Tag Archives: the journal Nature

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

SCIENCE EDITOR
Wednesday 07 May 2014

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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Woolly mammoths (and rhinos) ate flowers

Woolly mammoths (and rhinos) ate flowers

By Tia Ghose

Published February 06, 2014

  • pleistocene-arctic

    The Arctic had much more diverse flora than previously thought during the Pleistocene Era (Mauricio Anton)

Woolly mammoths, rhinos and other ice age beasts may have munched on high-protein wildflowers called forbs, new research suggests.

And far from living in a monotonous grassland, the mega-beasts inhabited a colorful Arctic landscape filled with flowering plants and diverse vegetation, the study researchers found.

The new research “paints a different picture of the Arctic,” thousands of years ago, said study co-author Joseph Craine, an ecosystem ecologist at Kansas State University. “It makes us rethink how the vegetation looked and how those animals thrived on the landscape.”

The ancient ecosystem was detailed Wednesday in the journal Nature.

Pretty landscape In the past, scientists imagined that the now-vast Arctic tundra was once a brown grassland steppe that teemed with wooly mammoths, rhinos and bison. But recreations of the ancient Arctic vegetation relied on fossilized pollen found in permafrost, or frozen soil. Because grasses and sedges tend to produce more pollen than other plants, those analyses produced a biased picture of the landscape. [Image Gallery: Ancient Beasts Roam an Arctic Landscape]

To understand the ancient landscape better, researchers analyzed the plant genetic material found in 242 samples of permafrost from across Siberia, Northern Europe and Alaska that dated as far back as 50,000 years ago.

They also analyzed the DNA found in the gut contents and fossilized poop, or coprolites, of eight Pleistocene beasts woolly mammoths, rhinos, bison and horses found in museums throughout the world.

The DNA analysis showed that the Arctic at the time had a varied landscape filled with wildflowers, grasses and other vegetation.

And the shaggy ice age beasts that roamed the landscape took advantage of that cornucopia. The grazers supplemented their grassy diet with a hefty helping of wildflowerlike plants known as forbs, the stomach content analysis found.

These forbs are high in protein and other nutrients, which may have helped the grazers put on weight and reproduce in the otherwise sparse Arctic environment, Craine told Live Science.

Vanishing wildflowers Between 10,000 and 15,000 years ago, forbs declined in the Arctic,study co-author Mary E. Edwards, a physical geographer at the University of Southampton in England, wrote in an email.

Though it’s not exactly clear why, “we do know from much other evidence that the climate changed at this time,” Edwards said.

The ice age was ending and warmer, wetter weather was prevailing. That climate “allowed trees and shrubs to flourish and these would have outgrown forbs by shading them for example,” Edwards said.

It’s also possible that the vanishing of these high-protein plants hastened the extinction of ice age beasts such as the woolly mammoth. For example, grasslands may have been delicately balanced, with poop from the grazers nourishing the plants, which in turn kept the animals alive. If a big jolt in climate disrupted one part of the chain for instance by depleting the forbs that may have led the whole system to collapse, Edwards speculated.

The findings also raise questions about modern grazers such as bison, Craine said. If the ancient beasts dined on forbs, it’s possible these wildflower-like plants play a bigger role in the diet of modern bison as well, he said.

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