Tag Archives: dna

Europeans’ white skin developed later than thought

Europeans' white skin developed later than thought

Sweden’s Crown Princess Victoria and Prince Daniel in 2011. Traits of white skin emerged more recently than thought in Europe. (AP Photo/Lehtikuva/Vesa Moilanen)

Science notes that Europe is often thought of as the “ancestral home of white people.” But a new DNA study suggests that pale skin and other traits we associate with the continent may have emerged only within the last 8,000 years—a “relatively recent” occurrence.

The study—published last month on the bioRxiv.com server and presented last week at the American Association of Physical Anthropologists’ annual meeting—compared genome DNA across three populations of farmers and hunter-gatherers who crossed over into Europe in discrete migrations within the past eight millennia, Science notes.

What scientists found: a handful of genes tied to diet and skin pigmentation that withstood natural selection and thrived in the northern regions. The data indicates hunter-gatherers who settled in Spain, Hungary, and Luxembourg about 8,500 years ago lacked two specific genes—SLC24A5 and SLC45A2—and had darker skin, Science notes.

But hunter-gatherers hunkered down further north in Sweden had both those light-skin genes and also a third gene that leads to blue eyes (and possibly fair skin and blond hair).

When the third demographic, the Near East farmers, arrived, they also carried the SLC24A5 and SLC45A2 genes, so paler skin started emerging throughout the continent as the populations interbred.

Although researchers don’t offer a definitive answer as to why natural selection picked those genes to thrive in the north, one paleoanthropologist speculated at the meeting that the lack of sun in the northern parts of Europe required people to adapt by developing lighter skin to better absorb more vitamin D, as well as the LCT gene that allowed them to digest the sugars their ancestors couldn’t in milk, also filled with vitamin D.

(This one infant could tell us where the first Americans came from.)

This article originally appeared on Newser: Europeans’ White Skin Came Later Than Thought

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New life: Scientists create first semi-synthetic organism with ‘alien’ DNA

SCIENCE EDITOR

The researchers believe the breakthrough is the first step towards creating new microbial life-forms with novel industrial or medical properties resulting from a potentially massive expansion of genetic information.

The semi-synthetic microbe, a genetically modified E. coli bacterium, has been endowed with an extra artificial piece of DNA with an expanded genetic alphabet – instead of the usual four “letters” of the alphabet its DNA molecule has six.

The natural genetic code of all living things is based on a sequence of four bases – G, C, T, A – which form two sets of bonded pairs, G to C and T to A, that link the two strands of the DNA double helix.

The DNA of the new semi-synthetic microbe, however, has a pair of extra base pairs, denoted by X and Y, which pair up together like the other base pairs and are fully integrated into the rest of the DNA’s genetic code.

The scientists said that the semi-synthetic E. coli bacterium replicates normally and is able to pass on the new genetic information to subsequent generations. However, it was not able to use the new encoded information to produce any novel proteins – the synthetic DNA was added as an extra circular strand that did not take part in the bacterium’s normal metabolic functions.

The study, published in the journal Nature, is the first time that scientists have managed to produce a genetically modified microbe that is able to function and replicate with a different genetic code to the one that is thought to have existed ever since life first started to evolve on Earth more than 3.5 billion years ago.

“Life on earth in all its diversity is encoded by only two pairs of DNA bases, A-T and C-G, and what we’ve made is an organism that stably contains those two plus a third, unnatural pair of bases,” said Professor Floyd Romesberg of the Scripps Research Institute in La Jolla, California.

“This shows that other solutions to storing information are possible and, of course, takes us closer to an expanded-DNA biology that will have many exciting applications, from new medicines to new kinds of nanotechnology,” Professor Romesberg said.

Expanding the genetic code with an extra base pair raises the prospect of building new kinds of proteins from a much wider range of amino acids than the 20 or so that exist in nature. A new code based on six base pairs could in theory deal with more than 200 amino acids, the scientists said.

“In principle, we could encode new proteins made from new, unnatural amino acids, which would give us greater power than ever to tailor protein therapeutics and diagnostics and laboratory reagents to have desired functions,” Professor Romesberg said.

“Other applications, such as nanomaterials, are also possible,” he added.

The researchers emphasised that there is little danger of the new life-forms living outside the confines of the laboratory, as they are not able to replicate with their synthetic DNA strand unless they are continuously fed the X and Y bases – synthetic chemicals called “d5SICS” and “dNaM”, that do not exist in nature.

The bacteria also need a special protein to transport the new bases around the cell of the microbe. The transporter protein comes from algae and if it, or the X and Y bases, are lacking, the microbial cells revert back to the natural genetic code, said Denis Malyshev of the Scripps Institute.

“Our new bases can only get into the cell if we turn on the “base transporter” protein. Without this transporter or when the new bases are not provided, the cell will revert back to A, T, G, C and the d5SICS and the dNaM will disappear from the genome,” Dr Malyshev said.

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Secret second code found hiding within human DNA

Secret second code found hiding within human DNA

Published December 13, 2013

news.com.au
  • dna molecules.jpg
    AP GRAPHICSBANK

Scientists have long believed that DNA tells the cells how to make proteins. But the discovery of a new, second DNA code overnight suggests the body speaks two different languages.

The findings in the journal Science may have big implications for how medical experts use the genomes of patients to interpret and diagnose diseases, researchers said.

The newfound genetic code within deoxyribonucleic acid, the hereditary material that exists in nearly every cell of the body, was written right on top of the DNA code scientists had already cracked.

‘A basic assumption about reading the human genome missed half of the picture.’

– John Stamatoyannopoulos, University of Washington associate professor of genome sciences and of medicine

Rather than concerning itself with proteins, this one instructs the cells on how genes are controlled.

Its discovery means DNA changes, or mutations that come with age or in response to viruses, may be doing more than what scientists previously thought, he said.

“For over 40 years we have assumed that DNA changes affecting the genetic code solely impact how proteins are made,” said lead author John Stamatoyannopoulos, University of Washington associate professor of genome sciences and of medicine.

“Now we know that this basic assumption about reading the human genome missed half of the picture,” he said.

“Many DNA changes that appear to alter protein sequences may actually cause disease by disrupting gene control programs or even both mechanisms simultaneously.”

Scientists already knew that the genetic code uses a 64-letter alphabet called codons.

But now researchers have figured out that some of these codons have two meanings. Coined duons, these new elements of DNA language have one meaning related to protein sequence and another that is related to gene control.

The latter instructions “appear to stabilise certain beneficial features of proteins and how they are made,” the study said.

The discovery was made as part of the international collaboration of research groups known as the Encyclopedia of DNA Elements Project, or ENCODE.

It is funded by the US National Human Genome Research Institute with the goal of finding out where and how the directions for biological functions are stored in the human genome.

Get more science and technology news at news.com.au.

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Ancient Europeans mysteriously vanished 4,500 years ago

Ancient Europeans mysteriously vanished 4,500 years ago

Published April 23, 2013

LiveScience

  • ancient-euros.jpg

    DNA taken from ancient European skeletons reveals that the genetic makeup of Europe mysteriously transformed about 4,500 years ago, new research suggests. Here, a skeleton, not used in the study, but from the same time period, that was excavated from a grave in Sweden. (öran Burenhult)

The genetic lineage of Europe mysteriously transformed about 4,500 years ago, new research suggests.

The findings, detailed today (April 23) in the journal Nature Communications, were drawn from several skeletons unearthed in central Europe that were up to 7,500 years old.

“What is intriguing is that the genetic markers of this first pan-European culture, which was clearly very successful, were then suddenly replaced around 4,500 years ago, and we don’t know why,” said study co-author Alan Cooper, of the University of Adelaide Australian Center for Ancient DNA, in a statement. “Something major happened, and the hunt is now on to find out what that was.”

The new study also confirms that people sweeping out from Turkey colonized Europe, likely as a part of the agricultural revolution, reaching Germany about 7,500 years ago.

For decades, researchers have wondered whether people, or just ideas, spread from the Middle East during the agricultural revolution that occurred after the Mesolithic period.

To find out, Cooper and his colleagues analyzed mitochondrial DNA, which resides in the cells’ energy-making structures and is passed on through the maternal line, from 37 skeletal remains from Germany and two from Italy; the skeletons belonged to humans who lived in several different cultures that flourished between 7,500 and 2,500 years ago. The team looked a DNA specifically from a certain genetic group, called haplogroup h, which is found widely throughout Europe but is less common in East and Central Asia.

The researchers found that the earliest farmers in Germany were closely related to Near Eastern and Anatolian people, suggesting that the agricultural revolution did indeed bring migrations of people into Europe who replaced early hunter-gatherers.

But that initial influx isn’t a major part of Europe’s genetic heritage today.

Instead, about 5,000 to 4,000 years ago, the genetic profile changes radically, suggesting that some mysterious event led to a huge turnover in the population that made up Europe.

The Bell Beaker culture, which emerged from the Iberian Peninsula around 2800 B.C., may have played a role in this genetic turnover. The culture, which may have been responsible for erecting some of the megaliths at Stonehenge, is named for its distinctive bell-shaped ceramics and its rich grave goods. The culture also played a role in the expansion of Celtic languages along the coast.

“We have established that the genetic foundations for modern Europe were only established in the Mid-Neolithic, after this major genetic transition around 4,000 years ago,” study co-author Wolfgang Haak, also of the Australian Center for Ancient DNA, said in a statement. “This genetic diversity was then modified further by a series of incoming and expanding cultures from Iberia and Eastern Europe through the Late Neolithic.”

Read more: http://www.foxnews.com/science/2013/04/23/ancient-europeans-mysteriously-vanished-4500-years-ago-660620043/?intcmp=features#ixzz2RQK3fgeo

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Woman Sought to Have Neanderthal Baby

Scientist seeks ‘adventurous woman’ to have Neanderthal baby

Published January 21, 2013

FoxNews.com

  • Homo Neanderthalensis

    Hyper-realistic busts of human ancestors — like this version of homo neandertal — give us a glimpse of what our ancient relatives may have looked like. (John Gurche)

  • An artist imagines the typical Neanderthal family.

    An artist imagines the typical Neanderthal family. (NASA/JPL-Caltech)

  • Neanderthal Tooth Fairy

    In this picture made available by Szczecin University’s Department of Archaelogy on Monday, Feb. 1, 2010 one of three Neanderthal teeth discovered in Poland is pictured . A team of Polish scientists say they have discovered three Neanderthal teeth in a cave in the southern part of the country. Mikolaj Urbanowski, an archaeologist and the lead researcher, said Monday that, although Neanderthal artifacts have been unearthed in Poland before, the teeth are the first remains of Neanderthals themselves discovered in the country. (AP)

EDITOR’S NOTE: The genetics professor quoted here, George Church, said after publication of this story that his quotes to the German magazine on which this article is based were distorted. An updated version of the story appears here.

Where’s Fred Flintstone when you need him?

A professor of genetics at Harvard’s Medical School believes he’s capable of bringing the long-extinct Neanderthal back to life — all he’s lacking is the right mother.

“I can create a Neanderthal baby, if I can find a willing woman,” George Church told German newspaper Spiegel Online. The DNA of the Neanderthal, a long extinct relative of man, has been more or less rebuilt, a process called genetic sequencing.

In 2005, 454 Life Sciences began a project with the Max Planck Institute to sequence the genetic code of a 30,000 year old Neanderthal woman. Now nearly complete, the sequence will let scientists look at the genetic blueprint of humankind’s nearest relative, understand its biology and maybe even create a living person.

And with that blueprint, it’s very possible to “resurrect” the Neanderthal, he argues — something Church has been pushing for years. Church did not respond to FoxNews.com requests to confirm the Spiegel Online story, but last year, he told Bloomberg he was keen on the idea.

“We have lots of Neanderthal parts around the lab. We are creating Neanderthal cells. Let’s say someone has a healthy, normal Neanderthal baby. Well, then, everyone will want to have a Neanderthal kid. Were they superstrong or supersmart? Who knows? But there’s one way to find out.”

Last year, researchers finished sequencing the genome of another extinct human relative, the denisovan — based solely off a piece of fingerbone and two molars.

Read more: http://www.foxnews.com/science/2013/01/21/scientist-seeks-adventurous-woman-to-have-neanderthal-baby/?intcmp=features#ixzz2LaOI7PjA

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DNA Storage Advance: Entire Genetics Textbook Encoded In Less Than One Trillionth Of A Gram

DNA used for computer storage!  Amazing new idea.

reposted from SicenceNow

By John Bohannon

When it comes to storing information, hard drives don’t hold a candle to DNA. Our genetic code packs billions of gigabytes into a single gram. A mere milligram of the molecule could encode the complete text of every book in the Library of Congress and have plenty of room to spare. All of this has been mostly theoretical—until now. In a new study, researchers stored an entire genetics textbook in less than a picogram of DNA—one trillionth of a gram—an advance that could revolutionize our ability to save data.

A few teams have tried to write data into the genomes of living cells. But the approach has a couple of disadvantages. First, cells die—not a good way to lose your term paper. They also replicate, introducing new mutations over time that can change the data.

To get around these problems, a team led by George Church, a synthetic biologist at Harvard Medical School in Boston, created a DNA information-archiving system that uses no cells at all. Instead, an inkjet printer embeds short fragments of chemically synthesized DNA onto the surface of a tiny glass chip. To encode a digital file, researchers divide it into tiny blocks of data and convert these data not into the 1s and 0s of typical digital storage media, but rather into DNA’s four-letter alphabet of As, Cs, Gs, and Ts. Each DNA fragment also contains a digital “barcode” that records its location in the original file. Reading the data requires a DNA sequencer and a computer to reassemble all of the fragments in order and convert them back into digital format. The computer also corrects for errors; each block of data is replicated thousands of times so that any chance glitch can be identified and fixed by comparing it to the other copies.

To demonstrate its system in action, the team used the DNA chips to encode a genetics book co-authored by Church. It worked. After converting the book into DNA and translating it back into digital form, the team’s system had a raw error rate of only two errors per million bits, amounting to a few single-letter typos. That is on par with DVDs and far better than magnetic hard drives. And because of their tiny size,DNA chips are now the storage medium with the highest known information density, the researchers report online today in Science.

Don’t replace your flash drive with genetic material just yet, however. The cost of the DNA sequencer and other instruments “currently makes this impractical for general use,” says Daniel Gibson, a synthetic biologist at the J. Craig Venter Institute in Rockville, Maryland, “but the field is moving fast and the technology will soon be cheaper, faster, and smaller.” Gibson led the team that created the first completely synthetic genome, which included a “watermark” of extra data encoded into the DNA. The researchers used a three-letter coding system that is less efficient than the Church team’s but has built-in safeguards to prevent living cells from translating the DNA into proteins. “If DNA is going to be used for this purpose, and outside a laboratory setting, then you would want to use DNA sequence that is least likely to be expressed in the environment,” he says. Church disagrees. Unless someone deliberately “subverts” his DNA data-archiving system, he sees little danger.

ScienceNOW, the daily online news service of the journal Science

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