Accessing your own genomic data is a civil right but requires strategies to manage safety [this right does not include most non-HIPPA collected as 23&me, Ancestry.com]

From 4 January 2018 Science Daily news item

The Genetic Information Nondiscrimination Act of 2008 expanded individuals’ access to genetic information by forcing changes to the HIPAA Privacy Rule. These amendments gave Americans a civil right to obtain copies of their own genetic test results stored at HIPAA-regulated laboratories. Researchers describe how civil rights and safety concerns collided after these changes and offers strategies to reconcile the two…….

…..”You only have an access right if the party that stores your data happens to be HIPAA-regulated. Most direct-to-consumer testing [as Ancestry.com and “23 & me”  and cloud data storage services are not HIPAA-regulated, so you may not have an access right if your data are there…

…..Giving people access to data from research laboratories is controversial because the genomic data they produce do not always contain clinically relevant information (only about 200 gene sequences have known clinical significance). Someone could misinterpret the data to pursue needless medical treatment or waste healthcare resources to clarify findings that they misunderstand.Giving people access to data from research laboratories is controversial because the genomic data they produce do not always contain clinically relevant information (only about 200 gene sequences have known clinical significance). Someone could misinterpret the data to pursue needless medical treatment or waste healthcare resources to clarify findings that they misunderstand……

……..”Having access to your own genomic data also lets you exercise important constitutional rights, such as your First Amendment rights to assemble and petition the government. You can go on social media and assemble groups of people with genes like yours and lobby Congress to spend more research dollars studying how those genes affect your health,” says Evans. “Like the right to vote, access to one’s own genomic data is a foundational civil right that empowers people to protect all their other civil rights.”

 

 

Extra DNA acts as a ‘spare tire’ for our genomes

Extra DNA acts as a ‘spare tire’ for our genomes.

From the  6 July 2015 American Chemical news release

Carrying around a spare tire is a good thing — you never know when you’ll get a flat. Turns out we’re all carrying around “spare tires” in our genomes, too. Today, in ACS Central Science, researchers report that an extra set of guanines (or “G”s) in our DNA may function just like a “spare” to help prevent many cancers from developing.

Various kinds of damage can happen to DNA, making it unstable, which is a hallmark of cancer. One common way that our genetic material can be harmed is from a phenomenon called oxidative stress. When our bodies process certain chemicals or even by simply breathing, one of the products is a form of oxygen that can acutely damage DNA bases, predominantly the Gs. In order to stay cancer-free, our bodies must repair this DNA. Interestingly, where it counts — in a regulatory DNA structure called a G-quadruplex — the damaged G is not repaired via the typical repair mechanisms. However, people somehow do not develop cancers at the high rate that these insults occur. Cynthia Burrows, Susan Wallace and colleagues sought to unravel this conundrum.

The researchers scanned the sequences of known human oncogenes associated with cancer, and found that many contain the four G-stretches necessary for quadruplex formation and a fifth G-stretch one or more bases downstream. The team showed that these extra Gs could act like a “spare tire,” getting swapped in as needed to allow damage removal by the typical repair machinery. When they exposed these quadruplex-forming sequences to oxidative stress in vitro, a series of different tests indicated that the extra Gs allowed the damages to fold out from the quadruplex structure, and become accessible to the repair enzymes. They further point out that G-quadruplexes are highly conserved in many genomes, indicating that this could be a factory-installed safety feature across many forms of life.

###

Due to a premature posting of this paper online, the embargo is now lifted as of July 6.

The authors acknowledge funding from the National Institutes of Health.

The paper will be available July 8, 2015, at this link: http://pubs.acs.org/doi/full/10.1021/acscentsci.5b00202.

[Research news article] DNA can’t explain all inherited biological traits, research shows

DNA can’t explain all inherited biological traits, research shows.

From the 2 April 2014 news release

Traits passed between generations are not decided only by DNA, but can be brought about by other materials in cells.

Edinburgh scientists studied proteins found in cells, known as histones, which are not part of the genetic code, but act as spools around which DNA is wound.

Histones are known to control whether or not genes are switched on.

Researchers found that naturally occurring changes to these proteins, which affect how they control genes, can be sustained from one generation to the next and so influence which characteristics are passed on.

Research avenues

The finding demonstrates for the first time that DNA is not solely responsible for how characteristics are inherited.

It paves the way for research into how and when this method of inheritance occurs in nature, and if it is linked to particular traits or health conditions.

It may also inform research into whether changes to the histone proteins that are caused by environmental conditions – such as stress or diet – can influence the function of genes passed on to offspring.

Theory confirmed

The research confirms a long-held expectation among scientists that genes could be controlled across generations by such changes.

However, it remains to be seen how common the process is, researchers say.

Scientists tested the theory by carrying out experiments in a yeast with similar gene control mechanisms to human cells.

They introduced changes to a histone protein, mimicking those that occur naturally, causing it to switch off nearby genes.

The effect was inherited by subsequent generations of yeast cells.

The study, published in Science, was supported by the Wellcome Trust and the EC EpiGeneSys Network.

We’ve shown without doubt that changes in the histone spools that make up chromosomes can be copied and passed through generations. Our finding settles the idea that inherited traits can be epigenetic, meaning that they are not solely down to changes in a gene’s DNA.

Professor Robin Allshire

School of Biological Sciences

[Press release] DNA clock helps predict lifespan

http://biocomicals.blogspot.com/2011_05_01_archive.html

Biocomicals by Dr. Alper Uzun is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License.

From the 30 January 2015 University of Edinburg press release

Scientists have identified a biological clock that provides vital clues about how long a person is likely to live.

Researchers studied chemical changes to DNA that take place over a lifetime, and can help them predict an individual’s age. By comparing individuals’ actual ages with their predicted biological clock age, scientists saw a pattern emerging.

Biological age

People whose biological age was greater than their true age were more likely to die sooner than those whose biological and actual ages were the same.

Four independent studies tracked the lives of almost 5,000 older people for up to 14 years. Each person’s biological age was measured from a blood sample at the outset, and participants were followed up throughout the study.

Researchers found that the link between having a faster-running biological clock and early death held true even after accounting for other factors such as smoking, diabetes and cardiovascular disease.

The same results in four studies indicated a link between the biological clock and deaths from all causes. At present, it is not clear what lifestyle or genetic factors influence a person’s biological age. We have several follow-up projects planned to investigate this in detail.

Dr Riccardo Marioni

Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh

DNA modification

Scientists from the University of Edinburgh, in collaboration with researchers in Australia and the US, measured each person’s biological age by studying a chemical modification to DNA, known as methylation.

The modification does not alter the DNA sequence, but plays an important role in biological processes and can influence how genes are turned off and on. Methylation changes can affect many genes and occur throughout a person’s life.

This new research increases our understanding of longevity and healthy ageing. It is exciting as it has identified a novel indicator of ageing, which improves the prediction of lifespan over and above the contribution of factors such as smoking, diabetes, and cardiovascular disease.

Professor Ian Deary

Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh

International collaboration

The study is published in the journal Genome Biology and was conducted by researchers from the University of Edinburgh, University of Queensland, Harvard University, University of California, Los Angeles (UCLA), Boston University, the Johns Hopkins University Lieber Institute for Brain Development and the U.S. National Heart, Lung and Blood Institute.

This study was carried out at the University of Edinburgh’s Centre for Cognitive Ageing and Epidemiology (CCACE), which is supported by the Medical Research Council (MRC) and the Biotechnology and Biological Sciences Research Council (BBSRC) as part of the Lifelong Health and Wellbeing programme, a collaboration between the UK’s Research Councils and Health Departments which is led by the MRC.

 

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[Press release] Did genetic links to modern maladies provide ancient benefits?

From the 28 January 2015 press release at University at Buffalo

study finds that humanity’s early ancestors had genetic variations associated with modern disease, and now the question is why

By Charlotte Hsu

The discovery highlights the importance of balancing selection, a poorly understood evolutionary dance in which dueling forces drive species to retain a diverse set of genetic features.

Credit: From Shaping Humanity, by John Gurche. Image may be republished ONLY in conjunction with stories about the research outlined in this press release.

Caption: A reconstruction ofHomo neanderthalensis, as created by artist John Gurche for the Smithsonian’s National Museum of Natural History. A study led by University at Buffalo biologist Omer Gokcumen compared the DNA of modern humans to Neanderthals and Denisovans (another ancient hominin). The research found that genetic deletions associated with various aspects of human health, including psoriasis and Crohn’s disease, likely originated in a common ancestor of the three species.

BUFFALO, N.Y. — Psoriasis, a chronic skin condition, can cause rashes that itch and sting.

So why would a genetic susceptibility to this and other ailments persist for hundreds of thousands of years, afflicting our ancient ancestors, and us?

That’s the question scientists are asking after discovering that genetic variations associated with some modern maladies are extremely old, predating the evolution of Neanderthals, Denisovans (another ancient hominin) and contemporary humans.

The study was published this month in Molecular Biology and Evolution.

“Our research shows that some genetic features associated with psoriasis, Crohn’s disease and other aspects of human health are ancient,” says senior scientist Omer Gokcumen, PhD, a University at Buffalo assistant professor of biological sciences.

Some of humanity’s early ancestors had the telltale features, called deletions, while others did not, mirroring the variation in modern humans, the scientists found. This genetic diversity may have arisen as far back as a million or more years ago in a common ancestor of humans, Denisovans and Neanderthals.

The discovery highlights the importance of balancing selection, a poorly understood evolutionary dance in which dueling forces drive species to retain a diverse set of genetic features.

The research raises the possibility that the diseases in question — or at least a genetic susceptibility to them — “may have been with us for a long time,” Gokcumen says.

Why this would happen is an open question, but one possibility is that certain traits that made humans susceptible to Crohn’s and psoriasis may also have afforded an evolutionary benefit to our ancient ancesto

– See more at: http://www.buffalo.edu/news/releases/2015/01/034.html#sthash.latn4ejg.dpuf

[Press release] NIH researchers tackle thorny side of gene therapy

NIH researchers tackle thorny side of gene therapy 

From the 20 January 2015 press release

 

NIH researchers tackle thorny side of gene therapy

Pre-clinical studies in mice reveal ways to reduce cancer risk with modified treatment

NHGRI researchers conduct laboratory investigations to advance gene therapy. Watch the video featuring Dr. Charles Venditti and Dr. Randy Chandler:  Methylmalonic Acidemia (MMA) Gene Therapy

Bethesda, Md., Tues., Jan. 20, 2015 – National Institutes of Health researchers have uncovered a key factor in understanding the elevated cancer risk associated with gene therapy. They conducted research on mice with a rare disease similar to one in humans, hoping their findings may eventually help improve gene therapy for humans. Researchers at the National Human Genome Research Institute (NHGRI), part of NIH, published their research in the Jan. 20, 2015, online issue of the Journal of Clinical Investigation.

“Effective and safe gene therapies have the potential to dramatically reverse diseases that are life-threatening for affected children,” said NHGRI Scientific Director Dan Kastner, M.D., Ph.D. “This study is an important step in developing gene therapies that can be safely used to benefit patients.”

Toxic side effects actually are rarely observed by researchers who have designed gene therapies using an adeno-associated virus (AAV) as a vector to deliver the corrected gene to a specific point in the cell’s DNA. AAVs are small viruses that infect humans but do not cause disease. A vector is a DNA molecule of AAV used as a vehicle to carry corrected genetic material into a cell. AAV viruses are uniquely suited for gene therapy applications.

But one prior study did find an association between AAV and the occurrence of liver cancer. The present research addresses this problem in gene therapy for an inherited disease in children called methylmalonic acidemia, or MMA. For 10 years, NHGRI researchers have worked toward a gene therapy to treat MMA. The condition affects as many as 1 in 67,000 children born in the United States. Affected children are unable to properly metabolize certain amino acids consumed in their diet, which can damage a number of organs and lead to kidney failure. MMA patients also suffer from severe metabolic instability, failure to thrive, intellectual and physical disabilities, pancreatitis, anemia, seizures, vision loss and strokes. The most common therapy is a restrictive diet, but doctors must resort to dialysis or kidney or liver transplants when the disease progresses.

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Smoking changes our genes

Smoking changes our genes.

From the 17 December 2013 ScienceDaily article

The fact that smoking means a considerable health risk is nowadays commonly accepted. New research findings from Uppsala University and Uppsala Clinical Research Center show that smoking alters several genes that can be associated with health problems for smokers, such as increased risk for cancer and diabetes.

We inherit our genes from our parents at birth. Later in life the genetic material can be changed by epigenetic modifications, i.e. chemical alterations of the DNA the affect the activity of the genes. Such alterations are normally caused by aging but can also result from environmental factors and lifestyle.

In a study recently published in the journal Human Molecular Genetics the researchers have examined how the genes are changed in smokers and users of non-smoke tobacco. They could identify a large number of genes that were altered in smokers but found no such effect of non-smoke tobacco.

…

t has been previously known that smokers have an increased risk of developing diabetes and many types of cancer, and have a reduced immune defence and lower sperm quality. The results from the study also showed that genes that increase the risk for cancer and diabetes, or are important for the immune response or sperm quality, are affected by smoking.

…..

Read the entire article here

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[News article] Vitamins: Potential Damage to Body’s Defences

From the 28 November 2013 ScienceDaily report

Vitamin supplements are a billion-dollar industry. We want to stay healthy and fit and help our bodies with this. But perhaps we are achieving precisely the opposite?

“We believe that antioxidants are good for us, since they protect the cells from oxidative stress that may harm our genes. However, our bodies have an enormous inherent ability to handle stress. Recent research results show that the body’s responses to stress in fact are important in preventing our DNA from eroding. I fear that the fragile balance in our cells can be upset when we supplement our diet with vitamin pills, says Hilde Nilsen to the research magazine Apollon. Nilsen is heading a research group at the Biotechnology Centre, University of Oslo.

Maintenance of genes

Our DNA – the genetic code that makes us who we are – is constantly exposed to damage.

In each of the hundred trillion cells in our body, up to two hundred thousand instances of damage to the DNA take place every day. These may stem from environmental causes such as smoking, stress, environmental pathogens or UV radiation, but the natural and life-sustaining processes in the organism are the primary sources of damage to our DNA.

How can the repair of damage to our DNA help us stay healthy and live long lives?

A small worm provides the answer

To answer this question, Hilde Nilsen and her group of researchers have allied themselves with a small organism – a one millimetre-long nematode called Caenorhabditis elegans (C. elegans). This roundworm, which lives for only 25 days, is surprisingly sophisticated with its 20,000 genes; we humans only have a couple of thousand more.

C. elegans is a fantastically powerful tool, because we can change its hereditary properties. We can increase its ability to repair DNA damage, or we can remove it altogether. We can also monitor what happens when damage to DNA is not repaired in several hundred specimens and through their entire lifespan. Different “repair proteins” take care of various types of damage to the DNA. The most common ones are repaired by “cutting out” and replacing a single damaged base by itself or as part of a larger fragment.

Affecting lifespan with the aid of genes

In some specimens that do not have the ability to repair the damage, the researchers observe that the aging process proceeds far faster than normal. Is it because the damage accumulates in the DNA and prevents the cells from producing the proteins they need for their normal operation? Most researchers have thought so, but Hilde Nilsen doubts it.

One of the genes studied by the researchers has a somewhat shortened lifespan: on average, this mutant lives three days less than normal. Translated into human terms, this means dying at the age of 60 rather than at 70. -“We were surprised when we saw that these mutants do not in fact accumulate the DNA damage that would cause aging. On the contrary: they have less DNA damage. This happens because the little nematode changes its metabolism into low gear and releases its own antioxidant defences. Nature uses this strategy to minimize the negative consequences of its inability to repair the DNA. So why is this not the normal state? Most likely because it comes at a cost: these organisms have less ability to respond to further stress ‒ they are quite fragile.

Hilde Nilsen and her colleagues have now -for the very first time -“shown that this response is under active genetic control and is not caused by passive accumulation of damage to the DNA, as has been widely believed.

…

Can do great harm

The balance between oxidants and antioxidants is crucial to our physiology, but exactly where this equilibrium is situated varies from one person to the next.

“This is where I start worrying about the synthetic antioxidants. The cells in our body use this fragile balance to establish the best possible conditions for themselves, and it is specially adapted for each of us. When we take supplements of antioxidants, such as C and E vitamins, we may upset this balance,” the researcher warns.

“It sounds intuitively correct that intake of a substance that may prevent accumulation of damage would benefit us, and that’s why so many of us supplement our diet with vitamins. Our research results indicate that at the same time, we may also cause a lot of harm. The health authorities recommend that instead, we should seek to have an appropriate diet. I’m all in favour of that. It’s far safer for us to take our vitamins through the food that we eat, rather than through pills,” Hilde Nilsen states emphatically.

 

Read the entire article here

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[Journal Article] Novel Genetic Patterns May Make Us Rethink Biology and Individuality

From the 7 November 2013 ScienceDaily article

Professor of Genetics Scott Williams, PhD, of the Institute for Quantitative Biomedical Sciences (iQBS) at Dartmouth’s Geisel School of Medicine, has made two novel discoveries: first, a person can have several DNA mutations in parts of their body, with their original DNA in the rest — resulting in several different genotypes in one individual — and second, some of the same genetic mutations occur in unrelated people. We think of each person’s DNA as unique, so if an individual can have more than one genotype, this may alter our very concept of what it means to be a human, and impact how we think about using forensic or criminal DNA analysis, paternity testing, prenatal testing, or genetic screening for breast cancer risk, for example. Williams’ surprising results indicate that genetic mutations do not always happen purely at random, as scientists have previously thought.

His work, done in collaboration with Professor of Genetics Jason Moore, PhD, and colleagues at Vanderbilt University, was published in PLOS Genetics journal on November 7, 2013.

Genetic mutations can occur in the cells that are passed on from parent to child and may cause birth defects. Other genetic mutations occur after an egg is fertilized, throughout childhood or adult life, after people are exposed to sunlight, radiation, carcinogenic chemicals, viruses, or other items that can damage DNA. These later or “somatic” mutations do not affect sperm or egg cells, so they are not inherited from parents or passed down to children. Somatic mutations can cause cancer or other diseases, but do not always do so. However, if the mutated cell continues to divide, the person can develop tissue, or a part thereof, with a different DNA sequence from the rest of his or her body.

….

f our human DNA changes, or mutates, in patterns, rather than randomly; if such mutations “match” among unrelated people; or if genetic changes happen only in part of the body of one individual, what does this mean for our understanding of what it means to be human? How may it impact our medical care, cancer screening, or treatment of disease? We don’t yet know, but ongoing research may help reveal the answers.

Christopher Amos, PhD, Director of the Center for Genomic Medicine and Associate Director for Population Sciences at the Cancer Center, says, “This paper identifies mutations that develop in multiple tissues, and provides novel insights that are relevant to aging. Mutations are noticed in several tissues in common across individuals, and the aging process is the most likely contributor. The theory would be that selected mutations confer a selective advantage to mitochondria, and these accumulate as we age.” Amos, who is also a Professor of Community and Family Medicine at Geisel, says, “To confirm whether aging is to blame, we would need to study tissues from multiple individuals at different ages.” Williams concurs, saying, “Clearly these do accumulate with age, but how and why is unknown — and needs to be determined.”

…

Just as our bodies’ immune systems have evolved to fight disease, interestingly, they can also stave off the effects of some genetic mutations. Williams states that, “Most genetic changes don’t cause disease, and if they did, we’d be in big trouble. Fortunately, it appears our systems filter a lot of that out.”

Mark Israel, MD, Director of Norris Cotton Cancer Center and Professor of Pediatrics and Genetics at Geisel, says, “The fact that somatic mutation occurs in mitochondrial DNA apparently non-randomly provides a new working hypothesis for the rest of the genome. If this non-randomness is general, it may affect cancer risks in ways we could not have previously predicted. This can have real impact in understanding and changing disease susceptibility.”

 

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New Genetics Education Resource

Genetics, Education, Discovery

From a recent email (National Library of Medicine)

The National Library of Medicine (NLM)  is pleased to announce the release of a new educational resource, GeneEd.

..a useful resource for students and teachers in grades 9 – 12 to learn genetics.

GeneEd allows students and teachers to explore topics such as Cell Biology, DNA, Genes, Chromosomes, Heredity/Inheritance Patterns, Epigenetics/Inheritance and the Environment, Genetic Conditions, Evolution, Biostatistics, Biotechnology, DNA Forensics, and Top Issues in Genetics.

Teachers can use the site to introduce topics, supplement existing materials, and provide as a reliable source to students conducting research.

 

The site links to categories such as research articles, animation, games, videos, interactive tutorials, and labs and experiments. 3D images, illustrations and text from NHRGI help to enrich the user experience by providing vivid imagery to reinforce genetic concepts.

Text varies from easy-to-read to advanced reading levels, which makes this a versatile tool both in and out of the classroom.
Specialty pages including Teacher Resources and Labs and Experiments highlight those tools that teachers may find particularly helpful.

Other specialty pages such as Careers in Genetics and Highlights allow students to see what is new and noteworthy in the field of Genetics along with links to different careers related to the science of Genetics.

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‘Junk DNA’ can sense viral infection

This image shows a consensus secondary structure for a ncRNA family called mascRNA-menRNA. The colouring gives an indication of the sequence conservation. (Photo credit: Wikipedia)

[Well, another thing to unlearn from biology classes in the late 70’s…. the DNA that doesn’t seem to be doing anything isn’t junk after all!]

From the 25 April 2012 article at EurekaAlert

Promising tool in the battle between pathogen and host, Tel Aviv University research confirms

Once considered unimportant “junk DNA,” scientists have learned that non-coding RNA (ncRNA) — RNA molecules that do not translate into proteins — play a crucial role in cellular function. Mutations in ncRNA are associated with a number of conditions, such as cancer, autism, and Alzheimer’s disease.

Now, through the use of “deep sequencing,” a technology used to sequence the genetic materials of the human genome, Dr. Noam Shomron of Tel Aviv University’s Sackler Faculty of Medicine has discovered that when infected with a virus, ncRNA gives off biological signals that indicate the presence of an infectious agent, known as a pathogen. Not only does this finding give researchers a more complete picture of the interactions between pathogens and the body, but it provides scientists with a new avenue for fighting off infections.

His findings have been published in the journal Nucleic Acid Research.

Another battleground between pathogen and host

“If we see that the number of particular RNA molecules increases during a specific viral infection, we can develop treatments to stop or slow their proliferation,” explains Dr. Shomron.

In the lab, the researchers conducted a blind study in which some cells were infected with the HIV virus and others were left uninfected. Using the deep sequencer, which can read tens of millions of sequences per experiment, they analyzed the ncRNA to discover if the infection could be detected in non-coding DNA materials. The researchers were able to identify with 100% accuracy both infected and non-infected cells — all because the ncRNA was giving off significant signals, explains Dr. Shomron.

These signals, which can include either the increase or decrease of specific ncRNA molecules within a cell, most likely have biological significance, he says. “With the introduction of a pathogen, there is a reaction in both the coding and non-coding genes. By adding a new layer of information about pathogen and host interactions, we better understand the entire picture. And understanding the reactions of the ncRNA following infection by different viruses can open up the battle against all pathogens.”

Finding an “Achilles heel” of infections

The researchers believe that if an ncRNA molecule significantly manifests itself during infection by a particular pathogen, the pathogen has co-opted this ncRNA to help the pathogen devastate the host — such as the human body. To help the body fight off the infection, drugs that stop or slow the molecules’ proliferation could be a novel and effective strategy.

This new finding allows researchers to develop treatments that attack a virus from two different directions at once, targeting both the coding and non-coding genetic materials, says Dr. Shomron. He suggests that ncRNA could prove to be the “Achilles heel” of pathogens.

Dr. Shomron and his team of researchers developed new software, called RandA, which stands for “ncRNA Read-and-Analyze,” that performs ncRNA profiling and analysis on data generated through deep sequencing technology. It’s this software that has helped them to uncover the features that characterize virus-infected cells.

The Economist—and the Truth About Microwave Radiation Emitted from Wireless Technologies

 

A Critique by Scientific Experts, Physicians and Oncologists

 Excerpt from the article

In its unsigned commentary on September 3, 2011, “Worrying about Wireless”, The Economistmakes a number of technical errors and misleading statements about microwave radiation that we write to correct. The governments of more than a dozen nations have issued precautionary advice and policies about wireless devices, including restricting cellphone use by children in France, India and Israel (See Worldwide Advisories at http://www.saferphonezone.com).  The Economist would do well to consult with experts in these and other tech-savvy nations to learn the science behind these countries’ decisions so that it can provide accurate reporting on wireless safety and health matters.

The Economist states:

“Let it be said, once and for all, that no matter how powerful a radio transmitter–whether an over-the-horizon radar station or a microwave tower–radio waves simply cannot produce ionising radiation. The only possible effect they can have on human tissue is to raise its temperature slightly.” 

This is a red herring.  Of course microwave radiation is non-ionizing radiation.  It has insufficient energy to directly break chemical bonds including mutating DNA. Independent studies show that microwave radiation from cellphones can damage genetic material and disrupt DNA repair without inducing heat.  Microwave radiation from cellphones can also increase the production of damaging free radicals, which can also indirectly damage DNA. ^[1a,b,c]

In 2000 the cellphone companies T-Mobil and DeTeMobil Deutsche Telekom Mobilnet commissioned the ECOLOG report.  This report acknowledged that microwave radiation damages genes, living cells, and the immune system.   Since then, the evidence base suggesting that prolonged cellphone use can harm human health has grown substantially.  In May 2011, after a rigorous review of the evidence, the World Health Organization’s (WHO) International Agency for Research on Cancer (IARC) classified radiation emitted by wireless devices including cellphones as “possibly carcinogenic.”

In addition, scientific studies carried out in Russia in the 1950s and 1960s and corroborated by European researchers more recently show that microwave radiation affects the heart, brain and liver, as well as the production of hormones and male human and animal fertility….

Read the entire article (medium long)

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How many genomes do you have? | SmartPlanet

How many genomes do you have? | SmartPlanet.

By John Rennie | November 29, 2011, 3:00 AM PST

The era of personal genomics is fast approaching, as headlines constantly remind us. With the cost of sequencing someone’s DNA rapidly falling toward just $1,000 (or less), it seems all but inevitable that soon we and our physicians will use that information to guide our health decisions.

 

 

454 Life Sciences gene sequencing machines. (Credit: Jon Callas, via Flickr)

 

But here’s an inconvenient biological truth that the triumphant talk about personal genomics sometimes skirts: we don’t each have just one genome. Yes, one may stand out most prominently for each of us, but we have others. And biology is still sorting out how much our health may depend on learning to pay attention to those we normally overlook.

 

All the cells in an organism like a human being certainly seem as though they should have the same genome. A fertilized egg divides repeatedly to give rise to the body’s cells, passing along the same set of chromosomes to every one of its cellular progeny. A few exceptional tissues might deviate from that rule — for example, red blood cells entirely discard the nucleus holding their genes, and the white blood cells called B lymphocytes scramble part of their DNA so that they can make an almost infinite number of different antibodies. But fundamentally, all the cells in the skin, the liver, the brain, the muscles and other tissues ought to share the same genome.

Or so it was thought. Yet exceptions to the rule keep cropping up, and they may help to explain some of the variation seen in tissues like the brain.

Variation on the brain

The hundred billion neurons in the human brain obviously differ from one another in their interconnections and in the specific neurochemical messenger molecules that they secrete. But a more subtle difference that has come to light over the past decade, largely thanks to the work of Michael J. McConnell and his colleagues at the Salk Institute for Biological Studies in La Jolla, Calif., resides in the DNA. They have shown extensive variation in the genomes of individual neurons, a condition called aneuploidy. The neurons have deleted, duplicated, and rearranged portions of their chromosomes, such that no two have exactly the same DNA sequence anymore…..

 

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Environment And Diet Leave Their Prints On The Heart

From the 30 November 2011 Medical News Today article 

A University of Cambridge study, which set out to investigate DNA methylation in the human heart and the ‘missing link’ between our lifestyle and our health, has now mapped the link in detail across the entire human genome.

The new data collected greatly benefits a field that is still in its scientific infancy and is a significant leap ahead of where the researchers were, even 18 months ago.

Researcher Roger Foo explains: “By going wider and scanning the genome in greater detail this time – we now have a clear picture of the ‘fingerprint’ of the missing link, where and how epigenetics in heart failuremay be changed and the parts of the genome where diet or environment or other external factors may affect outcomes.” …

…

DNA methylation leaves indicators, or “marks”, on the genome and there is evidence that these “marks” are strongly influenced by external factors such as the environment and diet. The researchers have found that this process is different in diseased and normal hearts. Linking all these things together suggest this may be the “missing link” between environmental factors and heart failure.

The findings deepen our understanding of the genetic changes that can lead to heart diseaseand how these can be influenced by our diet and our environment. The findings can potentially open new ways of identifying, managing and treating heart disease.

The DNA that makes up our genes is made up of four “bases” or nucleotides – cytosine, guanine, adenine and thymie, often abbreviated to C, G, A and T. DNA methylation is the addition of a methyl group (CH3) to cytosine.

When added to cytosine, the methyl group looks different and is recognised differently by proteins, altering how the gene is expressed i.e. turned on or off.

DNA methylation is a crucial part of normal development, allowing different cells to become different tissues despite having the same genes. As well as happening during development, DNA methylation continues throughout our lives in a response to environmental and dietary changes which can lead to disease.

As a result of the study, Foo likens DNA methylation to a fifth nucleotide: “We often think of DNA as being composed of four nucleotides. Now, we are beginning to think there is a fifth – the methylated C.”

Foo also alludes to what the future holds for the study: “…and more recent basic studies now show us that our genome has even got 6th, 7th and 8th nucleotides… in the form of further modifications of cytosines. These are hydroxy-methyl-Cytosine, formylCytosine and carboxylCytosine = hmC, fC and caC! These make up an amazing shift in the paradigm…”

As in most studies, as one question is resolved, another series of mysteries form in its place. The study shows that we are still on the frontier of Epigenetics and only just beginning to understand the link between the life we lead and the body we have. 

DNA methylation in E.coli

Related articles

• Environment and diet leave their prints on the heart (eurekalert.org)
• Diet, environment leave their prints on the heart (scienceblog.com)
• Controlling patterns of DNA methylation (medicalxpress.com)
• Epigenetic changes often don’t last, probably have limited effects on long-term evolution, research finds (sciencedaily.com)
• Epigenetics again: will it cause a revolution in evolution? (whyevolutionistrue.wordpress.com)
• Your Living Conditions as a Child May Be Detectable In Your DNA for Life By Clay Dillow (imullins89.wordpress.com)
• Welcome to the Genome Engineering Wordle (genome-engineering.com)
• Genome Engineering guest blog on BioNews: Europe leads the way in epigenome mapping (genome-engineering.com)
• Genome engineering – Method 3: Correction (genome-engineering.com)
• Carnival of Evolution #39 (genome-engineering.com)

DNA barcoding reveals fraud and secrets

http://www.barcodeoflife.org/content/about/what-dna-barcoding

Quack medicines, insect immigrants, and what eats what among secrets revealed by DNA barcodes

Global ‘barcode blitz’ accelerates; 450 experts converge on Adelaide Nov. 28-Dec. 3
Agenda in Adelaide: www.dnabarcodes2011.org/conference/program/schedule/index.php

This is the cover of the report: “Barcoding Life Highlights 2011.”

 

From the Eureka News Alert, Sun Nov 27, 2011 00:00 

(Consortium for the Barcode of Life (CBOL)) The newfound scientific power to quickly “fingerprint” species via DNA is being deployed to unmask quack herbal medicines, reveal types of ancient Arctic life frozen in permafrost, expose what eats what in nature, and halt agricultural and forestry pests at borders, among other applications across a wide array of public interests….

…

DNA barcode technology has already sparked US Congressional hearings by exposing widespread “fish fraud” — mislabelling cheap fish as more desirable and expensive species like tuna or snapper. Other studies this year revealed unlisted ingredients in herbal tea bags…..

Hot new applications include:

Substitute ingredients in herbal medicines

High demand is causing regular “adulteration or substitution of herbal drugs,” barcoding experts have discovered.

Indeed, notes Malaysian researcher Muhammad Sharir Abdul Rahman, one fraudster in his country treated rubber tree wood with quinine to give it a bitter taste similar to Eurycoma longifolia — a traditional medicine for malaria, diabetes and other ailments.

A library of DNA barcodes for Malaysia’s 1,200 plant species with potential medicinal value is in development, eventually offering “a quick one step detection kit” to reduce fraud in the lucrative herbal medicine industry, says Mr. Sharir….

…

Invasive pests

Until now, border inspection to keep agricultural pests, disease-carrying insects and invasive species from entering a country has been a hit-and-miss effort. Barcoding offers a tool to get same-day answers for accepting or rejecting imports, an issue of acute economic importance to Australia and New Zealand….

…

Assessing water quality

Scientists in Southern California and elsewhere are pioneering barcodes to assess freshwater marine water quality and its impact on marine life in, sand, sediment, and rocks or in mud in rivers and offshore.

Traditionally after collecting a bulk water sample, taxonomists must identify by sight several thousand invertebrates, a process requiring months and thousands of dollars. DNA barcodes enable them to analyze bulk samples in a fraction of the time at a fraction of the cost.

Similar projects underway in Korea, Iraq, Belgium and the Baltic region will be presented in Adelaide.

DNA barcoding is emerging as the tool of choice for monitoring water quality, DNA barcode libraries of aquatic insects under construction. New technologies are being developed and tested that will allow faster and more complete analyses of entire biological communities in streamwater on ‘DNA microchips’ and through next-generation sequencing.

Says Dr. Schindel: “It used to take weeks or months to analyze the organisms in streams to determine water quality. Now it takes hours at a fraction the cost.”…

Click here to see the entire medium long news release

Related articles

• Secrets Revealed By DNA Barcodes: Quack Medicines, Insect Immigrants, What Eats What And Much More (medicalnewstoday.com)
• Quack medicines, insect immigrants, and what eats what among secrets revealed by DNA barcodes (physorg.com)
• DNA barcoding catches food fraudsters, IDs animals (ctv.ca)
• Restaurants To Use DNA Barcoding To Prevent Seafood Fraud (huffingtonpost.com)
• Restaurants plan DNA-certified premium seafood (seattletimes.nwsource.com)
• Fish Barcode of Life Campaign (FISH-BOL) (bespacific.com)

The Case for Personalized Medicine: Interview with Edward Abrahams of PMC

This article in the 25 November Science Roll blog has interview Q and A’s with Edward Abrahams, Ph.D. of the Personalized Medicine Coalition. Topics include RNA sequencing, gene sequencing economics, and gene sequencing statistics.

The third edition of The Case for Personalized Medicine (PDF) was released a week ago

Some quotes….

The power in tailored therapeutics is for us to say more clearly to payers, providers, and patients—‘this drug is not for everyone, but it is for you.’ That is exceedingly powerful.”

John C. Lechleiter, Ph.D.
President and Chief Executive Officer, Eli Lilly and Company

 

 

As the field advances, we expect to see more efficient clinical  trials based on a more thorough understanding of the genetic  basis of disease. We also anticipate that some previously  failed medications will be recognized as safe and effective  and will be approved for subgroups of patients with specific genetic markers.”

Margaret Hamburg, M.D.

Commissioner, U.S. Food and Drug Administration

Francis Collins, M.D., Ph.D.

Director, National Institutes of Health

Related articles

• 72 Prominent Personalized Medicine Products Available; A Five-Fold Increase In Five Years (bioresearchonline.com)
• Personalized medicine’s opportunities and challenges for clinicians, business (medcitynews.com)
• CEPMED Hosts Pioneers in Personalized Medicine in Montreal at the International Economic Forum (prweb.com)
• Leading Health Executives to Speak at Dorland Health’s Care Coordination Summit, October 5th in Washington, DC (prweb.com)
• Personalized Medicine (hospitalphysicians.com)
• New and varied imaging techniques facilitate personalized medicine (jflahiff.wordpress.com)

Genetic sequencing alone doesn’t offer a true picture of human disease

Genetic sequencing alone doesn’t offer a true picture of human disease

From the January 23 Eureka news alert

DURHAM, N.C. – Despite what you might have heard, genetic sequencing alone is not enough to understand human disease. Researchers at Duke University Medical Center have shown that functional tests are absolutely necessary to understand the biological relevance of the results of sequencing studies as they relate to disease, using a suite of diseases known as the ciliopathies which can cause patients to have many different traits.

“Right now the paradigm is to sequence a number of patients and see what may be there in terms of variants,” said Nicholas Katsanis, Ph.D. “The key finding of this study says that this approach is important, but not sufficient. If you really want to be able to penetrate, you must have a robust way to test the functional relevance of mutations you find in patients. For a person at risk of type 2 diabetes, schizophrenia or atherosclerosis, getting their genome sequenced is not enough – you have to functionally interpret the data to get a sense of what might happen to the particular patient.”

“This is the message to people doing medical genomics,” said lead author Erica Davis, Ph.D., Assistant Professor in the Duke Department of Pediatrics, who works in the Duke Center for Human Disease Modeling. “We have to know the extent to which gene variants in question are detrimental – how do they affect individual cells or organs and what is the result on human development or disease? Every patient has his or her own set of genetic variants, and most of these will not be found at sufficient frequency in the general population so that anyone could make a clear medical statement about their case.”

Davis, working in the lab of Katsanis, and in collaboration with many ciliopathy labs worldwide, sequenced a gene, TTC21B, known to be a critical component of the primary cilium, an antenna-like projection critical to cell function.

While a few of the mutations could readily be shown to cause two main human disorders, a kidney disease and an asphyxiating thoracic condition, the significance of the majority of DNA variants could not be determined. Davis then tested these variants in a zebrafish model, in which many genes are similar to humans, and showed that TTC21B appears to contribute disease-related mutations to about 5 percent of human ciliopathy cases.

The study, which appears in Nature Genetics online on Jan. 23, shows how genetic variations both can cause ciliopathies and also interact with other disease-causing genes to yield very different sets of patient problems.

Katsanis, the Jean and George Brumley Jr., M.D., Professor of Pediatrics and Cell Biology, and Director of the Duke Center for Human Disease Modeling, is a world expert in ciliopathies such as Bardet-Biedl Syndrome, in which the primary cilium of cells is abnormal and leads to a host of problems. About one child in 1,000 live births will have a ciliopathy, an incidence that is in the range of Down’s syndrome, said Katsanis.

“By sequencing genes to identify genetic variation, followed by functional studies with a good experimental model, we can get a much better idea of the architecture of complex, inherited disorders,” Katsanis said. “Each individual with a disease is unique,” Davis said. “If you can overlay gene sequencing with functional information, then you will be able to increase the fidelity of your findings and it will become more meaningful for patients and families.”

It will take more laboratories doing more pointed studies like this one to get a fuller picture of the ciliopathies and other diseases, Davis said.

Katsanis noted that it will take true collaboration within many scientific disciplines as well as scientific finesse to get at the true roots of complex diseases.

“Brute force alone – sequencing – will not help,” he said. “Technology is of finite resolution. You must have synthesis of physiology, cell biology, biochemistry and other fields to get true penetration into medically relevant information.”

Texas A&M research shows bacteria provide example of one of nature’s first immune systems

From the December 23, 2010 Eureka news release

COLLEGE STATION, Texas, Dec. 23, 2010—Studying how bacteria incorporate foreign DNA from invading viruses into their own regulatory processes, Thomas Wood, professor in the Artie McFerrin Department of Chemical Engineering at Texas A&M University, is uncovering the secrets of one of nature’s most primitive immune systems.

His findings, which appear in “Nature Communications,” a multidisciplinary publication dedicated to research in all areas of the biological, physical and chemical sciences, shed light on how bacteria have throughout the course of millions of years developed resistance to antibiotics by co-opting the DNA of their natural enemies—viruses.

The battle between bacteria and bacteria-eating viruses, Wood explains, has been going on for millions of years, with viruses attempting to replicate themselves by – in one approach – invading bacteria cells and integrating themselves into the chromosomes of the bacteria. When this happens a bacterium makes a copy of its chromosome, which includes the virus particle. The virus then can choose at a later time to replicate itself, killing the bacterium—similar to a ticking time bomb, Wood says.

However, things can go radically wrong for the virus because of random but abundant mutations that occur within the chromosome of the bacterium. Having already integrated itself into the bacterium’s chromosome, the virus is subject to mutation as well, and some of these mutations, Wood explains, render the virus unable to replicate and kill the bacterium.

With this new diverse blend of genetic material, Wood says, a bacterium not only overcomes the virus’ lethal intentions but also flourishes at a greater rate than similar bacteria that have not incorporated viral DNA.

“Over millions of years, this virus becomes a normal part of the bacterium,” Wood says. “It brings in new tricks, new genes, new proteins, new enzymes, new things that it can do. The bacterium learns how to do things from this.

“What we have found is that with this new viral DNA that has been trapped over millions of years in the chromosome, the cell has created a new immune system,” Wood notes. “It has developed new proteins that have enabled it to resists antibiotics and other harmful things that attempt to oxidize cells, such as hydrogen peroxide. These cells that have the new viral set of tricks don’t die or don’t die as rapidly.”

Understanding the significance of viral DNA to bacteria required Wood’s research team to delete all of the viral DNA on the chromosome of a bacterium, in this case bacteria from a strain of E. coli. Wood’s team, led by postdoctoral researcher Xiaoxue Wang, used what in a sense could be described as “enzymatic scissors” to “cut out” the nine viral patches, which amounted to precisely removing 166,000 nucleotides. Once the viral patches were successfully removed, the team examined how the bacterium cell changed. What they found was a dramatically increased sensitivity to antibiotics by the bacterium.

While Wood studied this effect in E. coli bacteria, he says similar processes have taken place on a massive, widespread scale, noting that viral DNA can be found in nearly all bacteria, with some strains possessing as much as 20 percent viral DNA within their chromosome.

“To put this into perspective, for some bacteria, one-fifth of their chromosome came from their enemy, and until our study, people had largely neglected to study that 20 percent of the chromosome,” Wood says. “This viral DNA had been believed to be silent and unimportant, not having much impact on the cell.

“Our study is the first to show that we need to look at all bacteria and look at their old viral particles to see how they are affecting the bacteria’s current ability to withstand things like antibiotics. If we can figure out how the cells are more resistant to antibiotics because of this additional DNA, we can perhaps make new, effective antibiotics.”

 

The gene-environment enigma & personalized medicine

From the December 3, 2010 news item

Personalized medicine centers on being able to predict the risk of disease or response to a drug based on a person’s genetic makeup. But a study by scientists at Washington University School of Medicine in St. Louis suggests that, for most common diseases, genes alone only tell part of the story.

That’s because the environment interacts with DNA in ways that are difficult to predict, even in simple organisms like single-celled yeast, their research shows.

“The effects of a person’s genes – and, therefore, their risk of disease – are greatly influenced by their environment,” says senior author Barak Cohen, PhD, a geneticist at Washington University School of Medicine. “So, if personalized medicine is going to work, we need to find a way to measure a human’s environment.”

The research is available online in PLoS Genetics….

….

The new research raises many questions: what is a human’s environment and how can it be measured? Is the environment a person lived in during childhood important or the environment he lives in now?

Cohen suspects that any environment that matters is likely to leave a measurable molecular signature. For example, eating a lot of fatty foods raises triglycerides; smoking raises nicotine levels; and eating high-fat, high-sugar foods raises blood sugar levels, which increases the risk of diabetes. The key, he says, is to figure out what are good metabolic readouts of the environment and factor those into statistical models that assess genetic susceptibility to disease or response to medication.

“Measuring the environment becomes crucial when we try to understand how it interacts with genetics,” Cohen says. “Having a particular genetic variant may not have much of an effect but combined with a person’s environment, it may have a huge effect.”

Cohen says he’s not hopeless when it comes to personalized medicine. As scientists conduct ever-larger studies to identify rare and common variants underlying diseases such as cancer, diabetes and schizophrenia, they will be more likely to uncover variants that have larger effects on disease. Even then, however, a person’s environment will be important, he adds.

 

 

Genetic Testing Web Site

The US National Human Genome Institute (NHGRI) **publishes Genetic Testing, which serves as an introduction to non-scientists from a research perspective.

The Web site Genetic Testing includes the following

• Overview of Genetic Testing , with a link to A Brief Primer on Genetic Testing (a summary of current genetic testing)
• The Growth of Genetic Testing Raises Questions
• Legislation on Genetic Testing
• NHGRI Interest in Genetic Testing, including its concerns (as genetic discrimination) and activities (as providing information for genetic counselors)
• Policy Recommendations
• (Links to) Reports on Genetic Testing from government and nonprofit agencies

 

**[ From About the Insitute ]NHGRI’s  initial mission was to map the human genome.  Its role has been expanded to include applying genome technologies to the study of specific diseases and study the genetic components of complex disorders. Its human genome sequence database is available to scientists worldwide.

The NHGRI Web site includes information about

• NHGRI research
• Information about genetics and genomics, rare diseases, patient care and more (for patients, the public, and health professionals)
• Educational materials about genetics and genomics for students and teachers
• Policy, legal and ethical issues in genetic research
• Latest news, media resources and information from NHGRI
• Education, training, professional development and career opportunities at NHGRI
• (Under the For You tab)
  Specialized information for Students, Educators, Patients, Health Professionals

 

NCBI Develops Database of Genomic Structural Variations

From the October 21 NCBI announcement

The National Center for Biotechnology Information (NCBI) has developed a new tool to help scientists understand how differences in DNA sequences contribute to human health and disease.

The Database of Genomic Structural Variation, or dbVar, will help track large-scale variations in DNA sequences discovered in healthy individuals as well as people with conditions such as autism and cancer. The database also contains comparative data on wide variety of organisms, including plants and livestock, that are important to agriculture.

The human genome is made up of approximately 3 billion base pairs of DNA arranged into 23 chromosomes. In recent years, scientists have discovered that very large stretches of the genome can be rearranged, duplicated, or deleted. Some of these variations may be associated with disorders such as Down syndrome, while others do not have apparent impact on health. dbVar is one of several tools scientists can use to understand how genomic variations play a role in disease or affect a person’s characteristics.

“An enormous volume of data is now coming from studies that investigate genetic variation,” says NCBI Director, David Lipman, MD. “We are excited to be playing a role in this important area of scientific inquiry by making the data widely available to scientists and integrating it with other National Library of Medicine research tools and the scientific literature.”

dbVar was officially launched in September 2010. The database is part of an international collaboration that includes the recently-launched Database of Genomic Variants archive (DGVa) at the European Bioinformatics Institute (EBI) and theDatabase of Genomic Variants (DGV) in Toronto.  The databases are detailed in the October 2010 issue of Nature Genetics.

Members of the dbVar team are Deanna M. Church, John Garner, Timothy Hefferon, John Lopez, and Azat Mardanov.

 

Database to Help Scientists Understand How Differences in DNA Contribute to Human Health and Disease

From a National Institutes of Health (NIH) press release

The National Institutes of Health today announces the launch of a new resource, called the Database of Genomic Structural Variation, or dbVar, to help scientists understand how differences in DNA contribute to human health and disease.

The database will help track large-scale variations in DNA discovered in healthy individuals as well as those affected with disorders such as autism and cancer. Additionally, dbVar will collect data on a diverse array of organisms, including agriculturally important plants and livestock. The database was developed by the National Center for Biotechnology Information (NCBI), a division of the National Library of Medicine (NLM) at NIH.

“Jumping genes” make each person unique: study

“Transposons are sequences in the DNA code that can replicate themselves. They “jump” from one place to another on the chromosomes. Devine’s team found unique transposons in more than 90 percent of the 76 people they studied, they reported in the journal Cell.

These mutations can affect the functions of other genes. Stretches of DNA right in front of or behind a gene can turn it on, turn it off, or affect the way it functions.

That people have transposons is not new. “Forty-five percent of the genome is known to be transposon sequences,” Devine said. But most hopped in and are now inactive, passing down unchanged and in place from one generation to the next.

“What we are interested in are the ones that are moving around today. We found an average of 15 new insertions per person,” Devine said in a telephone interview.”

News item may be found here.