Category Archives: DNA

LEBANON, Ohio -- A DNA sample solved a rape cold case about 16 years after the crime, Warren County Prosecutor David Fornshell announced Thursday.

Sixteen years ago, nurses at Brookside Extended Care discovered one of their residents -- a 29-year-old woman with developmental disabilities so severe she could neither walk nor speak -- had been violently sexually assaulted by an unknown man overnight. Not one of them,Fornshell said, has ever been able to forget it.

"It's sickening to think that anybody would be capable of doing that to someone so vulnerable," he said.

The victim died in 2011. The only DNA evidence of the culprit's identity -- blood and semen found in the victim's diaper after the assault -- languished without matches for over a decade, and $6,000 in reward money didn't coax leads out of the surrounding community. Brookside made improvements to its security, including the installation of many alarms and surveillance cameras, but no suspects emerged.

Until Thursday.

Fornshell believes a DNA cross-check has successfully identified the culprit as Brian Sundin, a 42-year-old whose DNA was on file with the Florida Department of Corrections.

Sundin was with charged the rape in February after the match was made, but his indictment remained sealed while he was at large. According to a news release from Fornshell, he was recently arrested and convicted of a theft offense in Williamson County, Tennessee.

With Sundin already behind bars, Warren County authorities unsealed the indictment and began the process of extraditing him to Ohio.

Authorities believeSundin, who lived nearby at the time, entered Brookside through an unlocked door and assaulted the victim, according to the news release.

Although the victim is no longer living, Fornshell said everyone from doctors to detectives agreed the county should seek justice for her sake and that of her family.

"It's going to be a situation where no jury is going to believe she in any way consented to any of this happening," he said.

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DNA solved 'cold case' rape of developmentally disabled woman 16 ... - WCPO

July 6, 2017 Sequence-specific, twist-induced, kinked elastic configurations, generated by molecular dynamics simulations on supercomputers at the Texas Advanced Computing Center, help explain how long strands of DNA can fit in small spaces. Credit: Christopher G. Myers, B. Montgomery Pettitt, University of Texas Medical Branch

A biological mystery lies at the center of each of our cells, namely: how one meter of DNA can be wadded up into the space of a micron (or one millionth of a meter) within each nucleus of our body.

The nuclei of human cells are not even the most crowded biological place that we know of. Some bactiophagesviruses that infect and replicate within a bacteriumhave even more concentrated DNA.

"How does it get in there?" B. Montgomery (Monte) Pettitt, a biochemist and professor at the University of Texas Medical Branch, asks. "It's a charged polymer. How does it overcome the repulsion at its liquid crystalline density? How much order and disorder is allowed, and how does this play a role in nucleic acids?"

Using the Stampede and Lonestar5 supercomputers at The University of Texas at Austin's Texas Advanced Computing Center (TACC), Pettitt investigates how phages' DNA folds into hyper-confined spaces.

Writing in the June 2017 issue of the Journal of Computational Chemistry, he explained how DNA may overcome both electrostatic repulsion and its natural stiffness.

The key to doing so? Kinks.

The introduction of sharp twists or curves into configurations of DNA packaged within a spherical envelope significantly reduces the overall energies and pressures of the molecule, according to Pettitt.

He and his collaborators used a model that deforms and kinks the DNA every 24 base pairs, which is close to the average length that is predicted from the phage's DNA sequence. The introduction of such persistent defects not only reduces the total bending energy of confined DNA, but also reduces the electrostatic component of the energy and pressure.

"We show that a broad ensemble of polymer configurations is consistent with the structural data," he and collaborator Christopher Myers, also of University of Texas Medical Branch, wrote.

Insights like these cannot be gained strictly in the lab. They require supercomputers that serve as molecular microscopes, charting the movement of atoms and atomic bonds at length- and time-scales that are not feasible to study with physical experiments alone.

"In the field of molecular biology, there's a wonderful interplay between theory, experiment and simulation," Pettitt said. "We take parameters of experiments and see if they agree with the simulations and theories. This becomes the scientific method for how we now advance our hypotheses."

Problems like the ones Pettitt is interested in cannot be solved on a desktop computer or a typical campus cluster, but require hundreds of computer processors working in parallel to mimic the minute movements and physical forces of molecules in a cell.

Pettitt is able to access TACC's supercomputers in part because of a unique program known as the Journal of Computational Chemistry initiative, which makes TACC's computing resources, expertise and training available to researchers within the University of Texas Systems' 14 institutions.

"Computational research, like that of Dr. Pettitt, which seeks to bridge our understanding of physical, chemical, and ultimately biological phenomena, involves so many calculations that it's only really approachable on large supercomputers like TACC's Stampede or Lonestar5 systems," said Brian Beck, a life sciences researcher at TACC.

"Having TACC supercomputing resources available is critical to this style of research," Pettitt said.

FINDING THE ORDER IN DISORDERED PROTEINS

Another phenomenon that has long interested Pettitt is the behavior of Intrinsically Disordered Proteins (IDPs) and intrinsically disordered domains, where parts of a protein have a disordered shape.

Unlike crystals or the highly-packed DNA in viruses, which have distinct, rigid shapes, IDPs "fold up into a gooey mess," according to Pettitt. And yet they're critical for all forms of life.

It is believed that in eukaryotes (organisms whose cells have complex substructures like nuclei), roughly 30 percent of proteins have an intrinsically disordered domain. More than 60 percent of proteins involved in cell signaling (molecular processes that take signals from outside the cell or across cells that tell the cell what behaviors to turn on and off in response) have disordered domains. Similarly, 80 percent of cancer-related signaling proteins have IDP regions - making them important molecules to understand.

Among the IDPs Pettitt and his group are studying are nuclear transcription factors. These molecules control the expression of genes and have a signaling domain that is rich in the flexible amino acid, glycine.

The folding of the nuclear transcription factor signaling domain is not brought about by hydrogen bonding and hydrophobic effects, like most protein molecules, according to Pettitt. Rather, when the longer molecules find too many glycines in a space, they go beyond their solubility and start associating with each other in unusual ways.

"It's like adding too much sugar in your tea," Pettitt explains. "It won't get any sweeter. The sugar must fall out of solution and find a partner - precipitating into a lump."

Writing in Protein Science in 2015, he described molecular simulations performed on Stampede that helped to explain how and why IDPs collapse into globule-like structures.

The simulations calculated the forces from carbonyl (CO) dipole-dipole interactionsattractions between the positive end of one polar molecule and the negative end of another polar molecule. He determined that these interactions are more important in the collapse and aggregation of long strands of glycine than the formation of H-bonds.

"Given that the backbone is a feature of all proteins, CO interactions may also play a role in proteins of nontrivial sequence where structure is eventually determined by interior packing and the stabilizing effects of H-bonds and CO-CO interactions," he concluded.

The research was enabled by an allocation of compute time on Stampede through the Extreme Science and Engineering Discovery Environment (XSEDE) which is supported by the National Science Foundation.

Pettitt, a long-time champion of supercomputing, doesn't only use TACC resources himself. He encourages other scholars, including his colleagues at the Sealy Center for Structural Biology and Molecular Biophysics, to use supercomputers as well.

"Advanced computing is important for data analysis and data refinement from experiments, X-ray and electron microscopy, and informatics," he says. "All of these problems have big data processing issues that can be addressed using advanced computing."

When it comes to uncovering the mysteries of biology on the tiniest scales, nothing quite beats a giant supercomputer.

Explore further: Rosetta online server that includes everyone

More information: Christopher G. Myers et al, Phage-like packing structures with mean field sequence dependence, Journal of Computational Chemistry (2017). DOI: 10.1002/jcc.24727

Our bodies are made of biomolecules like proteins, nucleic acids, fats and sugars. These biomolecules are folded into specific 3D structurespredetermined by the DNA and RNA sequences that build themwhich allows them ...

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Using the largest computer in Japan - one of the most powerful in the world - research led by an MSU scientist has achieved breakthroughs in understanding how proteins are affected by realistic biological environments. The ...

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Marijuana is now legal for recreational or medicinal use in at least 28 states and the District of Columbia. But driving under the influence of marijuana is illegal no matter which state you're in. To enforce the law, authorities ...

Researchers at The University of Manchester in collaboration with Central South University (CSU), China, have created a new kind of ceramic coating that could revolutionise hypersonic travel for air, space and defense purposes.

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Researchers explore DNA folding, cellular packing with supercomputer simulations - Phys.Org

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

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

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.

Original post:
DNA testing - on the road to regenerative medicine - VatorNews

The mystery only deepened in 2013. Another team of researchers retrieved mitochondrial DNA from a Neanderthal-like fossil at Sima de los Huesos, dating back 430,000 years.

The researchers had expected the DNA to resemble that of later Neanderthals in Europe. Instead, the mitochondrial DNA looked like it belonged to Denisovans even though the Denisova cave was 4,000 miles away in Siberia.

Last year, the researchers announced they had gathered a small fraction of the nuclear DNA from the same Sima de los Huesos fossil. That genetic material looked like it belonged to a Neanderthal, not a Denisovan.

Dr. Krause and his colleagues have now discovered new Neanderthal DNA that they believe can solve the mystery of this genetic mismatch.

In 2013, one of Dr. Krauses graduate students, Cosimo Posth, examined a Neanderthal fossil from a German cave called Hohlenstein-Stadel. He was able to reconstruct all of its mitochondrial DNA.

Dr. Posth estimated that the Neanderthal fossil was 120,000 years old and, more important, that it belonged to a branch of the Neanderthal family tree with a long history. He and his colleagues determined that all known Neanderthals inherited their mitochondrial DNA from an ancestor who lived 270,000 years ago.

All the data pointed to a sequence of events that could solve the puzzle that had bedeviled Dr. Krause for so long.

The common ancestors of Neanderthals and Denisovans spread across Europe and Asia over half a million years ago. Gradually the eastern and western populations parted ways, genetically speaking.

In the east, they became Denisovans. In the west, they became Neanderthals. The 430,000-year-old fossils at Sima de los Huesos Neanderthals with Denisovanlike genes capture the early stage of that split.

At some point before 270,000 years ago, African humans closely related to us moved into Europe and interbred with Neanderthals. Their DNA entered the Neanderthal gene pool.

Over many generations, most of that new DNA disappeared. But the mitochondrial DNA survived, passed down from mothers to their children. In fact, eventually all the Neanderthals inherited it, for some reason discarding the mitochondrial DNA that the species once had.

Dr. Posth said it was possible that early members of our own species moved from North Africa into Europe. Supporting this idea was the discovery reported last month of fossils of Homo sapiens in Morocco dating back 300,000 years.

But Dr. Posth said it was too soon to rule out another possibility: that these migrants belonged to another species in Africa closely related to us that scientists have yet to document.

I feel uncomfortable to give a name to these humans, Dr. Posth said.

Adam C. Siepel, a geneticist at Cold Spring Harbor Laboratory on Long Island who was not involved in the new study, said the hypothesis fit the evidence. I think thats absolutely possible, he said.

The new study raises a host of tantalizing implications about human history.

It is not possible to know just how many times these early Africans interbred with Neanderthals. But somewhere in prehistory, at least one female human from Africa must have carried the child of a male Neanderthal.

Now you have this hybrid child, which is probably pretty unusual-looking, Dr. Siepel said. One way or another, this hybrid individual was absorbed into Neanderthal society.

Dr. Siepel warned that the hypothesis hinges on the new DNA found in the Hohlenstein-Stadel fossil. Dr. Krause and his colleagues are now trying to retrieve nuclear DNA from the fossil.

The research at Sima de los Huesos shows just how far back in time scientists can now search for genes. The most revealing DNA might come from the mountains of Morocco.

There, scientists may be able to find genes from the earliest Homo sapiens, which they can then compare to Neanderthals.

These are things that I never thought possible five years ago, Dr. Krause said.

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In Neanderthal DNA, Signs of a Mysterious Human Migration - New York Times

From long-distance running to sprinting is ability down to DNA or effort or both. Composite: Getty Images

Growing up, I was always the dumpy, unsporty one. Matt, my older brother, was the skinny one who did the running, jumping and anything requiring quickness and coordination. He seemed to excel with ease while I laboured away on a sluggish course towards sub-mediocrity. This pattern lasted until our late teens when Matt, being older, beat me to booze. While he was away on a year-long, round-the-world bender, I took up running with a vengeance. It was time to turn the tables.

By the time Matt got back, Id joined the local running club and was training every day. It turned out that becoming a competent runner didnt require special talent, just lots of miles driven on by the sense I was outrunning my former, slouchy self. Matt, visibly shaken by my transformation, threw himself into training to catch up stymied by his three-kilo beer belly.

'The biggest shock is my aerobic potential, rated "low". OK, I'm no Mo Farah, but but surely my aerobic capacity is at least middling'

Well skip the gory details the dozens of races where I beat Matt with ease and fast-forward to 2012. I had been training consistently for six years by now. Matt was swiftly catching up, but I still had a clear edge in any race of more than10 miles, so I decided to step up to the marathon. After putting in the hardest three months training of my life, I came away with a shiny new PB of 2hr 28 min 46 sec.

The point is not to revel in my glory. My time was decent club standard but hardly impressive against proper British marathoners, let alone African elites. The point is, it was amazing for me, given my widely presumed lack of ability. If only I had realised sooner that I had the potential

Imagine someone had tested my genes as a podgy kid and told me: dont worry, youre an athlete inside, its only your Sherbet Dip Dab habit holding you back. What wonderful reassurance and motivation that would have been. But wait. What if they had looked at my results and said: sorry, its not through lack of effort that you are sub-mediocre its down to your DNA. What then?

I was intrigued to find companies offering to do just that test my DNA to determine my sporting potential. Could it really work? I decided to find out.

I got in touch with DNAFit, the leading provider, and asked if they would blind-test my DNA plus a few other samples. To my surprise, they said yes. A call to some friends with connections in elite sport secured a sample from a multi-Olympian and world champion runner (on condition I wouldnt reveal his identity) lets call him Mr Swift and another from pro cyclist James McLaughlin. If their results tallied with their achievements, I figured, DNA testing would be worth taking notice of.

A few weeks later the results were in. Swifts read as follows: Aerobic potential: medium, which qualified as an intermediate VO2max tendency. Yet according to his physiologist, Swifts VO2max is above 77 quite definitely not an intermediate score. Furthermore, the report deems his power/endurance profile as favouring power over endurance by a ratio of 70/30. Swift is one of the greatest endurance runners in the history of the sport. His injury risk, marked medium, is also at odds with the actual evidence. He has had many, many injuries, his physiologist confides. Id say his injury risk is untypically high.

McLaughlins results are similarly at odds with his track record: his aerobic potential is rated medium, with a slight tendency towards power over endurance. It doesnt ring true at all, McLaughlin tells me. My VO2max is very high, nearly 82, and Im a pure endurance rider I fare far better in long, sustained efforts than in sprints.

My own results also suggest a predisposition towards power rather than endurance, 56/47. This flies in the face of my running experience: I am hopeless at shorter, power-based events; the longer the race, the better I do (relative to others). The biggest shock is my aerobic potential, rated low. OK, Im no Mo Farah, but surely my aerobic capacity is at least middling, or how could I have run a sub-2hr 30min marathon?

I owe it to DNAFit to give them a chance to explain after all, they have been generous in blind-testing samples, opening themselves up to journalistic scrutiny. The companys head of sport science is the former Olympic sprinter Craig Pickering, to whom I reveal the disparities between our results and our sporting track records.

You almost certainly cant use genes to tell who will be a good athlete or not a good athlete, he responds. There is no talent identification use in this.

Fair enough, but our world-class marathon runner was rated as having medium aerobic potential.

Thats a great example of how you cant use genetics to tell you what sport youll be good at.

OK, fine, so what can genetic testing tell us?

What the tests and reports do is give you information on which to base your training, to have a better informed programme.

Citing one DNAFit-supported study on a small group of athletes, Pickering says that the results provide enough information to guide training, either towards power (short, sharp) or endurance (longer, slower) sessions. This insight, he says, relates to genetically determined trainability rate of fitness gain rather than aptitude. Yet this wasnt the impression I had been given by the reports, covered as they are with the word potential.

I stress my concern to Pickering that, had I received my apparently bleak results as a newcomer to running, my athletic ambitions might have been crushed. But he thinks I am missing the subtleties. Because you have a low aerobic potential we have options, we can fine-tune and target other areas like movement economy and efficiency.

Low aerobic potential? We know that marathoners rely on their aerobic capacity, so surely this implies that my prospects were limited. No, that isnt what it means, he replies. I accept that potential does imply that. The title should be changed. I often call it your aerobic trainability.

By by this point, I have to admit, I am erring towards unconvinced. My scepticism deepens when I read the Athlome Projects consensus statement on direct-to-consumer (DTC) DNA tests:

The information provided by DTC is virtually meaningless for prediction and/or optimisation of sport performance. There is currently no evidence that existing genetic tests provide information that is useful regarding either predisposition for a particular sport, prediction of the training response likely to occur to a particular training programme, or predisposition to exercise-related injury.

Athlomes founder, Professor Yannis Pitsiladis, is even more damning: These results are pointless, throw them away. There are no grounds for any of it.

According to Pitsiladis, although there is vast, exciting scope for genetics-guided training, the science has a very long way to go: Were beginning to understand that performance is determined by hundreds, possibly even thousands of interacting genes. Even once they are known, we may not be able to make predictions with clinical significance; we will need to take into account the environmental factors as well.

Countering the criticism from Pitsiladis and his Athlome colleagues, Pickering alleges sour grapes: Theyre annoyed that weve done it before them and thats why theyre causing these problems. Their main goal was to sell genetic tests to people, in my opinion. They are frustrated that were one or two years ahead of them.

Pitsiladis doesnt deny having commercial interests in genetic testing but insists he is involved only in areas with demonstrable utility, such as using genetics to create improved anti-doping tests. He draws a sharp distinction between genetically testing elite athletes to assess their shared traits and testing amateurs who are almost as diverse a group as the general population.

Parents whove failed as athletes go buy this stuff, desperate for their kids to succeed Selling direct to consumers is the problem.

That is precisely my concern, too. Cant Pickering appreciate that for people such as myself, starting out as the unsporty sibling with every reason to doubt my genetic potential, my gloomy test results could have snuffed out my marathon dreams before I had even tried a 5k run?

I share your concern, he replies. Its something that, as a company, we try to communicate. Our reports use the word potential, and that needs to change We have to do a better job, and well continue to try.

Make no mistake, talent matters. Athletes such as McLaughlin and Swift are prodigiously genetically blessed. My older brother, too, is a natural. He overtook me and became a far superior athlete, as I always suspected he would. But being the best you can be isnt about biology, it is art as much as science. Talent isnt destiny decipherable from DNA; it waits to be realised through hard work, like a sculpture inside a boulder. So dont let anyone put you off get hammering.

Originally posted here:
Is running ability down to effort or DNA? And can it be proved? - The Guardian (blog)