dna

DNA revelations from Ötzi the Iceman’s leather and furs

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5,300-year-old mummy found in the Italian Alps wore clothes made from many different animals.

or the past two decades, scientists have analyzed every minute detail of Ötzi, a 5,300-year-old natural mummy found in the ice of the Italian Ötztal Alps. But one remaining mystery was the provenance of his clothing, made from leather and fur. Now, thanks to refined techniques in DNA sequencing, a team of scientists has identified how the clothing was made—and discovered something surprising about Ötzi’s domestic habits.

Ötzi lived during the Copper Age, when humans had been domesticating animals for a few thousand years, and our cutting-edge technologies included stone tools and fired pottery. From previous studies, we know that Ötzi was likely murdered by an arrow and a blow to the head. We also know he suffered from arthritis, and he ate a meal of deer and berries before he died.

The team’s new findings, published in Nature Scientific Reports, are as much a demonstration of DNA sequencing wizardry as they are about ancient fashion. It’s incredibly difficult to get genetic material out of tanned hides, because they’ve generally been scraped, heated, and exposed to fatty acids. Plus, the hides and furs themselves had disintegrated. But the researchers used several methods for extracting DNA from the hides that made up Ötzi’s shoelace, hat, loincloth, coats, leggings, and quiver. First they compared the strands of DNA they did find with other mapped genomes to identify species. Then the researchers targeted very small, specific regions in the DNA for reconstruction to learn more about the animals’ relationships with today’s domestic breeds.

 

Read at ArsTechnica

Large DNA study using 23andMe data finds 15 sites linked to depression

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Scientists announced on Monday that they had pinpointed 15 locations in our DNA that are associated with depression, one of the most common mental health conditions and one that is estimated to cost the world billions in health-care costs and lost productivity.

Although gene association studies — which link DNA inherited from our parents to particular diseases, conditions or even habits such as vegetarianism — are published practically every week, this is a particularly important one. It’s the first large study on major depressive disorder in people of European descent, and it shows that the genes that may be involved in the condition correspond to those involved in the development of neurons in the brain. There is also overlap between the genetic regions implicated in depression and those that have been linked to other psychiatric disorders such as schizophrenia. This finding supports another key study published in April that focused on genetic factors related to well-being and depression, which found that the genetic variants for those genes had some “moderate” overlap with those with schizophrenia and bipolar disorder. This may suggest that scientists study these genes and traits jointly in future work.

The new study, published in Nature Genetics, involved an analysis of genetic variations of 75,607 people of European ancestry who self-reported having depression and 231,747 healthy controls.

 

Read at Washington Post

Meet Luca, the Ancestor of All Living Things

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A surprisingly specific genetic portrait of the ancestor of all living things has been generated by scientists who say that the likeness sheds considerable light on the mystery of how life first emerged on Earth.

This venerable ancestor was a single-cell, bacterium-like organism. But it has a grand name, or at least an acronym. It is known as Luca, the Last Universal Common Ancestor, and is estimated to have lived some four billion years ago, when Earth was a mere 560 million years old.

The new finding sharpens the debate between those who believe life began in some extreme environment, such as in deep sea vents or the flanks of volcanoes, and others who favor more normal settings, such as the “warm little pond” proposed by Darwin.

Read at NYT

Panel Endorses ‘Gene Drive’ Technology That Can Alter Entire Species

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A revolutionary technology known as “gene drive,” which for the first time gives humans the power to alter or perhaps eliminate entire populations of organisms in the wild, has stirred both excitement and fear since scientists proposed a means to construct it two years ago.

Scientists dream of deploying gene drive, for example, to wipe out malaria-carrying mosquitoes that cause the deaths of 300,000 African children each year, or invasive rodents that damage island ecosystems. But some experts have warned that the technique could lead to unforeseen harm to the environment. Some scientists have called on the federal government to regulate it, and some environmental watchdogs have called for a moratorium.

On Wednesday, the National Academies of Sciences, Engineering and Medicine, the premier advisory group for the federal government on scientific matters, endorsed continued research on the technology, concluding after nearly a yearlong study that while it poses risks, its possible benefits make it crucial to pursue. The group also set out a path to conducting what it called “carefully controlled field trials,” despite what some scientists say is the substantial risk of inadvertent release into the environment.

Read at New York Times

Breast cancer: Scientists hail ‘milestone’ genetic find

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Scientists say they now have a near-perfect picture of the genetic events that cause breast cancer.

The study, published in Nature, has been described as a “milestone” moment that could help unlock new ways of treating and preventing the disease.

The largest study of its kind unpicked practically all the errors that cause healthy breast tissue to go rogue.

Cancer Research UK said the findings were an important stepping-stone to new drugs for treating cancer.

To understand the causes of the disease, scientists have to understand what goes wrong in our DNA that makes healthy tissue turn cancerous.

The international team looked at all 3 billion letters of people’s genetic code – their entire blueprint of life – in 560 breast cancers.

They uncovered 93 sets of instructions, or genes, that if mutated, can cause tumours. Some have been discovered before, but scientists expect this to be the definitive list, barring a few rare mutations.

 

Read at BBC

First child ‘DNA diagnoses’ in NHS project

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The first children with debilitating “mystery” diseases have finally been given a diagnosis as part of a huge scheme to analyse people’s DNA.

Four-year-old Georgia Walburn-Green’s damaged eyes and kidneys and her inability to talk had baffled doctors.

She is one of the first to have her precise genetic abnormality identified through the100,000 Genomes Project.

Her parents said the day Georgia was finally diagnosed was one of the biggest of their lives.

If a child is born with Down’s syndrome or a heart defect then families know what to expect.

Yet Georgia’s mum and dad – Amanda and Matt – had only 20 minutes of “worry-free cuddling” when Georgia was born before their “world went from totally happy to totally devastated”.

 

Full story on BBC site

Ghosts in the Genome How one generation’s experience can affect the next

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In one of the 20th century’s most disastrous collisions of political ideology and science, the Russian botanist Trofim Lysenko steered the USSR’s agricultural research policies to deemphasize the deterministic concepts of Mendelian inheritance. Instead, Lysenko was committed to the idea that, within the space of a single generation, the environment could alter the phenotype of future generations, an idea that is now often (imprecisely) referred to as “Lamarckian” inheritance. In Lysenko’s view, Mendelian inheritance, along with Darwinian evolution, emphasizes competition, whereas he believed that biology was based on cooperation, and that hard work in one generation should rapidly lead to the betterment of the species.

Lysenko was among the most infamous purveyors of the idea that the environment experienced by an organism could influence the phenotype in future generations, and he was rightly denounced as a charlatan because he falsified results in pursuit of his goal. However, the scientific community has discovered over the past few decades that the idea that acquired characters can be inherited may not be completely off the mark. It turns out that epigenetic marks, information not encoded in the genome’s sequence, do respond to environmental conditions within an organism’s lifetime, and recent evidence suggests that such information may be inherited.

These findings have helped motivate modern research into the oft-discredited study of transgenerational effects of the environment. Researchers are now beginning to understand the mechanisms of epigenetic inheritance and to generate evidence for the idea that the experiences of an ancestral population can influence future generations.

 

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New Letters Added to the Genetic Alphabet

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Scientists hope that new genetic letters, created in the lab, will endow DNA with new powers.

 

DNA stores our genetic code in an elegant double helix. But some argue that this elegance is overrated. “DNA as a molecule has many things wrong with it,” saidSteven Benner, an organic chemist at the Foundation for Applied Molecular Evolution in Florida.

Nearly 30 years ago, Benner sketched out better versions of both DNA and its chemical cousin RNA, adding new letters and other additions that would expand their repertoire of chemical feats. He wondered why these improvements haven’t occurred in living creatures. Nature has written the entire language of life using just four chemical letters: G, C, A and T. Did our genetic code settle on these four nucleotides for a reason? Or was this system one of many possibilities, selected by simple chance? Perhaps expanding the code could make it better.

Benner’s early attempts at synthesizing new chemical letters failed. But with each false start, his team learned more about what makes a good nucleotide and gained a better understanding of the precise molecular details that make DNA and RNA work. The researchers’ efforts progressed slowly, as they had to design new tools to manipulate the extended alphabet they were building. “We have had to re-create, for our artificially designed DNA, all of the molecular biology that evolution took 4 billion years to create for natural DNA,” Benner said.

 

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What’s Old Is New Again

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Revolutionary new methods for extracting, purifying, and sequencing ever-more-ancient DNA have opened an unprecedented window into the history of life on Earth.

 

Two researchers sit hunched in front of a fume hood dressed head-to-toe in stark white Tyvek suits, though the yellow-tinted window I’m viewing them through lends the entire scene a sulfurous hue. One of the scientists, a research associate named Hongjie Li, pipettes tiny volumes of solutions containing decades-old DNA into centrifuge tubes, while the other, PhD student Lu Yao, types information into a laptop. Airlock doors and a sensitive ventilation system minimize the incursion of outside air and the myriad bits of contaminating DNA it carries. Yao, reaching a point when she can take a break, looks up from her work and waves, a smile spreading beneath her face mask and crinkling the corners of her eyes.

This is the ancient-DNA lab at the University of Illinois, Urbana-Champaign, tucked in a corner of the basement at the Carl R. Woese Institute for Genomic Biology. Yao has spent hours in this space. Working under the guidance of molecular anthropologist Ripan Malhi, she hopes to answer questions about phylogeny, biogeography, and island dwarfism among long-tailed macaques (Macaca fascicularis) in Southeast Asia by sequencing decades- and even century-old mitochondrial DNA collected from the dried skulls of monkeys in museum collections. And thanks to recent methodological, computational, and conceptual advances in the study of ancient DNA, Yao, Li—who studies ancient DNA from native Californians—and other researchers are succeeding, compiling sequences at an unprecedented rate.

 

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Neanderthal-Human Hybrid Unearthed

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DNA from the 40,000-year-old bones of a modern human found in Europe contains Neanderthal genes.

 

Between 35,000 and 45,000 years ago, modern humans spread throughout Europe. Around the same time, Neanderthals disappeared from the landscape—but not before interbreeding with Homo sapiens. Recent research has revealed that all non-Africans living today retain a genetic trace—1-3 percent of the genome—of Neanderthal ancestry. And 40,000 years ago, human genomes may have contained twice as much Neanderthal DNA, according to a study published today (June 22) inNature.

Genetic material recovered from 40,000-year-old human bones unearthed in Romania harbors about 6-9 percent Neanderthal DNA, the study reports. Some of this DNA was contained in three relatively large chromosome segments, suggesting the individual had a Neanderthal ancestor only four to six generations back. “I think the conclusions are quite clear, and it’s really quite remarkable that they were lucky to find a hybrid that was so recent to be able to date it to a few generations back,” said Rasmus Nielsen, a University of California Berkeley population geneticist who was not involved with the work.

 

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