Daily Archives: July 5, 2017

Enlarge / The entrance to the cave where the Neanderthal thigh bone was found in 1937.

Modern humans and Neanderthals have a confusing genetic relationship. One set of data suggests our two species diverged around 650,000 years agobut other clues point to an ongoing close (that is, sexual) relationship between our ancestors that persisteduntil around 300,000 years ago. This is made all the more muddled by the fact that Neanderthals look like they were living in Eurasia 300,000 years ago whileour own ancestors were still in Africa. And then the two groups clearly intermingled once humans did leave Africa.

One way to account for all this contradictory information is to suggest that another group of humans left Africa sometime between the Neanderthals' departure and our own. An analysis of Neanderthal DNA, published this week in Nature Communications, adds new weight to this hypothesis.

When people talk about DNA, most often theyre talking about nuclear DNA. Thats the DNA that combines genetic material from a mother and a father and sits in the nucleus of each cell. But the mitochondrialittle energy-producing blobsthat sit inside cellshave their own DNA, which comes exclusively from the mother. Mitochondrial DNA (mtDNA) is a fantastically useful tool for understanding evolutionary lineages, in part because there's so much more of it that it's still detectable in very old samples.

The picture painted by nuclear DNA(nDNA) is that, between 765,000 and 550,000 years ago, our ancestors in Africa diverged into two groups. One group would eventually lead to our own species, although we wouldn'tmakean appearance until around 200,000 years ago. The other group would lead to Neanderthals and the closely related Denisovans. This proto-Neanderthal/Denisovan group left Africa for Eurasia at some point; sometime around 430,000 years ago, they diverged into distinct Neanderthals and Denisovans.

But the picture painted by mtDNA is different. Neanderthal mtDNA is more similar to modern humans than it is to Denisovan mtDNA. And the divergence date between us and them, when estimated based on mtDNA, is much more recentbetween 498,000 and 295,000 years ago.

Some researchers have suggested that you can explain this mixed genetic evidence if Neanderthals interbred with another, more recent African group of humans. This would provide them with different mtDNA after they split from Denisovans. And that, in turn, means that there must have been humans, closely related to our own species, who left Africa for Europe far earlier than previously suspected.

Some archaeological evidence supports this scenario: African and Eurasian technologies in this time period have some important similarities. Theres also corroborating evidence from very old Neanderthal DNA from Spain, which has Denisovan-like mtDNA. That matches up with the picture that Neanderthals started out with both nuclear and mtDNA closely related to their cousin Denisovans, but had their mtDNA replaced through breeding with other humans.

But there are some plausibility issues here. We know that our own species interbred with Neanderthals more recently, so thats not a problembut could low-level interbreeding on this small scale really result in such drastic changes to Neanderthal mtDNA, without leaving much of a mark on its nuclear genome? It also hasnt been possible to narrow down the window of whenall this interbreeding might have happened. This makes assessing the feasibility of the mtDNA-replacement scenario difficult.

A Neanderthal thigh bone from southwestern Germany has offered up some answers. The bone has been dubbed HST, after the Hohlenstein-Stadel cave where it was found in 1937. Itis the only human fossil from this region and time. Of course, a bone that has been handled by humans for that long is bound to have been subject to genetic contamination, and the researchers accounted for this in their analyses.

HST seems to have lived around 124,000 years ago, making this the second-oldest Neanderthal mtDNA to have been analyzed. The evidence pointed toward HSTs family line having diverged from other Neanderthal groups around 270,000 years ago.

That helps to narrow down the time frame of the genetic mixture with African humans: the mixing must have happened before 270,000 years ago. This suggests that the early migration out of Africa must have happened sometime before that. Given this timeframe, the researchers calculated that a huge mtDNA shift, based on low-level interbreeding, was, in fact, plausible.

Its a new point in favor of this early-migration hypothesis, but a lot more evidence is needed. Thestory is inordinately difficult to piece together because data is so scarce. Analyzing genomic DNAfrom the HST thigh bone would be fantastic, if it were possible, but modern contamination and the decay of itsincredibly ancient DNA make this a challenging prospect. We might get no more stories from HSTwell have to look to other Neanderthals for new puzzle pieces.

Nature Communication, 2016. DOI: 10.1038/ncomms16046 (About DOIs).

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Neanderthal DNA suggests yet another wave of human migration out of Africa - Ars Technica

TULSA -- What if your DNA could tell you about how to lose weight, or what foods and exercise are best for your health?

2 Works for You's Chera Kimikofollowed 98.5KVOO's Sunny Leigh for two months after she took the DNAFit test to see if knowing her DNA helped her shed the pounds for food.

Leigh, the bubbly morning personality on KVOO has no trouble getting people through their morning drive. But she does have trouble navigating her own health and weight loss goals.

"I weighed 130 pounds when I moved here," Leigh said. "I still had a big butt and big legs and I always fought that"

Dr. Mark Sherwood with Functional Medical Institute said the answer could be in her DNA.

"DNA makes up more than 20,000 genes, each carry instructions for a single protein," Sherwood said. "Together they determine how we look and how our bodies function."

First things first, Leigh went to see Dr. Sherwood, where doctors got her health information and sent if off to a lab.

Life-changing information for her was revealed on live radio.

"I've got to be honest, I am absolutely horrified because it seems like I have every possible bad thing against me," Leigh said. "But you said it is really not as terrible as I'm making it?"

"No, look at this as a standpoint of empowerment," Sherwood said. "Just because the genes say 'X' does not mean that is your destiny.

The DNAFit test let Leigh know what workouts are best for her DNA.

"You are a dominant endurance person," Sherwood said. "You don't need to go hard, you need to keep your heart rate below about 120-135, where you can carry on a conversation."

So Leigh hit the gym four days a week, doing 20 minutes of cardio and 40 minutes of leg, arm, abs and back exercises. Next, she changed up her eating habits to cut out things shedoesn't metabolize.

"Red meat, sugar, dairy, alcohol and caffeine, all a big no-no," Sherwood said.

"I am wondering what food there is left for me to eat," Leigh said.

Now, it's all about berries and lots of greens.

"According to my genetics, I need to be eating a whole lot more fruits and vegetables," Leigh said.

Halfway through the program in June, she checked in with Dr. Michelle Sherwood.

"It is going to tell us quite a few things," Sherwood said. "Your weight, it is going to tell us about your lean body mass, the percentage of fat you carry on your frame and your cellular health."

In one month, Leigh lost eight pounds of fat and gained four pounds of muscle. But the changes haven't come easy.

"Coffee has been really hard," Leigh said. "One of the big challenges, according to my DNA, is I don't process caffeine so I have gone to half calf. Eating healthy has been a lot more expensive than eating junk food so that has been a hit to my wallet. Having to buy all the fresh fruit and produce and fresh vegetable and fish, but in the long run it is a lot cheaper than having diabetes."

The payoff was worth it.

By July, she lost nine to 10 pounds of fat, and went up about eight pounds in lean body mass.

The DNAFit test at the institute costs about $380, but it can be paid for with a health savings account. The test can also show how people metabolize minerals and vitamins.

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Weight loss program tailored to your DNA - kjrh.com

Judge releases capital murder suspects

Tanya Eiserer, WFAA 3:48 PM. CDT July 05, 2017

A Dallas County district judge has ordered the release of two capital murder suspects after prosecutors failed for more than a year to send the DNA of one of the defendants to the lab to be tested.

On Monday the judge ordered that Leonte Stone, 24, and Konkun Tarpeh, 25, be released on electronic monitoring and house arrest.

The only thing keeping the two men in jail currently are holds from other counties. Tarpeh is being held on a Tarrant County violation on a protective order charge from Tarrant County. Stone is being held from Hunt County for evading arrest and child endangerment charges.

By state law, prosecutors have 90 days to announce that they're ready for trial from the day that a person is arrested. That's to keep indigent defendants from just being held in jail in perpetuity. In this case, prosecutors had failed to send Stones DNA to the lab to be tested against evidence collected in the case.

District Judge Brandon Birmingham ordered their release on a personal recognizance bond.

The DNA testing also cant be done quickly because of a recent issue with countys new DNA testing kits, which proved to be defective. The county crime lab suspended DNA testing in cases set for trial. The lab plans to restart testing in September with new testing kits.

Stone and Tarpeh are accused of killing Taydren Young and Dmydric Williams at an apartment complex on Forest Lane last March. Police said Young and Williams had gone there to buy marijuana.

Stone has been in jail since April. Tarpeh was picked up again in December. Their bail in the capital murder case had been set at $1 million each.

I am highly, highly upset, says Shokee Clay, Youngs mother. I'm very upset about the whole situation that there's even talk of anybody being released. There aren't words to explain how I feel about that.

Clay is angry that prosecutors did not tell her there was an issue with the case. She says the prosecutor on the case had assured her that she would keep her informed.

My son may not matter to them, but he matters to me, and I'm going to fight to the end for my son and I'm not going to let this ride, she says. I'm going to be up there tomorrow because I need some answers... because I need to know why I wasn't notified and how did they let DNA slip through.

She worries that if Stone and Tarpeh are released, they will just cut their ankle monitors and disappear.

The DAs office says that they will continue to vigorously pursue prosecution in the case. They said they could not comment further due to the ongoing nature of the case.

Shokee still cries every day over the loss of her son.

A video of Young freestyle dancing brought a smile to his mom's face. She misses his goofy, fun-loving personality.

I just wish I could reach in here and grab him out, but I know I can't, she says. Every day that go on, you know that he really, really not coming back.

Shokee and her husband had moved their boys out of Dallas to keep them safe.

Her middle son -- who is one year younger than Young -- is in college. Their other son is finishing high school.

Young's future had also looked bright.

He had graduated with honors from John Horn High School in Mesquite. He had a scholarship to Texas Southern University. He attended for two semesters before dropping out.

Young gravitated to a rougher crowd once back in Dallas.

On the day he died, Clay said she called her son. He asked her to pick him up in North Dallas. She told him she would pick him up after work. An hour later, Young was killed. He left behind an infant son.

I did everything I could, she said. Its not about how you raise your boys. It's about the company they keep.

As painful as it was, Shokee was there when they cremated Young.

This is all I have left of him, she says pointing to the wooden box containing his ashes. I walk by it every day and this is what I have and no mother should have to have one of these.

2017 WFAA-TV

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DNA not sent for testing; judge orders release of two capital murder suspects - WFAA

Parking bansigns installed on the Near West Sideaimed at curbing gang parties have been vandalized before the ban was set to begin. View Full Caption

DNAinfo/Stephanie Lulay

NEAR WEST SIDE Parking bansigns installed on the Near West Sideaimed at curbing gang parties have been vandalized before the ban was scheduled to begin.

Part of a larger plan to keep partiers from parking near Touhy-HerbertPark, the residential parking restrictions are set to go into effect July 24. But just days after the signs were installed, at least one sign nearWestAdams Street and SouthHamilton Avenue nearthe defunct Jelly Bean Garden was pushed to the ground, and at least one other parking sign was removed, neighbors reported.

The signs were installed June 27 and were torn down by Friday night, said one neighbor,who has asked not to be named for fear of retribution. Neighbors have reported the damaged signs to the city's 311 non-emergencycall center, he said.

"It seems like it was done in protest," said the man, who has lived in the area for six years. "I think the people who may have removed the signs are really just looking at any changes that are being made over as a sign that they are not wanted ... and they are trying to protest that in any way that they can."

A sign at Adams and Hamilton was pushed to the ground next to the neighborhood's defunct Jelly Bean Garden, an 8-year-old community lot across the street from Touhy-Herbertpark ruined by litter. [DNAinfo/Stephanie Lulay]

Some other residential parking ban signs recently installed onthe block were not vandalized or removed.

In the spring,Burnett pitched a plan toconvert a fewstreets near Touhy-HerbertPark to a residential permit parking zone, aiming to block partiers from parking near the park.

RELATED:Raucous, 200-Person Gang Parties Ruining Park Can Parking Ban Stop Them?

Near West Side police saidthe new parking rules could be a valuable tool, as the overnight restrictions would allow police to ticket and tow cars that don't have resident parkingstickers.

Burnett could not be reached for comment.

The parking bansigns were installed after araucous gang partybrought 1,000 people to the residential streets around Touhy-HerbertPark last month, a party that Burnett said was too large for police officers in 25 Chicago Police Department squadcars to break up. The police were outnumbered, he said.

"It's not just an inconvenience, it's very dangerous," Burnett said at the time."When you have that many people drinking, getting high, anything can happen."

RELATED:1,000-Person Gang Party Too Big For Police In 25 Squads To Stop, Ald. Says

At 8:40 p.m. June 20, days after the party,26-year-oldAntwon High was shot dead at Adams and Hoyne, just steps from the park. Two other men, ages 21 and 23, were wounded in the shooting.

RELATED:Antwon High, 26, Killed In Near West Side Shooting; 2 Others Wounded

Neighbors also had previously lobbied for a residential parking zone to be set up south of the park, saidKaterina Klopas, treasurer of theTouhy-Herbert Park Advisory Council.

The zone includes permit parking on the south end of Adams Street;LeavittStreetfrom Adams Street to Jackson Boulevard;Hamilton Avenuefrom Adams to Jackson; and Hoyne Avenue from Adams to Jackson, Burnettsaid. Parkingalso is prohibited onthe north of end of Adams overnight.

A residential parking ban sign was pushed to the ground at Adams and Hamilton, and another sign on the block was removed, neighbors report. [DNAinfo/Stephanie Lulay]

Before the signs were installed, the six-year neighbor said he was skeptical that a residential parking ban could help stop parties at Touhy-Herbertpark. Now that some signs have been defaced or removed, he said he's now even more skeptical the ban canmake a difference.

"I'm pretty skeptical,"the neighborsaid. "It's only going to make a difference if it's strictly enforced, and I don't have the confidence that it will be strictly enforced. I think a lot of people in the neighborhood are looking for a quick fix, and I don't think this was going to beit."

Another neighbor who has lived in the area for three years called the vandalism "disheartening."

"It's hard because the alderman and the neighborhood are putting up an effort," she said.

Here's parking sign at Hamilton Avenue and Jackson Boulevard that was not vandalized.[DNAinfo/Stephanie Lulay]

In a statement, Police Department spokesman Anthony Guglielmi said Near West Police District Cmdr. Edward Kulbida has increased patrols in the area in and around Touhy-Herbert Park.

"Iknow Cmdr. Kulbida has increased patrols overall in the park, and officers are going to be very strict on enforcing city park rules," Guglielmi wrote.

RELATED:Gun-Waving Teen, 14, Seen In Rap Video Arrested On Gun Charge Days Later

RELATED:A Music Video Was Shot In The Middle Of Last Week's 1,000-Person Gang Party

RELATED:Loud Gangbangers Party All Night Long at Near West Side Park, Neighbors Say

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Signs Aimed At Curbing Huge Gang Parties Near United Center Vandalized - DNAinfo

A few years ago, Harvard professor and bio-engineering rockstar George Church was a guest on The Colbert Report. As many of the talk show's guests did, he presented host Stephen Colbert with a copy of his book, which he'd co-authored with Ed Regis. Well, sort of. He actually handed Colbert 20 million copies of his book -- and they all fit in his front pocket.

How was that possible? Church had programmed 20 million copies of his book into DNA, which is known, rightly so, as the "information molecule" in biology. The incredible density of information that can be stored in DNA, and the potential to use it much like a traditional hard drive, has not been lost on technology companies scrambling to keep up with society's exponentially growing need for data storage.

Perhaps due to its having let the future pass it by on one too many occasions, Microsoft (NASDAQ: MSFT) is going all-in on the idea. It plans to deploy a proto-commercial, DNA-powered storage device about the size of a commercial Xerox copier by the end of the decade in one of its data centers. Even though it would cost billions using today's DNA synthesis technologies and only serve a niche application, the technology developed in the next three years will go a long way to ushering in digital-bio hybrid computing machines. It could be big for investors, too -- if it works.

Image source: Getty Images.

Microsoft and the rest of the information technology industry has spent billions of dollars on data centers to date in an endless battle to scale with the needs of consumers and growing demand for cloud computing. The most expensive part of a data center is power consumption, since it takes a lot of power to keep arrays of servers cool. That has become especially painful as traditional storage media have begun hitting their limits, which means tech companies won't be able to wring any further cost reductions out of scaling storage capacity with today's technology.

That's what makes DNA so intriguing, on paper at least. Volume for volume, it can store 10 million times more information than the magnetic tape drives commonly used today, which would drastically reduce power consumption per TB or square foot of space in a data center. One copy of your genome, held in just one of your body's cells, holds approximately 1.5 GB of information. And since your body contains trillions of cells, all of the DNA in all of your body's cells stores trillions of GB of information -- more than all of the digital data storage capacity in the entire world (although it's getting close).

There is one massive obstacle to commercializing this technology, however: cost. Consider that state-of-the-art technology today can produce synthetic DNA for genetic engineering applications at costs of about $0.05 per base pair, and experts I've spoken to attest it could be two orders of magnitude lower for DNA data storage applications. (The end use affects the cost of DNA because each application has different requirements for accuracy, length, and yield.)

Image source: Getty Images.

Either way, even with the best technology today, it would take several months and hundreds of thousands of dollars to synthesize an equivalent amount of DNA held in a single cell of E. coli -- something the bacterium does for free in about 20 minutes.

The good news is the cost has fallen quickly -- it was $1 per base pair not long ago. The not-so-good news is Microsoft estimates costs would need to fall by a factor of 10,000 before DNA data storage could really take off.

The company will likely be powerless to drive down the cost of DNA synthesis without outside help from biotech companies (supply) and fellow tech peers (demand). That's why Microsoft has partnered with the University of Washington and DNA synthesis leader Twist Bioscience, which has received investments from Illumina and Applied Materials, among others.

Earlier this year the trio made significant progress developing the basic technology required for DNA data storage, such as error-free read and write capabilities. The early-stage work also shows which areas need drastic improvement:

The biggest cost reductions will come from synthesizing DNA as close to free as possible (nature does this pretty efficiently), although improvements in technologies allowing us to more fully tap into the awesome storage density of DNA will greatly improve the cost-benefit ratio as well.

Put it all together and today's DNA synthesis and DNA data storage technologies would enable digital data storage devices at a cost of between $2 billion and $4 billion per TB. That's awfully expensive, but tremendous cost reductions -- more than 99.9% -- are possible with the proper effort and investments.

It may seem ridiculous, but investors should know there is precedent for dropping costs of biotechnologies over 99.9%. The amazing success of the Human Genome Project, which was initiated to spur innovation in DNA sequencing ("reading genes"), serves as a great example of what's possible. The cost of sequencing a human genome fell from $3 billion at the start of the project to just $1,000 today. Illumina thinks it can reduce that to $100 in the near future.

The recently announced Genome Write Project, which aims to spur innovation in DNA synthesis and construction ("writing genes"), is the logical follow-up to the Human Genome Project. Catalyzing a similar cost reduction to its scientific predecessor would drop DNA data storage costs from $2 billion to $4 billion per TB today to market-ready prices in the next 15 to 20 years, perhaps much sooner for data-center applications when power consumption and footprint costs are factored in.

However, the Genome Write Project's main problem is a lack of funding: Other than a $250,000 grant from Autodesk, there isn't much funding to speak of, despite interest in DNA data storage for data centers from across the industry. If Microsoft is serious about delivering DNA data storage technology to the market, it may want to consider funding the public research project in addition to its in-house R&D. Otherwise, it may be difficult to drum up support from tech peers -- who represent future synthetic DNA demand.

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Microsoft's DNA-Powered Server Cost $2 Billion -- but Prices Could Drop Over 99.9% - Madison.com

We recently had Dr. Craig Venter speak at our Splash Health 2017 event. Dr. Venter is the first person to sequence a human genome, simply put: the instructions and information about human development, physiology, and evolution. In his interview, he points out that 15 years ago, sequencing a human genome would have cost $100 million and take over nine months.

Oh how far weve come. Today, there are a number of companies helping us to analyze our genes, or basically our DNA, which make up genes, to understand our physiology. Advances in sequencing the human genome have been the foundation for this knowledge, and is ultimately paving the path toward personalized medicine - therapies that are personalized to a persons genetic code, and its cousin regenerative medicine - therapies that replace or enable damaged cells, organs to regenerate.

One company, Orig3n, is doing both. Boston-based Orig3n started out in 2014 collecting blood samples to conduct regenerative medicine studies, but later added in the ability to conduct DNA testing to learn more about a persons intelligence, or predisposition to learning languages, to knowing what vitamins theyre deficient in.

Its an interesting an unique funnel the company has created for itself on its way to solve big problems with regenerative medicine, which seems more in its infancy than DNA testing.

To that end, Orig3ns DNA testing business has taken off.

In order to be tested, you take a cotton swab and swab the inside of your cheek to collect DNA samples from the cells inside your mouth. Alternatively, one could spit in a tube, which is how 23andMe collects samples of DNA.

From there, Orig3n breaks down the cells to open up the DNA, which is inside the nucleus of the cell. The DNA is then purified and put into a genetic test panel. Your DNA is then analyzed against other DNA that have been collected and studied.

The analysis of the DNA is pretty standard. What differentiates its products, according to Robin Smith, Founder and CEO, is how the analysis is packaged and how quickly the results are turned around. The whole genome sequencing world has been around for 15 years and is fairly commoditized, said Smith. The same thing is happening with DNA detection. The biggest differentiator for Orig3n is that it delivers the data in ways that are understandable, said Smith.

For instance, on Orig3n, tests focus on an analysis of your skin to perfect your skincare routine, or about your strength and intelligence. Tests range from $20 to $100.

On Everlywell, you can take a DNA test to measure your sensitivity to foods. Or for around $239, it appears you can test to see if you have HIV, Herpes Type 2 and other sexual diseases.

On 23andMe, you can pay $199 to learn what proportion of your genes come from 31 populations worldwide, or what your genetic weight predisposes you to weigh vs an average and what are some healthy habits of people with your genetic makeup [though personally these habits seem to be good for anyone regardless of genetic makeup].

But for Orig3n, the DNA tests are just a good business while also a funnel to the bigger problem theyre trying to solve, and for which they recently raised $20 million for: Regenerative medicine.

Before offering the DNA tests, Orig3n was taking and continues to take blood samples, reprogramming cells to go back to a state three days prior. And from there, they can grow certain tissues. The purpose of Orig3n is to create cell therapies for various diseases and disorders.

In the next fives year, there will be real live therapies to repairing the degeneration of your eyes or performing some cardiac repair, Smith predicted. It feels like 1993 when I used a phone line to dial into the Internet, then seven years later we had the boom. We think regenerative medicine - getting your body to induce itself to rejuvenate parts that are broken - is where the Internet was in 1993.

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DNA testing - on the road to regenerative medicine - VatorNews