ-line Avy silencing may be well maintained through gametogenesis, fertilization, and development. Theirs is the first demonstration that a germ-line epigenetic change can be induced at a specific gene. They provide a mechanism for transgenerational epigenetic effects.

 

. . .

 

. . .. Other grandmaternal effects that appear to be epigenetic include diabetes in rats and humans. Transgenerational diabetes (F1 and F2 generations) can be induced by infusing pregnant rats (P1) with glucose during the last week of pregnancy (third trimester) (15). In humans, maternal (F1) and grandmaternal (P1) non-insulin-dependent diabetes mellitus (NIDDM) is associated with gestational diabetes (F2) (16). At least some of these models involve the recapitulation of epigenetic silencing in each generation (e.g., based on maternal behavior toward offspring; ref. 14) and probably do not require the tenacity of silencing evident in Avy.

 

Epigenetics at particular loci may have evolved to provide a range of phenotypes to suit a range of environmental conditions.

We do not know what range of phenotypes to expect when epigenetic systems that evolved over millions of years respond to new environmental variables such as refined foods, drugs, and xenobiotics. Glucose (15–17) and endocrine disrupters (18) are examples of factors leading to apparent epigenetic transgenerational effects in mammals; however, the genes responsible for the effects are not known. Now Cropley et al. (5) show that methyl donors have transgenerational effects attributed to a known allele, Avy.

 

. . .

 

In humans, the possibility, even the likelihood, that grandmaternal diets contributed to the incidence of obesity and diabetes in the current generation and that today's dietary habits will have effects for generations to come make the work of Cropley et al. (5) especially important.

Their demonstration of a transgenerational effect of midgestational maternal methyl supplementation is a significant advance that should stimulate much needed research in this area.

Germ cells carry the epigenetic benefits of grandmother's diet

Bit of a heavy article to start sorry it just popped on my screen for some bizzare reason.

Given the "English' diet of my forbears it is lucky i am alive at all. Mum used to boil greens for an hour then, when they had lost all their colour, she would add a teaspoon of bi-carb (which i loathed) to "green them back up"!! Might as well eat cardboard.

PS (thinks) At least two generations of (mainly paternal) alcoholics too. Gives one pause.. . .

Both father and grandfathers produced offspring after a world war. I wonder what Wars do to inheritance?

 

methylation is an important word, I can't remember why

[lemit]

I didn't know there were midwife toads. So, "The Wind In The Willows" was right after all?

 

Don't others remember when Toad got Mrs. Toad pregnant and thought the midwife was coming to help Mrs. Toad with the eggs, but was greatly surprised when instead the midwife put all the eggs on his back and insisted he carry them, thus causing him great discomfort whilst driving his brand new auto? It's one of my favorite stories. If you'd like, I can retell it in full sometime.

 

--lemit

[Michaelangelica]

Wiki on Biological methylation

[edit] Epigenetics

 

Methylation contributing to epigenetic inheritance can occur either through DNA methylation or protein methylation.

 

DNA methylation in vertebrates typically occurs at CpG sites (cytosine-phosphate-guanine sites; that is, where a cytosine is directly followed by a guanine in the DNA sequence); this methylation results in the conversion of the cytosine to 5-methylcytosine. The formation of Me-CpG is catalyzed by the enzyme DNA methyltransferase. The bulk of mammalian DNA has about 40% of CpG sites methylated but there are certain areas, know as CpG islands which are GC rich (made up of about 65% CG residues) where none are methylated. These are associated with the promoters of 56% of mammalian genes, including all ubiquitously expressed genes. 1-2% of the human genome are CpG clusters and there is an inverse relationship between CpG methylation and transcriptional activity.

 

Protein methylation typically takes place on arginine or lysine amino acid residues in the protein sequence.[1] Arginine can be methylated once (monomethylated arginine) or twice, with either both methyl groups on one terminal nitrogen (asymmetric dimethylated arginine) or one on both nitrogens (symmetric dimethylated arginine) by peptidylarginine methyltransferases (PRMTs). Lysine can be methylated once, twice or three times by lysine methyltransferases. Protein methylation has been most well studied in the histones. The transfer of methyl groups from S-adenosyl methionine to histones is catalyzed by enzymes known as histone methyltransferases. Histones which are methylated on certain residues can act epigenetically to repress or activate gene expression.[2][3] Protein methylation is one type of post-translational modification.

[edit] Embryonic development

 

In early mammalian development (fertilization to eight-cell stage), the genome is demethylated. From the eight-cell stage to the morula, de novo methylation of the genome occurs, modifying and adding epigenetic information to the genome. By blastula stage, the methylation is complete. This process is referred to as "epigenetic reprogramming"[4]. The importance of methylation was shown in knockout mutants without DNA methyltransferase which all died at the morula stage.[citation needed]

[edit] Postnatal development

 

Increasing evidence is revealing a role of methylation in the interaction of environmental factors with genetic expression. Differences in maternal care during the first 6 days of life in the rat induce differential methylation patterns in some promoter regions and thus influencing gene expression.[5] Furthermore, even-more-dynamic processes such as interleukin signaling have been shown to be regulated by methylation.[6]

[edit] Cancer. . .

Methylation - Wikipedia, the free encyclopedia

Well I HAVE had too much sleep last night and Am suffering from a fuzzy brain. so is it me. or is this bloody hard to understand?

[Michaelangelica]

So, if I save my own seed, eventually i will have plants better adapted to grow in my backyard?

The 'epigenetic' component is like an extra dimension on top of the genetic code of a living organism that is affected by the environment and in turn changes the activity of the genes.

The efficiency of energy production is strongly related to its epigenetic code.

By using a 'smart' selection adapting the epigenetic code, Bayer BioScience's hope is to use the technology in breeding and to develop improved yield varieties.

 

Using this method in rapeseed it has been proved that rapeseed varieties can be selected yielding between 8% and 20% more than the common varieties.

Flemish Researchers Develop Revolutionary Technology For Use In Plant Breeding

 

 

I don't understand how this can be done.

Scientists Take Early Steps Toward Mapping Epigenetic Variability

 

ScienceDaily (Aug. 17, 2009) — Brown University and other scientists have taken the first steps toward mapping epigenetic variability in cells and tissues. Mapping the human epigenome, similar to the human genome project in the 1990s, could someday allow for quicker and more precise disease diagnoses and more targeted treatments of many chronic ailments.

 

Details are published online in the latest edition of PLoS Genetics.

 

Epigenetics, a relatively new endeavor in science, refers to the control of the patterns of gene expression in cells, which gives rise to the necessary differences responsible for creating the complex and interacting tissues in the body.

 

Scientists globally have begun working on a Human Epigenome Project in a bid to compile detailed data documenting, within a person, the epigenetic changes in different types of cells and tissues, something that will complement the already-completed Human Genome Project.

Scientists Take Early Steps Toward Mapping Epigenetic Variability

[JMJones0424]

So, if I save my own seed, eventually i will have plants better adapted to grow in my backyard?

 

Short answer is yes, long answer is far more complicated.

 

Success would depend on many things, most importantly whether or not the seed stock is from a true-breeding line or a hybrid. First generation hybrids are generally marketed because they tend to contain the "best" of both parents, however, offspring of hybrids are extremely variable. For some edible species like apples and avocados, propagation is almost always done by cuttings, as there are no true breeding lines. Unless you have the area or time to plant many thousands of individuals from each of the subsequent generations, and the patience to back cross back to the parent stock in order to maintain desireable traits, you're better off starting with a true breeding line to begin with. Ensure that cross-polination does not occur by bagging a few of the flowers of the variety you want to save seeds from. Without bagging the flowers, wind-pollinated plants will need a setback of a few thousand feet from other varieties of the same species, but insect pollinated plants will need to be at least a few miles (bees have quite a long range) from other varieties to ensure that the seeds you are saving contain the traits you are trying to preserve and enhance. It generally takes at least five generations of back-crossing and selection of the best individuals among thousands from each generation in order to produce a new true-breeding line. However, adaptation of a true breeding line to your environment can slowly be accomplished with relatively low numbers of individuals per generation, as long as you are diligent in selecting a few primary traits to monitor and always save seed for the next generation from the plant with the best expression of those traits.

 

I am not sure how epigenetics plays a role in trait expression, but it seems to me that it is part of the underlying mechanism that has always been there, but until recently has not been understood or even imagined. I do not see how hobby-level gardeners would be able to incorporate any new techniques with this knowledge though.

 

It sure would be nice though, if you could do something simple like pH shocking parent stock at a specific stage of seed development in order to increase the expression of a desireable trait.

[HydrogenBond]

The DNA is the like hard drive of the cell. It contains all the data, programs and processes for the cell. But like a computer, once processes and programs are active, they can alter the contents of the hard drive, which is this case is done via epi-genetics.

 

If you were a soldier interacting in the field, one would have learned procedures for dealing with a wide range of anticipated situations. But you can't anticipate everything in that one book of procedures. Built into the DNA hard drive are the common procedures for that cell. Real time improvisation, is done with epi-genetics.

 

Sometimes the cell may need to alter the existing procedures to deal with the stress. Turning genes off via methylation, is one of the many options for adapting on the fly. This could be part of an energy saver mode. Finite resources need to be diverted, when trying to deal with an unknown stress on the fly.

 

We are being very careful to keep the two effects separate, genetic and epi-genetics, due to the philosophical wall. But I will take it one step further, can epi-genetics also be used to alter the hard drive procedures, in more than a random way? Life not only tries to adjusts to any stress in real time, but eventually adapts a routine, which we call selective advantage. Satisfying unknowns on the fly, will often lead to new things being written in the next book of procedures.

[lawcat]

So, if I am understanding correctly, the idea is simply to turn off undesirable genes? (Not to reengineer genes, but to simply turn them off.)

 

So, the premise is, the species are what they are, and they have some undesirable genetic traits. To make the species better, we should turn those bad genes off?

[freeztar]

So, if I am understanding correctly, the idea is simply to turn off undesirable genes? (Not to reengineer genes, but to simply turn them off.)

 

Or on...and it doesn't have to be undesirable genes.

So, the premise is, the species are what they are, and they have some undesirable genetic traits. To make the species better, we should turn those bad genes off?

 

What premise?

[Michaelangelica]

Short answer is yes, long answer is far more complicated.

. I do not see how hobby-level gardeners would be able to incorporate any new techniques with this knowledge though.

 

It sure would be nice though, if you could do something simple like pH shocking parent stock at a specific stage of seed development in order to increase the expression of a desirable trait.

Laving aside hybrids which as you say increases the complexity, just growing sage in my garden for ten years saving the seed and replanting it every year MAY result in epigenetic changes

I choose sage as I am climate zone 9. Sage is viable up to 8 Then it gets picky--and usually dies on me. So if i save my seed eventually. . .?

 

I had a friend who was "re-native-ing" her small farm. She was after a particular native grass seed that used to grow on her farm. Eventually she found some in Queensland about 2,000 miles north. She grew it but it never thrived. She later found that the reason was that it was blooming about 6-8 weeks earlier than its native pollinators would appear locally.

ISTM that the grass had adapted to its warmer northern climate. Bringing it back however it was out of synch. with the environmental processes around it!

[Moontanman]

Coral farming shows the effects of epigenetics. Coral collected from the wild is much harder to grow in aquaria than coral that has been grown over many years and divided by "fraging" As the coral is grown in aquariums it slowly adapts to the conditions and grows better and better. Since there is no sexual reproduction involved but only cutting pieces from one piece of coral and effectively cloning the coral epigenes would seem to explain how coral that has been divided many times in captivity and grown this way over many years adapts to the condition of aquaria much better than wild caught coral. Some times even the form of the corals change even though it is genetically identical to the original wild collected coral.

[lemit]

So, if I save my own seed, eventually i will have plants better adapted to grow in my backyard?

 

 

No, but maybe you can father lots of children.

 

But seriously, I'm curious about something. Is epigenesis the process of mutation described so luridly--and improbably--by the Japanese and American movies of the 'Fifties? Instead of giant insects or shrinking humans, are we seeing an increase in asthma and possibly in autism, as well as lots of new flu varieties?

 

If I am making sense here--an unlikely prospect--what do we do in this undramatic but potentially new environment of many potential environments, in which our immune systems are increasingly put at risk and are in turn putting us at risk?

 

Thanks. (And sorry about the joke.)

 

--lemit

[Michaelangelica]

I don't often leave myself open to such jokes; but when I do I never get away with it here! LOL

 

No i don't see it as mutations although the "jumping genes" seem to be a factor in this. Some of the "geography' and 'mechanics" of the gene is a bit beyond me.

It seems to me Epigenetics is a way for DNA to change far more rapidly than we ever thought possible (in 1-2 generations) in response to environmental change.

Does this mean that pants will adapt quickly to global Warming/Climate Change? I don't know--you might assume so-- but it many cases, reported, that does NOT seem to be the case

 

PS

i just Googled "Are plants adapting to climate change?"

and got

 

Animals and Plants Adapting to Climate Change

By Ker Than, Special to LiveScience

posted: 21 June, 2005

 

 

Land animals

 

Reindeer are expected to disappear from large portions of their current range by the end of the century.

 

Marmots are ending their hibernations about three weeks earlier than they did 30 years ago.

 

Canadian red squirrels are breeding about 18 days earlier.

 

Red foxes are spreading northward, encroaching on territory normally occupied by their artic cousins.

 

North American Fowler's toads are breeding six days later than they did a decade ago.

 

Polar bears today are thinner and less healthy than those of 20 years ago.

. . . . . .

Plants

 

Some plants are thriving in areas where their growth was limited before, thanks to temperature changes that provide more water, heat and sunlight.

 

American flowering plants like columbines and wild geraniums are blooming earlier than before.

http://www.livescience.com/environment/050621_warming_list.html

and

Some Plants Can Adapt To Widespread Climate Change

 

ScienceDaily (July 9, 2008) — While many plant species move to a new location or go extinct as a result of climate change, grasslands clinging to a steep, rocky dale-side in Northern England seem to defy the odds and adapt to long-term changes in temperature and rainfall

http://www.sciencedaily.com/releases/2008/07/080708155608.htm

So why some, and not others? Always the $64 question in evolution?!