Monthly Archives: June 2017

One of the DNA nanomachines and the shapes it can switch between.

Song et al.

DNA-based computers are one step closer to full realisation following the creation of simple DNA machines that can switch between two shapes with only a single trigger.

The switching ability, which is fully reversible, means that information is being relayed at a molecular level transferred between DNA structural units in a manner than is both self-sustaining and controllable.

Lead researcher Yonggang Ke of the Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech, US, says the micromachines can be used to either relay specific pieces of information through a DNA-constructed system, or to amplify a signal emanating from another part of it.

In the field of DNA-based computing, the DNA contains the information, but the molecules are floating around in solution, Ke says.

Whats new here is that we are linking the parts together in a physical machine.

Ke and colleagues constructed two different nanomachines, each comprising a number of artificial DNA double helixes stacked on each other, in two orientations, providing strength and stability.

The completed design looks rather like an accordion, or a foldable trellis.

One extra strand at the edge of each machine is attached, and functions as a trigger. When activated it compels the first DNA strand of the machine array to contract (or expand, depending on its initial state). This in turn transfers energy to the next strand, causing it to move in the same way, and so on, a little like dominoes falling.

The machines, fully built, are just a few hundred nanometres long slightly smaller than an influenza virus. To see them, Ke and colleagues used a powerful imaging technique known as atomic force microscopy.

Constructing machines on a nanometric scale would seem to require some impossibly fine hand-eye coordination on the part of the molecular engineers, but the compulsion of DNAs chemical structures to automatically bond means that, in solution, they seek out the complimentary strands of their neighbours, making construction a guided, rather than mechanical, process.

Although the machines built by Ke and his colleagues are very simple, they provide a powerful pathway towards construction of more complex structures. In research published in the journal Science, the team include blueprints for rectangles, cubes and tubes built by the same process.

Read more:
DNA nanomachines can transmit information - Cosmos

A Lincoln judge has given the OK for the Nebraska Department of Correctional Services to use reasonable force to collect DNA from an inmate refusing to give it voluntarily.

It was the fifth time the state prison system had sought permission to use force to get DNA samples from the 78 inmates who still hadn't provided it to prison staff as of February.

The other motions were in Omaha cases. One since has led to new charges against Brandon Weathers in connection to serial rapes of four women in 2002 and 2004.

DNA can be an important tool used to solve crimes or lead to suspects.

The Nebraska Attorney General's office recently asked a Lincoln judge for an order to allow a Phoenix police officer to get an additional DNA sample from an inmate at the Nebraska State Penitentiary.

After the inmate went to prison in September for a sex assault in Douglas County, his DNA sample was collected.

In December, the Nebraska State Patrol Crime Laboratory matched his DNA, which was uploaded into the Combined DNA Index System, to DNA on a toothbrush taken from a Phoenix home in 2010 by investigators looking into the homicide of a man who had been shot dead in a car outside, according to court records.

State law says a person who had been convicted of a felony or other specified offense as of July 15, 2010, who did not have a sample in the state DNA Sample Bank, was required to have one collected at his or her own expense. The law also applied to people already serving a sentence.

Still, some inmates refused to comply.

In the Lincoln case, Assistant Nebraska Attorney General Kale Burdick said prison employees notified Reuben J. Reyes of his obligation to provide his DNA in April 2013, about two months after he went to prison, and again this May.

Reyes refused, Burdick said in the motion filed June 14.

The same day, Lancaster County District Judge Lori Maret authorized the use of force to get it from the man serving a 20- to 25-year sentence for attempted first-degree assault and use of a firearm to commit a felony for pointing a .380 handgun at his cousin and firing once into the air, then twice more in his cousin's direction, in 2012.

Lincoln police said one of the rounds hit an apartment building. Another hit a car.

Reyes later pleaded no contest.

By Monday, state prisons spokeswoman Dawn-Renee Smith said the number of inmates who hadn't provided DNA was down to six.

She said she couldn't provide a list of the inmates' names because the information is related to their conduct in prison and protected by state statute.

Earlier this month, Corrections Director Scott Frakes said he is committed to collecting DNA samples from every incarcerated person to be in full compliance with state statute.

By policy, inmates who have not provided a DNA sample are ordered to submit it monthly and get written up for each refusal. Misconduct reports that result are referred to the institutional disciplinary committee.

Repeated refusals can lead to up to 90 days of lost good time.

More here:
Use of force may be applied to collect DNA samples from inmates ... - Beatrice Daily Sun

Doctors at Zuckerberg San Francisco General Hospital could not figure out what was wrong with the 29-year-old man sitting before them. An otherwise healthy construction worker from Nicaragua, the patient was suffering from a splitting headache, double vision and ringing in his ears. Part of his face was also numb. The cause could have been anythingfrom an infection to a stroke, a tumor or some kind of autoimmune disease. The Emergency Department (ED) staff took a magnetic resonance imaging scan of the mans brain, performed a spinal tap and completed a series of other tests that did not turn up any obvious reason for the swelling in his braina condition that is formally known as encephalitis.

Most likely, it was some kind of infection. But what kind? Nineteen standard tests are available to help clinicians try to pin down the source of encephalitis, but they test for the presence of only the most common infections; more than 60 percent of cases go unsolved each year. Physicians looked in the patients cerebrospinal fluid (which surrounds the brain and protects it) for evidence of Lyme disease, syphilis and valley fever, among other things. Nothing matched. So the S.F. General ED staff settled on the most likely culprit as a diagnosis: a form of tuberculosis (TB) that causes brain inflammation but cannot always be detected with typical tests. Doctors gave the man a prescription for some steroids to reduce the swelling plus some anti-TB drugs and sent him home.

Soon he was back, however, with the same symptoms. This time the physicians assumed the man, whose life was chaotic, had not been taking his drugs properly. (Even people with regular jobs and schedules often find taking TB medications fairly difficult.) The ED staff sent him away with another prescription but he returned again and againeven after he could prove that he was taking his medication correctly and on time. The drugs helped briefly after each visit, but the symptoms always returned. During that year his medical bills reached $580,000. Finally, S.F. General turned to an experimental test that is designed to uncover the source of virtually any neurological infection.

The test is the brainchild of researchers at the nearby University of California, San Francisco, led by neurologist Michael Wilson, biochemist Joseph DeRisi and infectious disease expert Charles Chiu. The group uses genetic-sequencing technology to identify mystery illnesses in people with encephalitis or meningitis (inflammation of the meninges, the membranes around the brain and spinal cord). This so-called metagenomic test analyzes all the DNA and RNA found in a sample of cerebrospinal fluid (meta means beyond in Greek). So any DNA or RNA that does not belong to the patientincluding that from viruses, bacteria, parasites or fungishows up in the results.

Done correctly, metagenomic testing could radically change the way infections of the brain are diagnosed. An element of circular logic underlies most standard infectious disease tests. Doctors order individual tests for each bug they suspect might be causing the problem. But how do they know what is causing the problem if they have not yet done the test? Metagenomic sequencing, in contrast, casts the broadest possible net, which allows it to pick up unexpected or previously unknown pathogens. Were looking at everything at once, which has the potential of replacing the myriad of lab tests with a single test, Chiu says.

The U.C. San Francisco team ran a sample of the mans cerebrospinal fluid through their investigative diagnostic procedure. Thats when we found the worm, Wilson says. Genetic sequencing and analysis revealed DNA from the kind of tapeworm found in pigs. The patient did not get better on TB drugs because he did not have TBhe had tapeworms living in his brain.

In Nicaragua and other developing countries tapeworm infections are common, and the larvae can migrate into the braina condition called neurocysticercosis. Usually the infection causes seizures as well as large brain cysts that are obvious on an MRI. This man had neither, however, which had led the medical staff to dismiss neurocysticercosis as a possibility. When this guy first presented, they absolutely thought of it, Wilson says. But when they scanned him in his brain and spinal cord, there were no cysts. He would improve briefly, because the steroids they gave him temporarily reduced the swelling in his brain, but the TB drugs were useless, so he would soon relapse again. Now that they knew the cause, the team started him right away on anti-worm drugs, which cannot eliminate the infection but will keep it under control. Its very treatable, Wilson says. Hes doing great.

The construction worker is one of nearly 300 patients who has participated since June 2016 in a metagenomic sequencing study based at U.C. San Francisco. Participants consist of anyone who has been admitted to one of eight medical centers, mostly in California, with an apparent neurological infection and no clear diagnosis. Metagenomic sequencing is done alongside traditional testing, for a head-to-head comparison.

Wilson and colleagues hope to prove their test, which will be more widely available this summer for about $2,400, can be an efficient and reliable solution for the sorts of medical mysteries that befuddle doctors, aggravate patients and can run up huge medical bills. The challenge is in making sense of the output, Chiu says. Sequencing does not produce a yes or no answer. The group developed a standard set of procedures to make it easy for an infectious disease doctor to pinpoint what the most likely bug might be.

On July 1 the U.C. San Francisco group will begin offering this test as a custom-ordered service to a broader group of people so that hospitals and labs in the U.S., and eventually anywhere in the world, can send cerebrospinal fluid for analysis. They plan to eventually expand their metagenomic testing to include pneumonia (infection of the lungs) and sepsis (infection of the bloodstream)two other ailments that often cause diagnostic dilemmas.

A similar metagenomic test for pneumonia, developed by researchers at the University of Utah, Arup Laboratories and start-up IDbyDNA, is also expected to debut this summer. In both cases the teams first do extensive work to make it easier for physicians to understand the complex and ambiguous genomic information garnered by the test.

These two tests will be the first commercially available metagenomic tests for infection in the U.S., but they are part of a growing trend. Two academic groups in Europe recently introduced tests for sepsis. And researchers at computational geneticist Pardis Sabetis lab at Harvard University are currently running a study on a similar test for encephalitis, says Anne Piantadosi, an infectious disease physician at Massachusetts General Hospital and a postdoctoral research fellow with the Sabeti group. She envisions a time in the next few years when future clinicians will be able to look back say, That was a really big improvement in how we diagnose infections.

Read the original post:
Brain-Invading Tapeworm That Eluded Doctors Spotted by New DNA Test - Scientific American

FootJoy has launched the latest version of the DNA (DryJoys Next Advancement) franchise, the DNA Helix.Featuring a wider platform and a lightweight construction to create power from the ground up, DNA Helix is available on footjoy.com and wherever FootJoy golf shoes are sold.

DNA Helix was developed based on specific feedback from the worlds best players who value the combination of flexibility and comfort but requested more platform stability, particularly in the heel area of the shoe.

Ive worn every version of DNA and this is by far the best for me, said Scott Stallings. The additional support they built in, especially laterally as I move back and through the ball, is fantastic.

The new NitroThin 3.0 TPU (thermoplastic polyurethane) outsole foundation in DNA Helix was developed to deliver the additional stability requested by Tour players. In fact, FootJoy says DNA Helix is 38 percent more stable than its predecessor. This was achieved by increasing the width between the cleat receptacles in the heel by 13 percent for more surface coverage. In addition, a new fit-bed was developed with more lateral stability and the integration of a 3D FoamCollar also helps to lock the players foot in place.

The new outsole also features strategically placed cut-outs in the TPU to expose more of the softer midsole which contributes to this outsole being 23 percent lighter than the previous version as well as being more flexible.

While it was certainly a challenge to improve upon a shoe as successful as DNA, the continued dialog we have with our Tour staff revealed there was an opportunity to improve the overall performance of the category, said Keith Duffy, Senior Product Manager, Footwear. But this isnt just an update for us. DNA Helix is a completely new golf shoe built from the ground up to deliver Tour-level performance and lightweight comfort for all players.

DNA Helix comes with a two-year waterproof warranty. Suggsted retail price is $209.99 (laced) or $239.99 (Boa System).

See the original post:
FootJoy introduces DNA Helix shoe - Golf Channel

Water treatment is vital to maintain human health but a method widely used in developing countries could be damaging the DNA of those drinking it. Despite poor evidence of their effectiveness as a water disinfectant, colloidal silver and silver nanoparticles are increasingly being promoted for treating potentially contaminated drinking water in low income countries.

Despite poor evidence of their effectiveness as a water disinfectant, colloidal silver and silver nanoparticles are increasingly being promoted for treating potentially contaminated drinking water in low income countries.

A study led by the University of East Anglia has concluded that there is a risk these treatments could in fact cause genotoxicity, which is damage to DNA, and affect reproduction and future generations. Prof Paul Hunter from UEAs Norwich Medical School, said the study brings together existing research to highlight the potential risks. Colloidal silver as a water treatment is sold across Africa and in countries like Haiti, despite the fact it doesnt treat water very effectively. The World Health Organization (WHO) advises against its use as a primary water treatment. If it isnt doing any good, we wanted to investigate if in fact it could be causing harm. The research looked at previous studies where the effects of silver, silver nitrate and silver nanoparticles have been measured in vivo on living animals. They found that, although results varied, more studies than they expected showed some evidence of genotoxicity, reporting effects including chromosomal aberrations, DNA fragmentation and damage to sperm. Prof Hunter said: We already know that there is little evidence that silver in water has any benefit. But this study brings together a body of work which shows it is potentially damaging DNA, and harming reproductive success. Colloidal silver is also widely marketed as an alternative health substance which can treat everything from skin complaints to bacterial and viral infections, cancer and AIDS. Again, little research exists to show any beneficial effects, but there are known side effects. One of the more obvious signs of over-exposure to silver is argyria, where the skin and hair turns a blue-grey colour.

One of the more obvious signs of over-exposure to silver is argyria, where the skin and hair turns a blue-grey colour.

WHO guidelines for drinking water quality dont currently include a value for silver in water, but indicate that a concentration of 0.1 milligrams per litre could be tolerated without risk to health. However, this was determined as a level unlikely to cause argyria, and didnt take into account potential damage to DNA. Prof Hunter said: While none of the previous studies alone are definitive, and we cant use them to determine a safe level of consumption from this review, we consider that the balance of evidence suggests there is the chance of damage to DNA. There is an urgent need for more research on this area to determine if people drinking water treated with silver have evidence of DNA damage.

See original here:
Water treatment could be damaging DNA - The Hippocratic Post (blog)