Tag: DNA

In A Lost Baby Tooth, Scientists Find Ancient Denisovan DNA

Denisovans

More than 100,000 years ago in a Siberian cave there lived a child with a loose tooth. One day her molar fell out, and fossilized over many millenniums, keeping it safe from the elements and the tooth fairy.

But she wasn’t just any child. Scientists say she belonged to a species of extinct cousins of Neanderthals and modern humans known today as the Denisovans.

And in a paper published last Friday in the journal Science Advances, a team of paleoanthropologists reported that she is only the fourth individual of this species ever discovered.

“We only have relatively little data from this archaic group, so having any additional individuals is something we’re very excited about,” said Viviane Slon, a doctoral candidate at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, and lead author of the study.

Denisovans cave

The scant fossil record for these ancient hominins previously included only two adult molars and a finger bone. The Denisovans were only correctly identified in 2010 by a team of researchers led by Svante Paabo.

Scientists exploring Denisova Cave in the Altai Mountains discovered the worn baby tooth in 1984 and labeled it ‘Denisova 2.’ At the time, its origins were a mystery.

But now, after performing DNA analysis on the deciduous, or baby tooth, researchers say it was one of the elusive Denisovans.

“We think based on the DNA sequences that ‘Denisova 2’ is at least 100,000 years, possibly 150,000 years old. Or a bit more,” said Ms. Slon. “So far it makes it the oldest Denisovan.”

Denisovans

To determine the origins of ‘Denisova 2’ the team first performed a CT scan of the tooth to preserve its structure for future studies.

After sequencing the DNA she compared genetic information from the sample with genetic data already collected from Denisovans, Neanderthals and modern humans.

“We saw it was most similar to Denisovan mitochondrial genomes,” she said. “That was exciting because that was a good indication that this was another Denisovan individual.”

Bence Viola, a paleoanthropologist from the University of Toronto and an author on the paper, said there was not too much to be learned from studying the tooth’s morphology or appearance.




The genetic analysis, on the other hand, provided the keys to learning more about the species. He said the genetic study was something the team most likely could not have done five years ago without destroying the tooth.

“For a long time we didn’t want to work on it because it’s such a small specimen,” he said.

But by drilling into the tooth and performing the genetic analysis the scientists were able to not only figure out who it belonged to, but also provide relative dates for when the Denisovan lived.

The study also suggests that the species had less genetic variability than modern humans, but more genetic diversity than seen in Neanderthal nuclear DNA.

Dr. Bernard A. Wood, a professor of human origins at the Center for the Advanced Study of Human Paleobiology at George Washington University, said the paper demonstrated the power of molecular biology as a tool for paleoanthropology.

“Talk about extracting blood from a stone,” he said, “this is extracting treasure from a tooth.”

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Here’s What You Need to Know Before You Buy A DNA Testing Kit

It’s amazing how much information there is hiding in one tiny globule of spit.

In 2003, scientists announced that they had, after more than a decade, completed sequencing the human genome.

In 2018, you can spit in a test tube and, for the same price as a pair of Apple Air Pods, find out a host of fascinating information about your ancestry and health.

But there are things you should know before you spit: Namely that you’re you’re handing over access to extremely sensitive information about things including your health, personality, and family history.




It’s all there in the fine print if you bother to read it: Testing companies can claim rights to your genetic information, allow third parties to access it, and simply by virtue of possessing it make your DNA vulnerable to hackers.

This isn’t because DNA testing companies like AncestryDNA or 23andMe are doing anything especially fishy. Sharing sensitive personal information is inherently risky.

And the truth is, we likely don’t even fully understand what some of those risks are. It’s possible you could one day face employment or insurance discrimination, or even social stigma, based on your genes.

We’re guessing you might not have thought about all this before you became one of the millions of people curious to find out what their DNA might say about them.

And, as I explored in a recent feature, the accuracy of the information you get back from these companies is dubious. So we’ll leave you with one important piece of advice: Think before you spit!

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Gene Editing Fixes Harmful Mutation In Human Embryos

GENE

Scientists have successfully edited the DNA of human embryos to erase a heritable heart condition that is known for causing sudden death in young competitive athletes, cracking open the doors to a controversial new era in medicine.

This is the first time gene editing on human embryos has been conducted in the United States. Researchers said in interviews this week that they consider their work very basic.




The embryos were allowed to grow for only a few days, and there was never any intention to implant them to create a pregnancy.

But they also acknowledged that they will continue to move forward with the science, with the ultimate goal of being able to “correct” disease-causing genes in embryos that will develop into babies.

News of the remarkable experiment began to circulate last week, but details became public Wednesday with a paper in the journal Nature.

The experiment is the latest example of how the laboratory tool known as CRISPR (or Clustered Regularly Interspaced Short Palindromic Repeats), a type of “molecular scissors,” is pushing the boundaries of our ability to manipulate life, and it has been received with both excitement and horror.

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A Mysterious New Form Of DNA Was Just Discovered In Human Cells

When you think of DNA, odds are, you picture the famous double helix, a ladder-like structure elegantly twisted like a corkscrew.

But DNA doesn’t always assume this form. The existence of one shape of DNA in humans, in particular — a four-stranded knot of genetic code — has been controversial among scientists for years.

Because this so-called i-motif loves acidic environments (a condition that scientists can create in the lab but doesn’t naturally occur in the body), many scientists thought that it couldn’t possibly exist in human cells.

But in recent years, studies have pointed to the possibility that this bizarre form of DNA could, in fact, exist in living humans.

Now, a new study published last April 23 in the journal Nature Chemistry provides the first direct evidence that it does exist and that it may play an important role in regulating our genes.




To spot the i-motifs, Dinger and his team designed an antibody — a protein that targets foreign invaders in the body — to specifically find and latch onto i-motifs.

They tagged these antibodies with a fluorescent dye and then injected them into human cells in the lab.

Using powerful microscopes, they spotted a bunch of tiny, glowing, green dots — colored antibodies holding onto elusive i-motifs.

According to Dinger, the hardest part about publishing this paper was proving that the antibody latched only onto i-motifs and not onto other shapes of DNA.

They did this by testing how the antibody interacted with other forms of DNA, such as the classic double helix and a better-studied structure related to the i-motif, called the G4 quadruplex.

Sure enough, the antibody proved faithful — it didn’t bind to either of these other forms.

This is a very exciting discovery,” said Zoe Waller, a senior lecturer in chemical biology at the University of East Anglia in the United Kingdom who was not involved with the study.

“This work is the icing on what is now quite a large cake of evidence that these [forms of DNA] do exist in vivo and are worthy of further study.”

What really fascinated the team, Dinger told Live Science, was not only that these i-motifs existed in living cells but that these green lightstwinkled on and off — meaning the i-motifs folded into existence and then unfurled, repeatedly.

In particular, the researchers found that the DNA folded into i-motifs at higher rates during a specific stage of transcription — the process that kicks off the translation of genes into proteins — when the DNA was just beginning to actively transcribe.

Later, the DNA unfolded back into its usual form, and the i-motifs disappeared. According to Dinger, this probably means the i-motifs play a very specific role in regulating the transcription process.

Indeed, this study supports previous research in lab dishes that these folds occur in areas that regulate genes.

These areas include the very ends of chromosomes called “telomeres” that are thought to play a role in aging and regions called promoters which are tasked with turning genes on and off.

But despite knowing some of the regions in which these folds can appear, the researchers don’t yet know which genes the folds control or what happens when you disturb the cell so that it can’t form these structures.

These types of drugs could be helpful for cancer treatment, for example.

One problem with certain cancer treatments is that they aren’t selective enough in targeting the problematic stretches of DNA, said Laurence Hurley, a professor at the University of Arizona and the chief scientific officer of Reglagene, a company that designs therapeutic molecules to target four-stranded DNA like i-motifs.

Instead, cancer drugs may attach to other parts of DNA as well, leading to possibly harmful side effects, said Hurley, who was not part of the new study.

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DNA Proves ‘Alien’ Was Actually Human Girl—Who Was She?

The mummified fetus from the Atacama region of Chile.

Before the media frenzy, before the documentary about aliens, before her bone fragments were ground up for DNA analysis, she was a girl.

She was tiny when she died. Six inches. Perhaps she was stillborn or died very young.

Her body was reportedly found wrapped in cloth with a purple ribbon and buried—with intentionality, it would seem—near a church in La Noria, an abandoned town in the Atacama desert in northern Chile.

As for everything else, well, it went like this. In 2003, a local man who regularly scavenged La Noria for historical trinkets found her body. He noted the unusual conical shape of her head.




Almost immediately, photos of her began to circulate, and ufologists eager for evidence of aliens came calling. A businessman bought her body and brought it to Spain.

She featured prominently, as the “Atacama humanoid,” in a documentary called Sirius, which alleges, among other things, contact between aliens and ancient civilizations.

On screen, the filmmakers are shown cutting her skull open, and removing a rib fragment for DNA analysis.

That DNA analysis was published last week—in Genome Research, a legitimate journal, and authored by a team of legitimate biologists led by Garry Nolan of Stanford University.

Museums were mad for skeletons around the turn of the 20th century.

That Nolan came to work with the makers of an alien-conspiracy documentary is unorthodox, to say the least.

But it was an opportunity to study rare mutations that could explain her unusual bones as well as an opportunity to restore to her a small measure of dignity.

The DNA analysis proved what scientists had been saying all along: She is human. She could have died as recently as decades ago based on the preservation of her DNA.

In interviews, Nolan told journalists he believed her body should be returned to Chile.

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Meet Cheddar Man: First Modern Britons Had Dark Skin And Blue Eyes

They call him Cheddar Man.

He lived more than 10,000 years ago, had brown hair, blue eyes and “dark to black” skin. To the surprise of many, he is believed to have been the first modern Briton.

A new project from London’s Natural History Museum and University College London has revealed groundbreaking DNA results that give a much clearer image of early British inhabitants.

Cheddar Man’s skeleton was discovered in 1903 in Gough’s Cave, located in Cheddar Gorge in Somerset, England. It is thought that the cool temperature in the cave helped to preserve the skeleton’s valuable DNA.

If the body was deposited in a good environment, where there was a cool and constant temperature, then the petrous bone is a good place to find useful ancient DNA,” said the Natural History Museum’s Selina Brace, who specializes in the study of ancient DNA.

Scientists obtained DNA from Cheddar Man by drilling a 2-millimeter hole in his skull and extracting bone powder.




Initially, it was assumed that the man, who died in his 20s, had pale skin, but new analysis and facial reconstruction have revealed quite the opposite.

It is now believed that Cheddar Man’s ancestors arrived in Britain via the Middle East after leaving Africa.

Cheddar Man is special because he represents the population occupying Europe at the time,” said Tom Booth, a bio-archaeologist at the museum.

They had dark skin, and most of them had pigmented eyes, either blue or green.” Data and software used in forensics gave Booth and the team a clearer understanding of Cheddar Man’s skin pigmentation and how dark it was.

The investigation into the skeletal remains revealed that Cheddar Man had “genetic markers of skin pigmentation usually associated with sub-Saharan Africa.”

The skull of Cheddar Man

Cheddar Man’s skeleton revealed damage to the front of the skull, which led us to believe he had a violent death. But when we looked again, it appeared likely that the damage occurred since being dug up,” Booth explained.

“It’s quite hard to figure out from the bones how he died, as most illnesses don’t leave a trace on human remains.”

Using 3-D printing, Adrie and Alfons Kennis were able to bring Cheddar Man to life. The model took several months to build and is described as “truly unique.”

Booth described their work as “amazing” and said the two brothers are skilled “wizards” who were able to bring years of hard work and research to life.

Experts say the ancestor was a Mesolithic hunter-gatherer who would have spent his days carving tools, fishing and hunting animals. Researchers say he was around 166 centimeters (5’4 inches) in height.

It is believed that Cheddar Man is related to 1 in 10 people living across the United Kingdom today.

It didn’t take long for Cheddar Man to trend worldwide on Twitter. Reactions to the extraordinary findings were mixed. Some praised the work of those involved with the reconstruction of Britain’s oldest skeleton.

Others focused on the racial tension in Britain and pointed out that perhaps not all Brits would be happy about their ties to the ancient human.

Cheddar Man’s complete skeleton has been lent to the museum and is currently on display.

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Scientists Find Jawbone Fossil From Oldest Modern Human Out Of Africa In A Cave In Israel

Scientists on Thursday announced the discovery of a fossilized human jawbone in a collapsed cave in Israel that they said is between 177,000 and 194,000 years old.

If confirmed, the find may rewrite the early migration story of our species, pushing back by about 50,000 years the time that Homo sapiens first ventured out of Africa.

Previous discoveries in Israel had convinced some anthropologists that modern humans began leaving Africa between 90,000 and 120,000 years ago. But the recently dated jawbone is unraveling that narrative.

This would be the earliest modern human anyone has found outside of Africa, ever,” said John Hawks, a paleoanthropologist from the University of Wisconsin, Madison who was not involved in the study.




The upper jawbone — which includes seven intact teeth and one broken incisor, and was described in a paper in the journal Science — provides fossil evidence that lends support to genetic studies that have suggested modern humans moved from Africa far earlier than had been suspected.

Dr. Hawks and other researchers advised caution in interpreting the discovery.

Although this ancient person may have shared some anatomical characteristics with present-day people, this “modern human” would have probably looked much different from anyone living in the world today.

Early modern humans in many respects were not so modern,” said Jean-Jacques Hublin, director of the department of human evolution at the Max Planck Institute for Evolutionary Anthropology in Germany.

Dr. Hublin said that by concluding the jawbone came from a “modern human,” the authors were simply saying that the ancient person was morphologically more closely related to us than to Neanderthals.

 

That does not mean that this person contributed to the DNA of anyone living today, he added. It is possible that the jawbone belonged to a previously unknown population of Homo sapiens that departed Africa and then died off.

That explanation would need to be tested with DNA samples, which are difficult to collect from fossils found in the arid Levant.

The upper jawbone, or maxilla, was found by a team led by Israel Hershkovitz, a paleoanthropologist at Tel Aviv University and lead author of the new paper, while excavating the Misliya Cave on the western slopes of Mount Carmel in Israel.

The jawbone was discovered in 2002 by a freshman on his first archaeological dig with the group.

The team had long known that ancient people lived in the Misliya Cave, which is a rock shelter with an overhanging ceiling carved into a limestone cliff.

By dating burned flint flakes found at the site, archaeologists had determined that it was occupied between 250,000 to 160,000 years ago, during an era known as the Early Middle Paleolithic.

Evidence, including bedding, showed that the people who lived there used it as a base camp. They hunted deer, gazelles and aurochs, and feasted on turtles, hares and ostrich eggs.

Dr. Hershkovitz and Mina Weinstein-Evron, an archaeologist at the University of Haifa, felt that the jawbone looked modern, but they needed to confirm their hunch.

The Misliya finding is just the latest in a series of discoveries that are changing the story of our evolutionary past.

One study, not yet confirmed, suggested that modern humans may have interbred with Neanderthals in Eurasia about as far back as 220,000 years ago.

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Chinese Scientists Have Successfully Cloned Monkeys

Two monkeys are the first ever primates to be cloned using the technique that created Dolly the sheep.

The technique brings the prospect of cloned human beings even more closer.

But scientists caution that there may be no good reason to create such clones, and that ethical and legal questions need to be answered about such research.

More immediately, the technique will allow researchers to create whole labs full of genetically identical monkeys.




That could prove tremendously useful in scientific and medical research – allowing doctors to watch how specific treatments affect the genetic makeup of animals that are otherwise exactly the same, for instance.

The two identical long-tailed macaques – named Zhong Zhong and Hua Hua – were born eight and six weeks ago at a laboratory in China. They represent the furthest reaches of cloning technology, genetically resembling each other entirely.

They aren’t, strictly, the first primates to have been cloned. But they are the first to be produced using the single cell nuclear transfer (SCNT) technique, which involves transferring cell nucleus DNA to a donated egg cell that is then prompted to develop into an embryo, and is the same process used for Dolly the sheep.

Previous work has relied on splitting embryos, which is the same phenomenon that happens when twins are born and can only produce four offspring.

The two monkeys were part of a total of 79 different transfer attempts, which used different techniques. Scientists had some luck cloning monkeys using adult cells, but those were only able to survive for a few days.

That genetic symmetry of the monkeys means that scientists could create a whole experiment’s worth of identical monkeys, save for the specific genetic changes that they want to study.

But the research has already led to fears about where it could lead.

The scientists stress they did the work under strict international codes, and co-author Muming Poo said the team was aware “that future research using non-human primates anywhere in the world depends on scientists following very strict ethical standards”.

The breakthrough means that it would theoretically be easier to clone a human, since primates share so much of their makeup with us.

But actually doing so is much less likely, given the ethical and regulatory objections there would be to any such plan.

Scientists will keep watch on Zhong Zhong and Hua Hua, who for now appear to be growing and developing like normal monkeys. They expect more clones to be born in the coming months.

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Taking Gene-Editing To The Next Level

Researchers who discovered a molecular “scissors” for snipping genes have now developed a similar approach for targeting and cutting RNA.

The new cutting tool should help researchers better understand RNA’s role in cells and diseases, and some believe it could one day be useful in treatments for illnesses from Huntington’s to heart disease.

To develop the “blades” for the process, researchers led by Feng Zhang at the Broad Institute used CRISPR (clustered regularly interspaced short palindromic repeats)—a system that bacteria evolved to fight off pathogens.

CRISPR has previously been used to edit DNA but had been theorized to work on RNA as well.

The new findings, reported Thursday in Science, came from systematically exploring different aspects of that natural defense system that protects bacteria—and may eventually be put to use helping people.

Nature has already invented all these really interesting mechanisms,” Zhang says, comparing himself with a treasure hunter.

We’re just trying to play with that and learn how they work…then turn them into tools that will be useful to us.




 

Zhang says the new paper will not affect an ongoing patent dispute over who owns rights to the gene-editing approach known as CRISPR–Cas9. His team was the first to use CRISPR–Cas9 in mammalian cells.

Another team—led by Jennifer Doudna, at the University of California, Berkeley, and French researcher Emmanuelle Charpentier—was first to publish on CRISPR–Cas9, showing its activity in bacteria.

Ironically, Doudna was a co-author on a March paper in Cell that used CRISPR–Cas9 to cut RNA in mammalian cells whereas Zhang’s new paper focuses on bacteria.

The two RNA manipulation methods may be complementary ways to approach the same ends or one may turn out to be more efficient than the other.

In interviews this week each group praised the other’s work while touting the advantages of their own respective approaches.

Zhang says his new method—using the enzyme C2c2 to target RNA—relies on an existing natural system and therefore may be more effective than an approach that requires more manipulation.

Gene Yeo, senior author on the Cell paper, says he has collaborated with both Doudna and Zhang, and described the new paper as a continuation of the kind of “friendly competition” that drives science.

There’s always a bit of a race between a lot of the groups, including mine,” he says. “I think scientific competition is good. People tend to push the boundaries more.

Although Yeo pointed out that the C2c2 system has not yet been shown to work in mammalian cells, Zhang says unpublished results make him optimistic that it will.

Both RNA-targeting approaches have a long way to go before they could be tested in people—but the promise is there, says Yeo, a professor of cellular and molecular medicine at the University of California, San Diego.

Targeting RNA may also offer new insights into how changes in RNA lead to changes in biology and the development of disease.

I think we’ll see an avalanche of these tools that will enable us to monitor and study RNA,” Yeo says.

This helps us think about RNA as not just an intermediate molecule between DNA and protein,” but as a therapeutic tool for treating diseases and problems of development.

Genes consist of double-stranded DNA, which makes single-stranded RNA—which in turn makes the proteins needed for life. Many diseases result from too much or too little protein.

Theoretically, acting on the RNA could push those protein levels up or down, thereby offering treatments.

Manipulating RNA poses fewer ethical concerns than tinkering with the underlying DNA, although gene editing will remain a better approach for treating some diseases.

The problem with DNA editing is that it’s permanent,” Yeo says. “That could be good, but what if you make a mistake?

In some cases, such as with brain cells, DNA repair mechanisms are so strong that it may be more effective to act on the RNA rather than cutting the DNA, says Yeo, who has started a company that’s still in stealth mode to begin looking at treating diseases with this approach.

Zhang says he has long been interested in developing systems to target RNA. His team decided to survey the different kinds of CRISPR systems to figure out their functions.

C2c2 turned out to be an RNA-targeting system, according to the new study, which includes researchers from the National Institutes of Health, Rutgers University and the Skolkovo Institute of Science and Technology in Russia, in addition to Harvard University and Massachusetts Institute of Technology.

Like the Cas9 system that targets specific DNA, C2c2 can be aimed directly at desired RNA sequences, with seemingly few off-target effects.

The reason that it has evolved is to be able to use RNA guides to target RNA,” Zhang says.

His colleague, Eugene Koonin, a co-author on the new paper, puts it more poetically: “Evolution of life to a very large extent is a story of host–parasite interactions,” says Koonin, an expert in evolutionary genomics at the National Center for Biotechnology Information.

As we explore this arms race between host and parasite, we discover more and more intricate, novel ways in which cellular organisms cope with parasites and parasites counteract.

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DNA Of Man Who Died In 1827 Recreated Without His Remains

Recreating a deceased person or animal’s DNA has required that DNA be extracted from the remains of the individual, but a new study has shown that may not be the only way.

The DNA of a man who died nearly 200 years ago has been recreated from his living descendants rather than his physical remains — something that has never been done before.

deCODE Genetics, a biopharmaceutical company in Iceland, achieved this feat by taking DNA samples from 182 Icelandic descendants of Hans Jonatan, a man who is quite an icon in Iceland, most well known for having freed himself from slavery in a heroic series of seemingly impossible events.




It was the unique circumstances of Hans Jonatan’s life that made it possible for his DNA to be recreated after his death. For one, Jonatan was the first Icelandic inhabitant with African heritage.

Iceland also boasts an extensive and highly detailed collection of genealogical records.

The combination of Jonatan’s unique heritage and the country’s record-keeping for inhabitants’ family trees made this remarkable recreation possible.

deCODE used DNA screened from 182 relatives, first reconstructing 38 percent of Jonatan’s mother Emilia’s DNA (which accounted for 19 percent of Jonatan’s).

Published in Nature Genetics, this elaborate study began with a whopping 788 of Jonatan’s known descendants, but was able to be narrowed down to 182 through DNA screening against known markers.

While this is truly an amazing feat, according to Robin Allaby of the University of Warwick in the United Kingdom,  it “seems to be the sort of analysis you could only do under particular circumstances when an immigrant genome is of a very rare type.

Despite these limitations, deCODE believes the technique could have extensive applications.

Kári Stefánsson of deCODE said that “It’s all a question of the amount of data you have. In principle, it could be done anywhere with any ancestors, but what made it easy in Iceland was that there were no other Africans.”

Allaby does believe the results of this study could give us additional avenues to explore the DNA of those who have long since passed.

“It’s the sort of study that could, for instance, be used to recover genomes of explorers who had interbred with isolated native communities.”

Theoretically, a technique like this could help researchers create “virtual ancient DNA,” which would allow scientists to recreate the DNA of historical figures.

Agnar Helgason of deCODE stated that “Any historic figure born after 1500 who has known descendants could be reconstructed.”

While it’s exciting, there are still major hurdles to overcome in terms of the potential future applications.

The quantity, scale, and detail of the DNA from living ancestors required to recreate a person’s DNA make it impractical for use within most families.

Additionally, with each new generation identifiable DNA fragments get smaller and more difficult to work with.

To that end, more immediate applications might involve repairing and filling in spaces within family trees.

But if it’s honed, it could become a valuable historical tool, giving us an in-depth look at what life was like for historical figures like Jonatan.

Scientists could genetically resurrect anyone, providing us with a more thorough understanding of our species both from our own personal familial perspectives and through the more macrocosmic lens of human history.

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