The Epigenetics Revolution

This epigentics book looks interesting. I'll order a copy today.

The Epigenetics Revolution: How Modern Biology Is Rewriting Our Understanding of Genetics, Disease, and Inheritance by Nessa Carey

Epigenetics can potentially revolutionize our understanding of the structure and behavior of biological life on Earth. It explains why mapping an organism's genetic code is not enough to determine how it develops or acts and shows how nurture combines with nature to engineer biological diversity. Surveying the twenty-year history of the field while also highlighting its latest findings and innovations, this volume provides a readily understandable introduction to the foundations of epigenetics.

Nessa Carey, a leading epigenetics researcher, connects the field's arguments to such diverse phenomena as how ants and queen bees control their colonies; why tortoiseshell cats are always female; why some plants need cold weather before they can flower; and how our bodies age and develop disease. Reaching beyond biology, epigenetics now informs work on drug addiction, the long-term effects of famine, and the physical and psychological consequences of childhood trauma. Carey concludes with a discussion of the future directions for this research and its ability to improve human health and well-being.

 Biography
Here's the official version...
Nessa Carey has a virology PhD from the University of Edinburgh and is a former Senior Lecturer in Molecular Biology at Imperial College, London. She has worked in the biotech and pharmaceutical industry for ten years. She lives in Bedfordshire and this is her first book.
And what else?
After leaving school I went to the University of Edinburgh to become a vet. This didn't last because I was allergic to fur, unable to think in 3D (not good for anatomy), quite bored and really rubbish at the course. So I dropped out and at Catford Job Centre, in amongst the ads for short order chefs (I couldn't cook) and van drivers (I couldn't drive), was one for a forensic scientist. And oddly enough I had always wanted to work at this end of crime - I must have been the only kid in the UK who had read a biography of Bernard Spilsbury by the age of 11.
So for five years I worked at the Metropolitan Police Forensic Science Lab in London and studied part-time. I then realised that I loved academic science and went off to do a PhD. At the University of Edinburgh. In the veterinary faculty.
After that, it was the academic route of post-doc, Lecturer and Senior Lecturer. But I had a tendency to wander off on routes that intrigued me - degree in Immunology, PhD in Virology, post-doc in Human Genetics, academic position in Molecular Biology. Such wandering isn't necessarily the best idea in academia but the breadth of experience is really valued in industry. I've spent 10 years in biotech and have recently moved to the pharmaceutical sector.
And outside of work? I love birdwatching (no, I don't have a life-list), cycling, scavenging stuff from skips, and growing vegetables. I have a fantasy about one day having a smallholding (where I will starve to death if I really have to be self-sufficient) and I can't wait to write my next book. And I can now cook. And drive.

More on the "Project ENCODE" DNA Breakthrough Research

by Stephanie Pappas, LiveScience Senior Writer

September 05, 2012



UW genome scientist Dr. John A. Stamatoyannopolous led several major Project ENCODE related studies.


The ENCODE project has looked deeper into "junk DNA" than ever before. And junk it is not: According to more than 30 research papers published today (Sept. 5) in a number of journals including Science and Nature, at least 80 percent of the genome is biologically active, with much non-protein-coding DNA regulating nearby genes in a complex dance of influence. [Mysteries of Human Evolution]

The findings reveal that the genetic basis of many diseases may not be in protein-coding genes at all, but in their regulatory neighbors. For example, genetic variants related to metabolic diseases pop up in genetic regions that activated only in liver cells. Likewise, regions activated in immune cells hold variants that have been associated with autoimmune disorders such as lupus.

"These breakthrough studies provide the first extensive maps of the DNA switches that control human genes," study researcher John Stamatoyannopoulos, associate professor of genome sciences and medicine at the University of Washington, said in a statement. "This information is vital to understanding how the body makes different kinds of cells, and how normal gene circuitry gets rewired in disease. We are now able to read the living human genome at an unprecedented level of detail, and to begin to make sense of the complex instruction set that ultimately influences a wide range of human biology."

In the News: New DNA project shows us living beyond our genes

Well, once again, one man's junk is another man's treasure!

New DNA project shows us living beyond our genes

by Robert Bazell and Maggie Fox, NBC News
In what many scientists say is a revolution in biology, a giant new project is rewriting our understanding not only of what causes diseases or what makes our eyes a certain color, but what makes us human. And it turns out scientists have been looking in the wrong place for a very long time.

The bounty of new discoveries, released in a batch of 40 research papers on Wednesday, shows the stretches of DNA that we call genes are only a very small piece of what makes the body work. Much more important is the stuff in between the genes – stuff once dismissed as “junk DNA”. It turns out that junk DNA is what is in control, they report in the series of papers in the journals Nature, Science and elsewhere.

“This has opened up whole new galaxies.  It’s like having a bigger telescope,” says Dr. Bruce Stillman, president of Cold Spring Harbor Laboratory, which played a major role in the work.

Scientists already knew in 2003, as they finished the giant Human Genome Project, that they did not have the understanding they had hoped for.  It turned out that humans had just a measly 22,000 genes – fewer than some animals and far fewer even than a plant such as rice. How could something as complex and advanced as a human be boiled down into something so simple?

“We understood precious little about the processes that turns genes on and off. In short we had more questions than answers about how the human genome works,” said Dr. Eric Green, director of the National Human Genome Research Institute, which conducted the study.

The next phase of work, called ENCODE for Encyclopedia of DNA Elements, shows there’s nothing simple about it. As many as 40 million different switches are controlling these genes, turning them on and off in complex and subtle ways.

“The genome is loaded with gene controlling switches. There are literally millions of these,” Dr. John Stamatoyannopoulos of the University of Washington, who worked on the studies, told reporters in a telephone briefing.

Dr. Francis Collins, director of the National Institutes of Health, calls the findings “awesome and elegant.”

“This is the first truly comprehensive view, of how the three billion letter instruction book for human biology actually carries out its work, across many tissues and over the course of development,” he told NBC News in an interview.

Stanford University genomic expert Michael Snyder says it looks like gene mutations -- the changes in DNA sequences that we associate with causing diseases -- may only affect rare diseases. Common diseases, like heart disease, cancer, and allergy, are probably controlled elsewhere. “We think that most of the changes that affect disease don’t lie in the genes themselves, but the switches,” Snyder says.

So treating these common diseases may lie in trying to affect the switches. “The pharmaceutical industry has largely given up on genomics and the genome in favor of older approaches,” said Stamatoyannopoulos. These new findings may reinvigorate new drug research, he said. “Now we have a huge amount of genetic data about human disease that we can actually put to work to find the right kind of genes and proteins to target,” he said.

This new data will also help doctors diagnose disease in the first place, predict which treatments will work best for patients, and monitor their progress. It  points the way to studies to determine the causes of hundreds of diseases including  all kinds of cancer, Alzheimer’s disease, schizophrenia, heart disease, type 1 and type 2 diabetes, lupus, rheumatoid arthritis and asthma. 

It also may lead to a better understanding of how our genetics determine such non-disease factors as height, weight and expected life span.

Not only that – it can help explain why humans and chimpanzees share 98 percent or more of our genes, yet are so different.

"Genes occupy only a tiny fraction of the genome, and most efforts to map the genetic causes of disease were frustrated by signals that pointed away from genes. Now we know that these efforts were not in vain, and that the signals were in fact pointing to the genome's 'operating system' -- the instructions for which are hidden in millions of locations around the genome," said Stamatoyannopoulos. "The findings provide a new lens through which to view the role of genetics and genome function in disease."

Another surprising finding was that the regulatory circuitry blueprints could be used to pinpoint cell types that play a role in specific diseases -- without requiring any prior knowledge about how the disease worked. For example, DNA changes associated with Crohn's disease (a common type of inflammatory bowel disease) are concentrated in the switches controlling two types of immune cells.

Researchers can use this same method to identify cell types not previously known to play a role in a particular disease, expanding our understanding of the disease process and potentially leading to new therapies.

"We now have a parts list of what makes us human," says Mark Gerstein of Yale university, who worked on the project. "What we are doing is figuring out the wiring diagram of how it all works."

The findings rewrite biology 101 for most of us.  Each gene, we were taught, provided the code for a single protein. The proteins were the building blocks of cells, and the products made by the cells, from compounds called growth factors to signal-carrying chemicals. An intermediary genetic structure called RNA carried this information. ENCODE shows this is not quite so straightforward, that RNA generates the 40 million switches that can affect how and when many things happen within the cells.

“This is another grand chapter in the ongoing and historic research story that is unraveling the details about how life works, and how disease occurs,” Collins said.

Albert-László Barabási at TEDMED 2012

Networks guru and author Albert-László Barabási says diseases are the results of system breakdowns within the body, and mapping intracellular protein networks will help us discover cures.

http://www.youtube.com/watch?v=10oQMHadGos


Q & A video:

http://www.youtube.com/watch?v=SkurtDHFnac&feature=relmfu

An Interview with Stafford Lightman, Endocrinologist, Bristol University, England

Q:  What are the origins of the stress response?

A:  Stress is an extremely important protective mechanism for human beings, and in fact for all animals, because if you're being chased by a lion it's important to get away. In order to get away you need to give as much oxygen and as much sugar to your muscles to make them work as fast as they can, so your blood flow needs to go faster. When you're being frightened, your brain detects the danger, it sends signals down your spinal cord to your adrenal medulla to release adrenaline. The adrenaline increases the amount of sugar in your blood and increases your heart rate, and this helps your efficiency of getting away from the lion. Your brain also sends signals down to the pituitary gland, which releases another hormone which acts on the outside of the adrenal, the adrenal cortex, and that releases cortisol. Cortisol is also very important in keeping your blood sugar up, keeping your blood pressure up, and helping allow the body to have maximal exertion to get away from danger.

Q:  What happens to the body as a result of the stress response in the brain?

A:  One of the fascinating things that happens is [that] the body is being prepared only to use its really essential functions, so the muscles work well, the liver releases more sugar, for energy, but things are actually being turned off as well. Although the heart rate is going up and more blood is going round the body, parts of the body which aren't needed urgently are being turned off. The blood supply to the gut and areas like this is actually decreased, so your digestion diminishes—you don't need digestion when you're running away from a lion—obviously your sexual function is turned off, and a lot of the non-essential activities of the body just decrease so that you preserve the really essential ones to get away from the dangerous situation.

In a modern situation we don't have these same sorts of dangerous problems, but what we have are other very stressful situations. And the interesting thing, of course, is that your blood sugar goes up, your heart rate goes up and your blood pressure goes up, but you're not utilizing all of this, you're not running away, you're not having energy, so all of these hormonal responses are happening, but they're actually not being used.

Q:  When does the stress response become dangerous?

A:  The important thing about the stress response is it's adapted for short-term responses. It becomes dangerous when you get multiple stress responses, one after the other, or experience chronic stress that goes on for weeks or years. When that happens your levels of cortisol can be raised for very prolonged periods of time, and it can have lots of nasty effects on the body. It can damp down your immune system, for instance, so that you can't respond to diseases as well as you should. It can also have effects on the brain, actually decreasing the number of brain cells in certain parts of the brain and decreasing your memory. It also can affect your blood pressure, and it can affect the fats in the blood and make it more likely for you to have heart attacks and strokes. So when you have chronic stress, that's when stress becomes dangerous.

Q:  Can caring for people with chronic illnesses actually lead to illnesses in caregivers?

A:  There's been quite a lot of interest recently about what chronic stress can do to cause disease. We did a study on caregivers of patients with Alzheimer's disease…We've looked at their hormones and we find that their cortisol is indeed raised, so they have a hormonal stress response which is prolonged for a very long period of time. We've also looked at their immune function by giving them influenza vaccination, which is routinely given to elderly people, and we've found that their antibody response to the influenza vaccination is much poorer than equivalent people of the same age who aren't caring for a loved one with Alzheimer's or some other disease.

So it's clear that chronic stress does damp down the immune system. And other people have also shown that chronic stress can decrease your ability to heal wounds, so that if you've got small wounds they just don't heal as well. The body just doesn't function quite as well when you have large, high levels of cortisol circulating through it for long periods of time.

Q:  Has stress been linked to depression and other mental illnesses?

A:  It's quite clear that chronic stress is related with depression. Depression is a very major common disease in our society, and it is undoubtedly related to the chronic stress that we have in our society.

The ability of stress to cause depression as well as other problems like heart disease and high blood pressure are connected in an interesting way. [Patients who are depressed after a] heart attack are much more likely to die within the next few years than people who've had heart attacks and who aren't depressed. So again this depression, which is related to chronic stress, actually has a major effect on life expectancy.

Q:  Might there someday be a pill to reduce the effects of stress?

A:  We are involved in an intensive program to develop an anti-stress pill, and the only way we can do this really is to try and block the beginning of the pathway in the brain that causes the response to stress. And this happens at the hypothalamus, which makes a hormone called CRH. We're making a pill that blocks the effect of CRH, and therefore blocks all of the effects of stress on the body, including the effects of stress in causing an increase in cortisol. We're not designing a drug to give to everybody who's stressed. But this can be very important and hopefully should actually be an extremely useful treatment for … depression that's associated with severe stress.