Monthly Archives: March 2017

Gif: ScienceRobotics

Living things: Theyre mostinspiring, but also difficult things to try to replicate in robotics. With that aim, researchers in Japan have managed to designa tiny robotic system that moves like a living cell. The scientists described the robotlast week in the journal Science Robotics.

The system, called a molecular robot, is about the size and consistency of an amoeba. It is a fluid-filled sac containingonlybiological and chemical componentsabout 27 of them,says Shin-ichiro Nomura, abioengineer at Tohoku University in Sendai, Japan and one of the robots inventors. The molecular componentswork in concert tostretch and change the shape of the sac, propelling it with cell-like motion through a fluid environment. The motioncan be turned on and off with DNA signals that respond to light.

Other than puttering around, the amoeba-like robot cant do much. But thats the beauty of the invention, says Nomura. The bot serves as a vehicle to house whatever researchers can dream up: tiny computers, sensors, and even drugs.Outfitted with those tools, the system could then be used to explore the biomolecular environment. It could seekout toxins or check the surface of other cells or the content of a Petri dish.

Nomura and his colleagues have figured out a way to package and ship the tool as a kit so that other scientists can play with the robots and incorporate their own components, he says. He hopes the platform will be used to build increasingly complex molecular robots with controllable motility.

Ultimately, Nomura would like to seethe robot function inside a cell. Thats kind of a frontier,says Nomura. A robot that can dive into a cell and itsnucleus can act as a diagnostic, seeking out problems with cellular machinery. Its a little dreamy,Nomura says, but notes that his robot can bereduced in size to less than one micrometersmallenough to fit inside a cell.

Researchers have developed many proof-of-concept micro- and nanoscale robots that can move and communicate within the body. Many of these tiny robots are made with biodegradable materials and are driven by magnetic, chemical, or ultrasonic forces.

Nomuras molecular robot differsin that it is composed entirely of biological and chemical components, moves like a cell, and is controlled by DNA. Other molecular robots have been developed, but none with this kind of controllable motility, Nomura says.

It took about a year and half and 27 different chemical components to make the molecular bot, Nomura says.Alipid membrane serves as a the malleablerobot body. Inside, specialproteins bump into the membrane, causing it to change shapekind of like bagbeing punched from the inside.

The punchingonly happens when key proteins called kinesins and microtubules connect to the membrane viaanchor units. That connection is provided by light-sensitive DNA. When UV light shines on therobot, the light-sensitive DNA inside cleaves into a single strand. It can then latch onto the anchor units and the kinesin-microtubule structure, forming a bridge between them.

The microtubules, which are rigid, long structures, slide along the kinesin proteins with the help ofadenosine triphosphate, or ATPthemolecule of intracellular energy transport. As they slide, they punch the bots outermembrane, causing it to change shape.

With this combination of molecules,Nomura and his colleagues succeeded in mimicking the movement of a cell. But if the thing is assembledsolely withbiological components and chemically powered by ATP,can we really call it a robot?The definition of robot is wide, says Nomura. If something has a body and can sense and process information to carry outa function,its a robot, he says.

Robot orcell-bot, we look forward to seeing what engineers stick inside it.

IEEE Spectrums biomedical blog, featuring the wearable sensors, big data analytics, and implanted devices that enable new ventures in personalized medicine.

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With new design advances, nanorobots are inching closer to medical use 1Mar

This sleek yet rugged sensor measures better and lasts longer 27Feb

Battery technology inspires a flexible, organic, nonvolatile device for neuromorphic circuits that needs only millivolts to change state 22Feb

And auto-complete software should dramatically boost performance for this brain-computer interface 21Feb

A consumer-friendly gadget could help tDCS treatment catch on 21Feb

Researchers squeeze a three-step optogenetics process into one nifty probe and demonstrate it in mice 20Feb

Expert evaluators of medical devices raise caution about direct-to-consumer products 10Feb

Swallowable electronics could transmit data for nearly a week 6Feb

The Korean company's consumer-friendly tDCS gadget could help this electric treatment catch on 26Jan

First clinical trials will take on postpartum hemorrhage in the developing world 20Jan

The Indiegogo campaign took backers' money, enjoyed the media attention, then went silent 19Jan

An implantable sleeve mimics the motion of the heart and reverses heart failure in pigs 18Jan

Swiss researchers harness the heart's energy using one of their most famous inventions: the watch 11Jan

Super-thin graphene-based health monitor could have wide range of benefits 11Jan

A wearable device made from cheap household materials could spread the benefits of health monitoring 9Jan

Scientists are developing screening tools to distinguish complex chains of amino acids and carbohydrates 6Jan

Implanted in the body, a tiny micromachine dispenses a dose of medication with each tick 4Jan

Survival rates are boosted by an oscillating field that attacks dividing cancer cells 4Jan

"Kissenger" device uses haptic tech to send and receive kisses 23Dec2016

Silicon nanowires swallowed by human cells provide new bioelectronic tool 19Dec2016

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Amoeba-Like Robot Programmed With DNA - IEEE Spectrum

wbur

March 07, 2017Updated 03/07/2017 2:22 PM

Telling one identical twin from another poses problems for police. And it goes beyond appearances.

That's because DNA profiling may be the gold standard for bringing criminals to justice, but when it comes to identical twins, standard testing cant tell the difference.

So when crime scene DNA showed a match to a suspect in two rape cases in Boston in 2004, it showed a match to his twin brother as well.

Now, aSuffolk County prosecutor is trying to persuade a state judge to make her court the first in the country to admit a new forensic test that points to one of the twins and not the other.

The Scientific Legal Loophole Of Identical Twins

The case of 36-year-old Dwayne McNair of Dedham demonstrates the already long and powerful reach of DNA science that first came to a courtroom trial in 1987.

And Suffolk County prosecutors hope to extend that reach even farther.

The issue begins with thesavage and separate assaults of two women abducted, pistol-whipped and raped by two men in Dorchester.

Prosecutor David Deakin said that as the victim of the second assault was putting her clothes back on, she did something extraordinarily brave.

"Nearby was a used condom that one of the perpetrators had used during the sexual assault," Deakin said, "and she scooped the condom up in the cups of her bra, and then put the bra in her pocket."

That gave police a semen sample from the unknown rapist and thus a DNA "fingerprint." Several years later, when a couple of Boston cops got a tip that McNair might be worth investigating, they tailed him to work. They watched him smoke a cigarette, then picked up his discarded stub-- the source of another DNA fingerprint. It matched the DNA in the condom.

Case solved, you might think. Except the detectives learned McNair has a twin brother.

"We obtained a court order for the twins to submit DNA samples, which they did," Deakin said, "and the DNA testing of those samples revealed that they are in fact identical twins. And therefore both of their DNA matched the crime scene sample."

Here was the scientific legal loophole of identical twins: The prosecution could prove to a jury that it was either Dwayneor Dwight McNair who committed the crimes. But it couldn't prove which one.

"Ordinary DNA science, the kind of science that's used around the world every day in courts to identify people, can't differentiate between identical twins," Deakin said.

Scientists in general accept that not every cell in identical twins is exactly alike, that identical twins arent exactly identical. But its been widely assumed there was no way to tell them apart.

"The understanding was that you just couldn't do it," said Penn State law professor David Kaye, an expert in forensic science, "because they were so similar that the kinds of differences that genetic tests that are used in forensics would pick up just wouldn't be seen in any pair of identical twins."

'Next Generation' Sequencing

Ten years after the crimes, in 2014, Dwayne McNair was about to go to trial when prosecutor Deakin read about advanced technology successfully applied by a German company to tell one identical twin from another.

"Next generation," or "massive parallel," sequencing, as its called, enables scientists to map out the genome of each twin. That's the entire set of genetic instructions in the bundles of DNA the chromosomes found in every cell.

The goalis to findmutations, those rare events in the process of cell division that occur while each cell is otherwise faithfully copying some 3billion letters of genetic code. Inevitably, as with every typist, there's going to be a typo.

"You can have a miscopy, if you will, at some point in the DNA sequence," Kaye said. "We'll callthat a mutation."

Mutations occur both randomly and rarely. And if a mutation occurs after the twinning process, that gives rise to separate identical twin; its thought that the mutation will show up in one twin or the other, but not both.

In its experiment with identical brothers, that German company, Eurofins Forensic, used semen samples to map out the genomes of each twin. When it compared the two genomes, it found five mutations in one twin that were not in the other, thereby demonstrating identical twins could be differentiated.

Then Eurofins sequenced the genome of a child of one of the two brothers on the basis of a blood sample. Researchers found the child had the same five genetic mutations found in one of the identical twins, indicating who was the father and who was the uncle. The experiment offered evidence that mutations will carry to body tissue and semen.

Deakin realized the possibility the Eurofins test could compare the sperm sample of the unknown suspect with the saliva of the two McNair brothers.

"What Eurofins did was the first to publish a study showing that using this technique, you can identify the source of an unknown sample," Deakin said.

With time running out before Dwayne McNair went to trial in Boston in 2014, the Suffolk County district attorney hired Eurofins to test the McNair brothers saliva samples and the semen from the crime scene. And Deakin went to court to withdraw the charges against Dwayne McNair to wait for the results of genome sequencing on the twins.

They found nine differences out of 3 billion.

Now came the novel and controversial part of the test. After establishing the genetic differences, Eurofins compared both DNA profiles from the saliva with the DNA of the semen found in the suspect's condom.

Analysts found seven locations where the DNA of Dwayne McNair's saliva showed a match, and two where his brother Dwight matched.

Even more telling, scientists found two of the mutations in Dwayne's saliva were also present in the semen sample. In Dwights case, none were present.

On that basis, Eurofins concluded Dwayne McNair was 2 billion times more likely than Dwight to be the source of the semen and therefore the rapist. And in September 2014, Dwayne was once again indicted on charges of rape and armed robbery.

Ready For 'Prime Time'?

McNair's defense was to try to exclude the new tests and evidence from trial.

RobertTobin, his attorney, characterized the defense by saying"that the test isn't ready yet for forensics."Tobin added: "It hasn't been vetted and researched by independent scientists. ... I mean, its an interesting experiment but it just isn't ready for prime time."

In hearings over the course of three weeks and just concluded, the defense and the prosecution called to the stand a string of molecular geneticists, biostatisticians, embryologists, forensic experts and a former top scientist at the FBIs DNA lab.

McNairs defense established that the technique that implicates him has never been admitted to a courtroom anywhere in the world. Its the product of only one experiment using only one set of twins. There has never been a DNA study of, say, 20or a hundred sets of identical twins, published and peer-reviewed, to corroborate the findings or the foundations of what Eurofins has done.

"Given the way that most forensic tests are validated, and should be validated according to many scientists, this test has not been validated yet in that manner," professor Kaye said.

One of the most complicating and controversial issues is that the DNA of the sperm is being compared to the DNA from saliva.

Professor David Housman of MIT, who has a long history of testifying for the prosecution, testified this time for the defense.

"If they had obtained semen samples from both twins and one of the twin's semen samples matched the crime scene samples, then I would not have a problem with it," Housman said.

It would be far simpler if scientists could sequence the DNA of both twins' semen and then match them against the semen taken from the crime scene. But compelling someone to provide semen samples would be a violation of his Fourth Amendment rights against unreasonable search and seizure. So saliva samples, considered minimally intrusive, had to substitute as a proxy tissue. And witnesses questioned whether the saliva and the semen all have the same DNA.

"The issue of which twin is necessarily the donor of the sperm cannot be ... proven beyond a reasonable doubt," Housman said.

This isn't the first time Deakin has prosecuted a rape casecomplicated by identical twins both matching the DNA. But his expert witnesses testified to the rock solid quality of the technology.

Deakin has confidence in the evolving science.

"While it is indisputably a novel approach, we expect to prove its a reliable one," he said.

Now Superior Court Judge Linda Giles must decide whether the test and its results are ready for prime time.

If the prosecution is denied the use of the new evidence, it will still have the evidence from conventional DNA testing that narrows the suspects to one brother or the other.

But the prosecution will also have as a witness a man who has admitted to being the other rapist of the two women in this case.

In still another example of the far reaching power of DNA, that defendant was identified by a national DNA database, which showed he matched the DNA in a rape kit from one of the victims.

Correction:An earlier version of this story incorrectly reported Robert Tobin's first name. We regret the error.

This story aired on March 7, 2017.

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Standard DNA Testing Can't Differentiate Between Identical Twins. A New Test Challenges That - WBUR

Newly discovered DNA enhancers help switch on colorectal cancer Science Daily In a breakthrough study published in Nature Communications, scientists discovered changes in specific regions of DNA, outside of colorectal cancer genes, that "enhance" harmful gene expression to help grow tumors. The changes are highly conserved ... and more »

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Newly discovered DNA enhancers help switch on colorectal cancer - Science Daily

Scientists have developed what they claim is the most efficient data storage technique ever, with a new DNA-encoding method that approaches the theoretical maximum for information stored per nucleotide.

Using an algorithm called DNA Fountain, the researchers squeezed six files into a single speck of DNA including a short film, an entire computer OS, and an Amazon gift card but that's just for starters. The team says the same technique could effectively compress all the world's data into a single room.

Not only is DNA data storage an amazing space saver; the technique could also enable us to preserve knowledge with extreme robustness and longevity unlike traditional technology media, which is known to succumb to all kinds of faults with time.

"DNA won't degrade over time like cassette tapes and CDs, and it won't become obsolete if it does, we have bigger problems," says computer scientist Yaniv Erlich from Columbia University.

DNA storage itself isn't new, with the technique pioneered in 2012 by researchers at Harvard University, who figured out how to compress a 53,400-word book into the genetic code of synthetic DNA molecules, and then read the data back using DNA sequencing.

Since then various other teams have been trying to optimise the technique, with Microsoft claiming last year that a method it had come up with was 20 times more efficient than the previous record.

In turn, Erlich and fellow researcher Dina Zielinski from the New York Genome Centre now say their own coding strategy is 100 times more efficient than the 2012 standard, and capable of recording 215 petabytes of data on a single gram of DNA.

For context, just 1 petabyte is equivalent to 13.3 years' worth of high-definition video, so if you feel like glancing disdainfully at the external hard drive on your computer desk right now, we won't judge.

At the heart of the researchers' system is an algorithm originally designed to detect and fix errors in streaming video applications.

According to the researchers, the same kind of mechanism can be used to avoid errors when reading back binary data (made up of 1s and 0s) that's been translated into the four nucleotide bases in DNA: A, G, C, and T.

"[N]ot all DNA molecules are created equally," Erlich told Dexter Johnson at IEEE Spectrum.

"If you have DNA molecules that have a long stretch of the same nucleotide, such as AAA, it is not very favourable for the informatics machinery. It's very hard to read this molecule without an error. So you want to avoid stretches like that."

The researchers' algorithm manages to avoid errors when reading back the DNA data by additionally encoding a series of hints about what the information should look like once decoded.

This mean that not only can you recreate any DNA fragments that get lost in the process it's also highly optimised.

"We showed that we can reliably store information on DNA, and that our organising of information approaches 'optimal packing,'", Erlich told Katherine Lindemann at ResearchGate, "meaning it is nearly impossible to fit more information on the same amount of DNA material."

To test the system, the team compressed six files: a computer OS; an 1895 French short film, Arrival of a train at La Ciotat; a US$50 Amazon gift card; a computer virus; a Pioneer plaque; and an academic paper by information theorist Claude Shannon.

The overall file size of the complete package was relatively tiny coming in at just 2MB but the important thing was testing to see if the DNA Fountain algorithm was able to encode the binary information into genetic data without losing any of the information.

After the digital data represented in a list of 72,000 DNA strands was converted into a speck of DNA molecules carried in a vial, the researchers were able to sequence the DNA and recover the files with zero errors.

While it's an impressive result, the team says it will be some time before the expense of storing and reading data in DNA makes sense for the rest of us. For their 2MB package, the researchers spent $7,000 to synthesise the DNA, and another $2,000 to sequence it.

Erlich thinks it could be more than a decade before DNA storage becomes accessible to the general public.

And even then, the technology might be reserved for things like recording patient data in medical systems, as opposed to being sold to consumers as the latest tech product.

"This is still the early stages of DNA storage. It's basic science," Erlich told Eva Botkin-Kowacki at The Christian Science Monitor.

"It's not that tomorrow you're going to go to Best Buy and get your DNA hard drive."

The findings are reported in Science.

The rest is here:
Scientists Have Stored a Movie, a Computer OS, and an Amazon Gift Card in a Single Speck of DNA - ScienceAlert