Daily Archives: March 29, 2017

Nearly a decade ago, Dallas police proposed a new program designed to get sex workers off the streets. Rather than just send them to jail, police would set up shop at truck stops, accompanied by counselors, social workers and nurses, and give the sex workers a choice of either prison or talking to a counselor. But the program also had a grimmer, more ethically fraught componentcollecting sex workers DNA in hopes of identifying their bodies should they wind up dead.

As a recent study from Duke University points out, for vulnerable populations, such data can be a double-edged sword. The same data that could help them also risks violating their genetic privacy, or worse, incriminating them should it be abused. Police have created, in essence, a DNA database of sex workers. Its not hard to imagine ways that could go wrong.

DNA databases have the potential to improve investigations into crimes impacting sex workers, who are more likely to be victims of murder than other populations, and often, do not carry any legitimate form of ID. Just as a decade ago some parents turned to fingerprinting to help identify their children in case they were kidnapped, the Dallas police started collecting DNA samples from sex workers just in case, god forbid, they wound up dead on the side of the highway. But while this kind of data might help police bring about justice for some of the grisliest crimes, it could also impinge upon sex workers privacy, coercing them into handing over information that could be indicting.

The social ramifications of collecting DNA from vulnerable populations (e.g., children, vagrant youth, sex workers, and victims of criminal acts) are considerable, and questions remain unanswered as to how best to protect individuals from misuse of their voluntarily provided DNA, write authors of the new study published in the International Journal of Criminal Justice Sciences.

Working with law enforcement, the authors went to Dallas to interview sex workers about the ongoing DNA collection program. Although many of the women said they do not trust police, they also said they willingly gave DNA samples because they want to be identified in the case of their death. The database has already helped to identify at least one woman, a sex worker who died in a Fort Worth ER in 2013.

My guy, the few times that I did talk to him while I was on the street, he always used to joke about the fact that they were going to tattoo my social security number and my address on my foot so that if I died that somebody knew who I belonged to, one focus group member said. That was one of the reasons why I did it. And then Ive had twofriends that have actually been identified through the program.

Still, some women were concerned about where their DNA might wind up.

One of my concerns would be who would have access to this information, once they got the DNA sample or whatever, who else would have access to it? another focus group participant said. Like would it be just for this simple organization or would everyonepolice, doctors, you know like people who go and donate sperm, sperm banks, stuff like thatlike who would have access to DNA?

As a society, we are just beginning to understand how important the right to genetic privacy is. Information about our DNA, if not properly handled and protected by law, could wind up not only incriminating people in criminal scenarios, but affecting access to things like insurance and employment. Right now, legislation is winding its way through Congress that seeks to undo some of the protections of the Genetic Information and Nondiscrimination Act. Many groups have spoken out against it, viewing it as a massive violation of public privacy.

The authors note that the police program has taken care to enact privacy protections, including only processing samples in the event of a death linked to a participant, and storing them in a facility not associated with law enforcement. But one participant suggested that a universal database, rather than one just for sex workers, and a program run outside of law enforcement entirely might make the program more egalitarian.

The Dallas program is a good example of the increasingly complicated position that DNA occupies in modern life. On the one hand, it can provide miraculous information that helps solve crimes, identify disease and help tell us about who we are. On the other hand, that same information can be damning.

And while the DNA sampling program is billed as voluntary, the authors question how voluntary it can really be when the request is coming from the police. At the time of DNA collection, the participants are either already under courtsupervision from an arrest or in a treatment program, which places them in a position under law enforcement authority, and perhaps less able to provide true consent, the authors write.

The authors point out that the only way to walk that fine line between benefit and disaster is to do so with careful consideration of all the ways things might go wrong. In this case, that means taking into account the opinions of the population the police are DNA testing, to make sure they arent coercing vulnerable people into unwillingly giving up a right to privacy.

[The Atlantic]

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DNA Is Being Collected to Protect Sex Workers, But It Could Also Be Used Against Them - Gizmodo

Print The draft policy says that before familial searching is done, local police have to certify that reasonable investigative efforts have been exhausted

By Anthony M. Destefano Newsday

NEW YORK A state panel of DNA experts approved on Monday a draft policy allowing familial searching, a new and controversial form of genetic testing, as a way of helping police solve homicide, certain sex crimes and terrorism cases.

By a unanimous vote, the DNA subcommittee of the state Commission on Forensic Science approved a short policy statement calling for familial searching, also known as FS, as well as a set of regulations to govern the procedure in New York.

The subcommittee also recommended that the commission approve the policy, which garnered interest as a result of the killing of Howard Beach jogger Karina Vetrano last August. Police got DNA from Vetranos body but couldnt get any matches with genetic profiles in the state DNA database.

The draft policy approved by the subcommittee said that before familial searching is done, the local police and prosecutors have to certify that reasonable investigative efforts had been exhausted or that emergency circumstances exist. It would also be used in investigations dealing with first-degree kidnapping and arson.

Interest increased in familial searching following a November 2016 story in Newsday which described familial searching and its potential use in the Vetrano investigation, which at that time seemed stalled. NYPD Commissioner James ONeill and Queens District Attorney Richard Brown issued strong statements calling for changes in state procedures to allow familial testing.

Todays action by the DNA Subcommittee of the NYS Commission on Forensic Science unanimously approving familial match DNA searches is an important step forward in identifying the guilty, excluding the innocent and bringing closure to the families of victims of unsolved homicides, Brown said in a statement. While the journey for justice for those families is not yet complete, this is an important milestone.

The Vetrano family also support the testing, even though police, using more traditional investigative methods, were finally able to make an arrest in early February of a suspect in Karinas homicide.

Some civil libertarians have voiced concerns about privacy and the fact that the existing state DNA database has a disproportionately high number of profiles of people of color. Proponents said familial searching is race-neutral.

2017 Newsday

McClatchy-Tribune News Service

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NY mulls use of DNA familial matching - Police News

Science Daily

Watching the passage of knotted DNA slip through nanopores ... Science Daily How can long DNA filaments, which have convoluted and highly knotted structure, manage to pass through the tiny pores of biological systems? Scientists used ... and more »

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Watching the passage of knotted DNA slip through nanopores ... - Science Daily

source: Stock Photo

If competitors didn't have enough to worry about concerning U.S. shale, another technological breakthrough has the potential to slash another 10 percent off of production costs for shale companies, further enhancing their ability to boost supply and generate a profit under most oil price points.

Among the more than dozen companies using Biota Technology's DNA testing are Statoil ASA (NYSE:STO) and EP Energy Corp. (NYSE:EPE).

To get an idea of the potential range of costs, shale wells are developed from $4 million to $8 million, depending on a variety of elements involved. Biota's take from those using the technology is under 1 percent, said Ajay Kshatriya, CEO and co-founder of Biota Technology.

Peter Lascelles, a geologist for EP Energy Corp., which was one of Biota's first customers, said DNA testing is superior to seismic and chemical analysis in understanding well performance and their potential.

What DNA testing is and does

The outcome of using DNA testing is it allows drillers to avoid mistakes which could limit the maximum output potential of a given well. It helps to more accurately measure the amount of pressure needed to reach shale oil, as well as allows drillers to know beforehand the distance needed between wells to generate the best results, among other improvements.

"The technique involves testing DNA extracts from microbes found in rock samples and comparing them to DNA extracted from oil. Similarities or differences can pinpoint areas with the biggest potential," according to Reuters.

Not only does this help companies engage in less costly production methods because of less accurate knowledge, but it also helps improve productivity by cutting the time it takes for a company to start pumping oil.

Being skeptical of yet another assertion of technology that can improve costs, EP Energy made Biota participate in a blind test to see how effective the technique was. It asked the company to make a determination on the origination of a specific oil sample from numerous wells in a targeted zone.

Lascelles said the company in fact did pinpoint the wells the oil sample came from and was as a result able to recommend ways it could improve drilling in the area.

At under 1 percent of costs to bring wells into production, it's easy to see why this is a very desirable technology to include in the output process.

source: Reuters via Biota

Concerns over increased supply misguided

Earlier in March, Bloomberg published an article where concern was aired over the lower costs of shale oil bringing more supply to the market, which would drive down the price of oil. In my view this is misguided and the result of not understanding how business works.

It would be no different than Wal-Mart at the height of its power being considered a weak investment because its low prices and margins generated more sales, which in turn may provide it the room to further lower prices. The same could be said about Amazon and it removing a lot of the costs out of distribution and delivery, which increases the sales at the company.

Rising supply is a major problem only if the costs are rising while the price of oil is falling. Otherwise, companies can profitably boost revenue and earnings at a lower price point than in the past.

Just like with retailers that turn over inventory far more than competitors and make money by increased sales, oil producers generate more revenue and earnings by increasing barrels sold, even if the price of oil has dropped. They make less per barrel but more from increased sales. Volume makes up for it.

I'm referring here to the new wells being completed, as the older wells aren't as efficient as the new wells. Once the old wells are worked through, the shale industry will emerge as among the lowest cost producers outside of a few state-owned companies in the Middle East. But even with that in mind, the shale costs are being driven down so much they could come close to those costs within the next year or two.

If you think that's too optimistic of an outlook, at CERAWeek some executives said breakeven was a low as $12 per barrel. Shell (NYSE:RDS.A) has said its new wells start to be profitable at about $20 per barrel. It's not going to be long before even those low numbers are improved.

EP Energy

At the end of 2016 EP Energy had drilling inventory of about 5,200 locations, with 2,900 of them located in the Wolfcamp.

The company noted in its latest earnings report that almost all of its locations are profitable "at today's strip pricing," and over 80 percent of them are profitable under $40 per barrel.

Cash costs in 4Q 2016 dropped 7 percent year-over-year, with most of the expense categories lower. Adjusted EBITDA was $255 million in the fourth quarter.

Also important on the cost side, the company was able to get its lease agreements amended with its landowner, the University Land System, which cut back on the royalty rates it will have to pay.

It's easy to see with increased productivity, lower costs and lower royalties, how the company has positioned itself for stronger earnings. Add to that the improvements it'll get from incorporating DNA testing into its operations, and you can see things are going to get better going forward.

And even if the price of oil finds support and royalties climb once again, it doesn't take away from the benefit it gets on the cost side from DNA testing.

Add to that its hedging of 75 percent of its 2017 oil product at $61.66 and its 76 percent of its natural gas production at $3.28, the company looks like it could outperform through the remainder of 2017.

Further out, the company has hedged about 20 percent of its 2017 production level at $60 per barrel, and over 25 percent of its natural gas swap at $3.11.

Statoil

Statoil doesn't have the same performance outlook at EP or others working shale have, as its locations aren't as profitable as the Permian is. Its major deposits are in the Bakken, Eagle Ford, and Marcellus.

So far Statoil hasn't been able to match many of its competitors on the efficiency side, as its breakeven point at the end of 2016 was a very high $66 per barrel. Even so, that's still an 35 percent improvement over 2015 costs. The company says by 2018 it should be able to cut breakeven down to $50 per barrel.

That is based upon existing inventory. If it were to acquire acreage in the Permian, it would be able to more rapidly lower its outlook for breakeven.

Embracing technology that can improve its cost structure will help Statoil, especially has it plays catch-up with competitors that have rapidly improved their ability to compete at most oil price levels.

Conclusion

Continuing to remove costs out of the production process is a positive for the shale industry, as it can continue to increase production profitably with their new wells.

Not only is this not bad, it's very good, as it puts more pressure on OPEC and Russia, which don't have a lot of room to lower costs. In regard to OPEC, I'm talking about the low-cost leaders, which also happen to be the top suppliers within the cartel. Russia actually has significant shale reserves, but its exposure to high-cost Artic oil and the ongoing restrictions on acquiring Western tech and equipment, which would boost its performance, makes it difficult for Russia to make cost improvements at this time.

Those with exposure to U.S. shale know that it's the future of oil for at least the next couple of decades. Costs are going to continue to improve, and when they're very close to the best OPEC has to offer, they'll crush the cartel. Already the U.S. is the swing producer. What happens when costs are removed to the point of being almost even with the best OPEC has to offer?

We're not going to see shale producers cutting back on production. It'll be measured and disciplined, but not relevant to concerns on rising supply and lower oil prices offsetting lower costs. It's U.S. shale that has the rest of the world on the ropes, not the other way around.

That doesn't mean high-cost shale producers won't come under pressure, because they will. What it means is the very best companies are starting to rise to the surface, and as they take more market share from competitors, the industry will consolidate further, and they will be in almost complete charge of the direction of oil in the not too distant future.

In my view this is OPEC's last time of attempting to manipulate the price of oil by cutting costs. Shale producers have responded to the cuts by ramping up production. The problem is many investors and analysts continue to interpret this as the result of moderately higher oil prices, when the reality is it's because they can generate profits with oil at a much lower level. That's why an increase in supply is to the benefit of shale producers; they don't have to provide for a country like its OPEC competitors do.

As for DNA testing, it's one more arrow in the quiver of shale producers who have another tool to use to cut costs even further.

Disclosure: I/we have no positions in any stocks mentioned, and no plans to initiate any positions within the next 72 hours.

I wrote this article myself, and it expresses my own opinions. I am not receiving compensation for it (other than from Seeking Alpha). I have no business relationship with any company whose stock is mentioned in this article.

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Shale Gets Another Efficiency Boost - DNA Testing Can Cut Costs By 10% - Seeking Alpha

Then, for Giddins' birthday, a friend gave him an AncestryDNA test kit. He put the $99 gift on the shelf and forgot about it.

"One day, in spring 2016, I took it down and looked at it. I thought to myself, 'I should take this thing. I've been looking for my mom all this time,'" Giddins recalls. "So, I did it. I took the test."

Using the kit's prepaid packaging, Giddins mailed a sample of his saliva to AncestryDNA for analysis of maternal and paternal genetic information ("autosomal DNA," or all 23 pairs of chromosomes). A few weeks later it can take six to eight weeks he was notified that his results were available online.

"They give you links to everyone [in the testing database] you share DNA with," Giddins says. "I found my mom and much more. I found a brother, two sisters, cousins, aunts and uncles. I found my history; I found my truth."

Giddins' biological mother, now 70 and living in Columbia, S.C., called him, knowing only that her family tree indicated that they somehow were related. As they talked, she asked for his birthday.

"Dec. 17," he answered.

"She said, 'I am the woman on your birth certificate.' We both cried," Giddins says. "She told me that on every Dec. 17, she had prayed to God that I was well."

Giddins, his wife, Lita, and their five children have since visited his rediscovered relatives in South Carolina, and he talks with his biological mother two or three times a week on the telephone.

"We have a lot to catch up on," he laughs.

Spokeswoman Crista Cowan said that while Lehi-based AncestryDNA provides clients with ethnicity breakdowns, it does not keep specific records of customers' race or religion. That said, there seems ample anecdotal evidence (a search of YouTube using the term "African-American DNA testing" turns up more than 40,000 results) of black people using AncestryDNA and other testing companies to plumb their roots.

"A lot of people are creating videos of their DNA 'reveals,'" Cowan says, adding that many customers are surprised at the ethnic diversity discovered within their chromosomes.

Overall, AncestryDNA has seen orders for its kits skyrocket since the service launched in May 2012. More than 3 million people have tested, with that number having jumped from just 2 million in spring 2016.

As life-changing as DNA testing has proved for African-American clients in general, it allows blacks who have embraced Mormonism to do what other Latter-day Saints take for granted identify ancestor candidates for baptismal temple rites for the dead.

Robert Burch Jr., president of the Utah chapter of the Afro-American Historical and Genealogical Society, found DNA results in 2016 that took him beyond his slave forebears, all the way to ancestors in the Cameroon and Congo regions several centuries ago.

"I encourage African-Americans to do DNA testing," Burch says. "It allows us to leap across the obstruction of 600 years of racial lies and historic deletions."

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For black Mormons, DNA testing a revelation of roots and faith - Salt Lake Tribune

March 29, 2017 How can long DNA filaments, which have convoluted and highly knotted structure, manage to pass through the tiny pores of various biological systems? This is the fascinating question addressed by Antonio Suma and Cristian Micheletti, researchers at the International School for Advanced Studies (SISSA) in Trieste who used computer simulations to investigate the options available to the genetic material in such situations. The study has just been published in PNAS, the journal of the National Academy of Sciences of the Unites States. Credit: Antonio Suma, SISSA

Anyone who has been on a sail boat knows that tying a knot is the best way to secure a rope to a hook and prevent slippage. Similarly, knots in sewing threads prevent them slipping through two pieces of fabric. How, then, can long DNA filaments, which have convoluted and highly knotted structure, manage to pass through the tiny pores of various biological systems? This is the fascinating question addressed by Antonio Suma and Cristian Micheletti, researchers at the International School for Advanced Studies (SISSA) in Trieste, who used computer simulations to investigate the dynamics of the molecule in such situations. The study has just been published in PNAS, the journal of the National Academy of Sciences of the Unites States.

"Our computational study sheds light on the latest experimental breakthroughs on knotted DNA manipulation, and adds interesting and unexpected elements," explains Micheletti. "We first observed how knotted DNA filaments pass through minuscule pores with a diameter of about 10 nanometers (10 billionths of a meter). The behaviour observed in our simulations was in good agreement with the experimental measurements obtained by an international research team led by Cees Dekker, which were published only a few months ago in Nature Biotechnology. These advanced and sophisticated experiments marked a turning point for understanding DNA knotting. However, current experiments cannot detect how DNA knots actually pass through the narrow pore.

"In fact, the phenomenon occurs over a tiny spatial scale that is inaccessible to microscopes. This is why our group resorted to what the great German biophysicist Klaus Schulten called 'the computational microscope,' that is, computer simulations."

Suma and Micheletti explain: "The simulations revealed that the passage of the knot can occur in two distinct ways: One where the knot is tight, and the other where the knot is more delocalised. In both cases, the knot not only passes through the pore, but it does so in a very brief time."

Moreover, the knot usually passes in the final stages of the translocation, when most of the DNA strand has already passed. "But there is something more that is counterintuitive," state the authors. "The size of the knot, whether small or large, does not seem to affect the pore obstruction time by much. The latter depends instead on the translocation speed, which, in turn, depends on the initial position of the knot along the filament." These results, say the researchers, ought to help the design of future experiments probing the spontaneous knotting of DNA, a still largely unexplored venue, especially regarding the size of DNA knots.

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Advancing our current understanding of knots in biological molecules is important to clarify their implications in biological contexts as well as in applicative ones, such as DNA sequencing using nanopores. Suma and Micheletti hope that the promising directions suggested by their study can lead to a more detailed and accurate profiling of entanglement in DNA, RNA and proteins.

Explore further: New study shows that proteins are 'virtually' knotted

More information: Antonio Suma et al. Pore translocation of knotted DNA rings, Proceedings of the National Academy of Sciences (2017). DOI: 10.1073/pnas.1701321114

Journal reference: Proceedings of the National Academy of Sciences Nature Biotechnology

Provided by: Scuola Internazionale Superiore di Studi Avanzati

Many of the processes essential to life involve proteins - long molecules which 'fold' into three-dimensional shapes allowing them to perform their biological role.

DNA has the nasty habit of getting tangled and forming knots. Scientists study these knots to understand their function and learn how to disentangle them (e.g. useful for gene sequencing techniques). Cristian Micheletti, ...

Nanotechnologies require a detailed knowledge of the molecular state. For instance, it is useful to know when and how a generic polymer, a long chain of polymers (chain of beads), knots. The study of molecular entanglement ...

A simple and effective way of unravelling the often tangled mass of DNA is to 'thread' the strand into a nano-channel. A study carried out with the participation of the International School for Advanced Studies in Trieste ...

As sailors and mountaineers know very well, every knot carries out a specific function. There's a knot that slides, one that "floats", and one that comes undone with a single pull. In the field of nanotechnology as well, ...

Scientists at The University of Manchester have produced the most tightly knotted physical structure ever known - a scientific achievement which has the potential to create a new generation of advanced materials.

(Phys.org)Researchers from the University of Sheffield report a new continuous-breathing metal-organic framework (MOF), SHF-61, that has two different solvent-specific forms, a narrow-pore structure that is the result ...

A method for diagnosing flu virus from breath samples could soon replace invasive nasal swabs and deliver better results faster.

A fluorescent probe developed by Michigan Tech chemist Haiying Liu illuminates the enzyme beta-galactosidase in a cell culture, which could help cancer surgeons.

In order for a fuel cell to work, it needs an oxidizing agent. TU Wien has now found a way to explain why oxygen does not always enter fuel cells effectively, rendering them unusable.

Researchers at the University of York and Simon Fraser University, Canada, revealed the 3-D structure of an enzyme that could provide a crucial step forward in treating neurodegenerative diseases.

The photodissociation of triiodide anion (I3-) is a classic textbook reaction that has been extensively studied both in solution and in gas phase. However, probing the ultrafast dynamics of this reaction in the solid state ...

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New study investigates the passage of knotted DNA through nanopores - Phys.Org