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General interest items edited by Janice Flahiff

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.

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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.

July 17, 2015 Posted by | Medical and Health Research News | , , , , , | Leave a comment

[Press release]NIH scientists determine how environment contributes to several human diseases

NIH scientists determine how environment contributes to several human diseases.
From the 25 November 2014 NIH Press Release

Using a new imaging technique, National Institutes of Health researchers have found that the biological machinery that builds DNA can insert molecules into the DNA strand that are damaged as a result of environmental exposures. These damaged molecules trigger cell death that produces some human diseases, according to the researchers. The work, appearing online Nov. 17 in the journal Nature, provides a possible explanation for how one type of DNA damage may lead to cancer, diabetes, hypertension, cardiovascular and lung disease, and Alzheimer’s disease.

Time-lapse crystallography was used by National Institute of Environmental Health Sciences (NIEHS) researchers to determine that DNA polymerase, the enzyme responsible for assembling the nucleotides or building blocks of DNA, incorporates nucleotides with a specific kind of damage into the DNA strand. Time-lapse crystallography is a technique that takes snapshots of biochemical reactions occurring in cells.

Samuel Wilson, M.D., senior NIEHS researcher on the team, explained that the damage is caused by oxidative stress, or the generation of free oxygen molecules, in response to environmental factors, such as ultraviolet exposure, diet, and chemical compounds in paints, plastics, and other consumer products. He said scientists suspected that the DNA polymerase was inserting nucleotides that were damaged by carrying an additional oxygen atom.

DNA polymerase

After the DNA polymerase (gray molecule in background) inserts a damaged nucleotide into DNA, the damaged nucleotide is unable to bond with its undamaged partner. As a result, the damaged nucleotide swings freely within the DNA, interfering with the repair function or causing double-strand breaks. These steps may ultimately lead to several human diseases. (Graphic courtesy of Bret Freudenthal)

 

“When one of these oxidized nucleotides is placed into the DNA strand, it can’t pair with the opposing nucleotide as usual, which leaves a gap in the DNA,” Wilson said. “Until this paper, no one had actually seen how the polymerase did it or understood the downstream implications.”

November 28, 2014 Posted by | environmental health, Medical and Health Research News | , , , , , , | Leave a comment

[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

 

November 27, 2013 Posted by | Nutrition | , , , , , | Leave a comment

   

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