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#430830 Biocomputers Made From Cells Can Now ...

When it comes to biomolecules, RNA doesn’t get a lot of love.
Maybe you haven’t even heard of the silent workhorse. RNA is the cell’s de facto translator: like a game of telephone, RNA takes DNA’s genetic code to a cellular factory called ribosomes. There, the cell makes proteins based on RNA’s message.
But RNA isn’t just a middleman. It controls what proteins are formed. Because proteins wiz around the cell completing all sorts of important processes, you can say that RNA is the gatekeeper: no RNA message, no proteins, no life.
In a new study published in Nature, RNA finally took center stage. By adding bits of genetic material to the E. Coli bacteria, a team of biohackers at the Wyss Institute hijacked the organism’s RNA messengers so that they only spring into action following certain inputs.
The result? A bacterial biocomputer capable of performing 12-input logic operations—AND, OR, and NOT—following specific inputs. Rather than outputting 0s and 1s, these biocircuits produce results based on the presence or absence of proteins and other molecules.
“It’s the greatest number of inputs in a circuit that a cell has been able to process,” says study author Dr. Alexander Green at Arizona State University. “To be able to analyze those signals and make a decision is the big advance here.”
When given a specific set of inputs, the bacteria spit out a protein that made them glow neon green under fluorescent light.
But synthetic biology promises far more than just a party trick—by tinkering with a cell’s RNA repertoire, scientists may one day coax them to photosynthesize, produce expensive drugs on the fly, or diagnose and hunt down rogue tumor cells.
Illustration of an RNA-based ‘ribocomputing’ device that makes logic-based decisions in living cells. The long gate RNA (blue) detects the binding of an input RNA (red). The ribosome (purple/mauve) reads the gate RNA to produce an output protein. Image Credit: Alexander Green / Arizona State University
The software of life
This isn’t the first time that scientists hijacked life’s algorithms to reprogram cells into nanocomputing systems. Previous work has already introduced to the world yeast cells that can make anti-malaria drugs from sugar or mammalian cells that can perform Boolean logic.
Yet circuits with multiple inputs and outputs remain hard to program. The reason is this: synthetic biologists have traditionally focused on snipping, fusing, or otherwise arranging a cell’s DNA to produce the outcomes they want.
But DNA is two steps removed from proteins, and tinkering with life’s code often leads to unexpected consequences. For one, the cell may not even accept and produce the extra bits of DNA code. For another, the added code, when transformed into proteins, may not act accordingly in the crowded and ever-changing environment of the cell.
What’s more, tinkering with one gene is often not enough to program an entirely new circuit. Scientists often need to amp up or shut down the activity of multiple genes, or multiple biological “modules” each made up of tens or hundreds of genes.
It’s like trying to fit new Lego pieces in a specific order into a room full of Lego constructions. Each new piece has the potential to wander off track and click onto something it’s not supposed to touch.
Getting every moving component to work in sync—as you might have guessed—is a giant headache.
The RNA way
With “ribocomputing,” Green and colleagues set off to tackle a main problem in synthetic biology: predictability.
Named after the “R (ribo)” in “RNA,” the method grew out of an idea that first struck Green back in 2012.
“The synthetic biological circuits to date have relied heavily on protein-based regulators that are difficult to scale up,” Green wrote at the time. We only have a limited handful of “designable parts” that work well, and these circuits require significant resources to encode and operate, he explains.
RNA, in comparison, is a lot more predictable. Like its more famous sibling DNA, RNA is composed of units that come in four different flavors: A, G, C, and U. Although RNA is only single-stranded, rather than the double helix for which DNA is known for, it can bind short DNA-like sequences in a very predictable manner: Gs always match up with Cs and As always with Us.
Because of this predictability, it’s possible to design RNA components that bind together perfectly. In other words, it reduces the chance that added RNA bits might go rogue in an unsuspecting cell.
Normally, once RNA is produced it immediately rushes to the ribosome—the cell’s protein-building factory. Think of it as a constantly “on” system.
However, Green and his team found a clever mechanism to slow them down. Dubbed the “toehold switch,” it works like this: the artificial RNA component is first incorporated into a chain of A, G, C, and U folded into a paperclip-like structure.
This blocks the RNA from accessing the ribosome. Because one RNA strand generally maps to one protein, the switch prevents that protein from ever getting made.
In this way, the switch is set to “off” by default—a “NOT” gate, in Boolean logic.
To activate the switch, the cell needs another component: a “trigger RNA,” which binds to the RNA toehold switch. This flips it on: the RNA grabs onto the ribosome, and bam—proteins.
BioLogic gates
String a few RNA switches together, with the activity of each one relying on the one before, and it forms an “AND” gate. Alternatively, if the activity of each switch is independent, that’s an “OR” gate.
“Basically, the toehold switches performed so well that we wanted to find a way to best exploit them for cellular applications,” says Green. They’re “kind of the equivalent of your first transistors,” he adds.
Once the team optimized the designs for different logic gates, they carefully condensed the switches into “gate RNA” molecules. These gate RNAs contain both codes for proteins and the logic operations needed to kickstart the process—a molecular logic circuit, so to speak.
If you’ve ever played around with an Arduino-controlled electrical circuit, you probably know the easiest way to test its function is with a light bulb.
That’s what the team did here, though with a biological bulb: green fluorescent protein, a light-sensing protein not normally present in bacteria that—when turned on—makes the microbugs glow neon green.
In a series of experiments, Green and his team genetically inserted gate RNAs into bacteria. Then, depending on the type of logical function, they added different combinations of trigger RNAs—the inputs.
When the input RNA matched up with its corresponding gate RNA, it flipped on the switch, causing the cell to light up.

Their most complex circuit contained five AND gates, five OR gates, and two NOTs—a 12-input ribocomputer that functioned exactly as designed.
That’s quite the achievement. “Everything is interacting with everything else and there are a million ways those interactions could flip the switch on accident,” says RNA researcher Dr. Julies Lucks at Northwestern University.
The specificity is thanks to RNA, the authors explain. Because RNAs bind to others so predictably, we can now design massive libraries of gate and trigger units to mix-and-match into all types of nano-biocomputers.
RNA BioNanobots
Although the technology doesn’t have any immediate applications, the team has high hopes.
For the first time, it’s now possible to massively scale up the process of programming new circuits into living cells. We’ve expanded the library of available biocomponents that can be used to reprogram life’s basic code, the authors say.
What’s more, when freeze-dried onto a piece of tissue paper, RNA keeps very well. We could potentially print RNA toehold switches onto paper that respond to viruses or to tumor cells, the authors say, essentially transforming the technology into highly accurate diagnostic platforms.
But Green’s hopes are even wilder for his RNA-based circuits.
“Because we’re using RNA, a universal molecule of life, we know these interactions can also work in other cells, so our method provides a general strategy that could be ported to other organisms,” he says.
Ultimately, the hope is to program neural network-like capabilities into the body’s other cells.
Imagine cells endowed with circuits capable of performing the kinds of computation the brain does, the authors say.
Perhaps one day, synthetic biology will transform our own cells into fully programmable entities, turning us all into biological cyborgs from the inside. How wild would that be?
Image Credit: Wyss Institute at Harvard University Continue reading

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#430814 The Age of Cyborgs Has Arrived

How many cyborgs did you see during your morning commute today? I would guess at least five. Did they make you nervous? Probably not; you likely didn’t even realize they were there.
In a presentation titled “Biohacking and the Connected Body” at Singularity University Global Summit, Hannes Sjoblad informed the audience that we’re already living in the age of cyborgs. Sjoblad is co-founder of the Sweden-based biohacker network Bionyfiken, a chartered non-profit that unites DIY-biologists, hackers, makers, body modification artists and health and performance devotees to explore human-machine integration.
Sjoblad said the cyborgs we see today don’t look like Hollywood prototypes; they’re regular people who have integrated technology into their bodies to improve or monitor some aspect of their health. Sjoblad defined biohacking as applying hacker ethic to biological systems. Some biohackers experiment with their biology with the goal of taking the human body’s experience beyond what nature intended.
Smart insulin monitoring systems, pacemakers, bionic eyes, and Cochlear implants are all examples of biohacking, according to Sjoblad. He told the audience, “We live in a time where, thanks to technology, we can make the deaf hear, the blind see, and the lame walk.” He is convinced that while biohacking could conceivably end up having Brave New World-like dystopian consequences, it can also be leveraged to improve and enhance our quality of life in multiple ways.
The field where biohacking can make the most positive impact is health. In addition to pacemakers and insulin monitors, several new technologies are being developed with the goal of improving our health and simplifying access to information about our bodies.
Ingestibles are a type of smart pill that use wireless technology to monitor internal reactions to medications, helping doctors determine optimum dosage levels and tailor treatments to different people. Your body doesn’t absorb or process medication exactly as your neighbor’s does, so shouldn’t you each have a treatment that works best with your unique system? Colonoscopies and endoscopies could one day be replaced by miniature pill-shaped video cameras that would collect and transmit images as they travel through the digestive tract.
Singularity University Global Summit is the culmination of the Exponential Conference Series and the definitive place to witness converging exponential technologies and understand how they’ll impact the world.
Security is another area where biohacking could be beneficial. One example Sjoblad gave was personalization of weapons: an invader in your house couldn’t fire your gun because it will have been matched to your fingerprint or synced with your body so that it only responds to you.
Biohacking can also simplify everyday tasks. In an impressive example of walking the walk rather than just talking the talk, Sjoblad had an NFC chip implanted in his hand. The chip contains data from everything he used to have to carry around in his pockets: credit and bank card information, key cards to enter his office building and gym, business cards, and frequent shopper loyalty cards. When he’s in line for a morning coffee or rushing to get to the office on time, he doesn’t have to root around in his pockets or bag to find the right card or key; he just waves his hand in front of a sensor and he’s good to go.
Evolved from radio frequency identification (RFID)—an old and widely distributed technology—NFC chips are activated by another chip, and small amounts of data can be transferred back and forth. No wireless connection is necessary. Sjoblad sees his NFC implant as a personal key to the Internet of Things, a simple way for him to talk to the smart, connected devices around him.
Sjoblad isn’t the only person who feels a need for connection.

When British science writer Frank Swain realized he was going to go deaf, he decided to hack his hearing to be able to hear Wi-Fi. Swain developed software that tunes into wireless communication fields and uses an inbuilt Wi-Fi sensor to pick up router name, encryption modes and distance from the device. This data is translated into an audio stream where distant signals click or pop, and strong signals sound their network ID in a looped melody. Swain hears it all through an upgraded hearing aid.
Global datastreams can also become sensory experiences. Spanish artist Moon Ribas developed and implanted a chip in her elbow that is connected to the global monitoring system for seismographic sensors; each time there’s an earthquake, she feels it through vibrations in her arm.
You can feel connected to our planet, too: North Sense makes a “standalone artificial sensory organ” that connects to your body and vibrates whenever you’re facing north. It’s a built-in compass; you’ll never get lost again.
Biohacking applications are likely to proliferate in the coming years, some of them more useful than others. But there are serious ethical questions that can’t be ignored during development and use of this technology. To what extent is it wise to tamper with nature, and who gets to decide?
Most of us are probably ok with waiting in line an extra 10 minutes or occasionally having to pull up a maps app on our phone if it means we don’t need to implant computer chips into our forearms. If it’s frightening to think of criminals stealing our wallets, imagine them cutting a chunk of our skin out to have instant access to and control over our personal data. The physical invasiveness and potential for something to go wrong seems to far outweigh the benefits the average person could derive from this technology.
But that may not always be the case. It’s worth noting the miniaturization of technology continues at a quick rate, and the smaller things get, the less invasive (and hopefully more useful) they’ll be. Even today, there are people already sensibly benefiting from biohacking. If you look closely enough, you’ll spot at least a couple cyborgs on your commute tomorrow morning.
Image Credit:Movement Control Laboratory/University of Washington – Deep Dream Generator Continue reading

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#428173 Next-Gen Robotics & Automation: ...


The fall in price of next-generation robots from hundreds to tens of thousands of pounds means that the business case just became stronger for automotive vehicle and parts manufacturers to implement robotic solutions across individual manufacturing lines.

Challenges and pitfalls remain though, with nearly 76% of the target audience lacking clarity on robotic capabilities and implementation best practice. From how to prepare process for automation, to the individual capabilities of each type of robot for individual production lines, OEMs need to know the next best step.

This year’s must attend Next-Generation Robotics & Automation: Automotive Manufacturing Europe 2016 Summit will be the only event focused on robotic upgrade and innovation, specifically for the automotive industry.

Co-located with our UK flagship Joining, Forming & Manufacturing Technologies Summit, on 29th-30th November, at the VOX in Birmingham, this must attend event addresses how to retain cutting edge in automotive manufacturing and the tactics needed to get next-generation robots right, first time.

Reasons To Attend:

The Only European Robotics Event Dedicated To The Automotive Industry

Discuss selection and implementation challenges specific to your sector:

8+ Robotic Capabilities Case Studies – Comprehensive access to exclusive manufacturer perspectives on Next-Generation Robotic applications – direct from the plant

5 Process Specific Breakout Groups – Grapple with application, maintenance & selection considerations particular to your production process: Body Shop, Paint Shop, Power Train & Final Assembly

4 Robot-Type Deep Dive Discussion Groups – Discuss with peers the capabilities and attributes of each specific next-generation robot type to address their relevance to your needs: Zero Speed Monitoring, Power & Force Limited, Speed & Separation & Hand Guided Robots

Strategic & Technical Focus – A blended programme offers access to business case and strategic considerations, as well as tactical robotic application techniques
Speakers Include:

Willem Grobler, Technology Project Leader, BMW
Rich McDonnell, Senior Manufacturing Manager TS-22,
Jaguar XE & F-Pace Body Construction, Jaguar Land Rover
Dan Lämkull , Methods Developer, Volvo Car Corporation
Ali Ackay, Control Technologies & Robotics – Manufacturing Engineering Development, Daimler AG & Mercedes-Benz Trucks

Register today to profit from the Super Early Bird Discount, and reserve your place at the innovation hub of the European Automotive sector in time!
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#428053 Omnidirectional Mobile Robot Has Just ...

Spherical Induction Motor Eliminates Robot’s Mechanical Drive System
PITTSBURGH— More than a decade ago, Ralph Hollis invented the ballbot, an elegantly simple robot whose tall, thin body glides atop a sphere slightly smaller than a bowling ball. The latest version, called SIMbot, has an equally elegant motor with just one moving part: the ball.
The only other active moving part of the robot is the body itself.
The spherical induction motor (SIM) invented by Hollis, a research professor in Carnegie Mellon University’s Robotics Institute, and Masaaki Kumagai, a professor of engineering at Tohoku Gakuin University in Tagajo, Japan, eliminates the mechanical drive systems that each used on previous ballbots. Because of this extreme mechanical simplicity, SIMbot requires less routine maintenance and is less likely to suffer mechanical failures.
The new motor can move the ball in any direction using only electronic controls. These movements keep SIMbot’s body balanced atop the ball.
Early comparisons between SIMbot and a mechanically driven ballbot suggest the new robot is capable of similar speed — about 1.9 meters per second, or the equivalent of a very fast walk — but is not yet as efficient, said Greg Seyfarth, a former member of Hollis’ lab who recently completed his master’s degree in robotics.
Induction motors are nothing new; they use magnetic fields to induce electric current in the motor’s rotor, rather than through an electrical connection. What is new here is that the rotor is spherical and, thanks to some fancy math and advanced software, can move in any combination of three axes, giving it omnidirectional capability. In contrast to other attempts to build a SIM, the design by Hollis and Kumagai enables the ball to turn all the way around, not just move back and forth a few degrees.
Though Hollis said it is too soon to compare the cost of the experimental motor with conventional motors, he said long-range trends favor the technologies at its heart.
“This motor relies on a lot of electronics and software,” he explained. “Electronics and software are getting cheaper. Mechanical systems are not getting cheaper, or at least not as fast as electronics and software are.”
SIMbot’s mechanical simplicity is a significant advance for ballbots, a type of robot that Hollis maintains is ideally suited for working with people in human environments. Because the robot’s body dynamically balances atop the motor’s ball, a ballbot can be as tall as a person, but remain thin enough to move through doorways and in between furniture. This type of robot is inherently compliant, so people can simply push it out of the way when necessary. Ballbots also can perform tasks such as helping a person out of a chair, helping to carry parcels and physically guiding a person.
Until now, moving the ball to maintain the robot’s balance has relied on mechanical means. Hollis’ ballbots, for instance, have used an “inverse mouse ball” method, in which four motors actuate rollers that press against the ball so that it can move in any direction across a floor, while a fifth motor controls the yaw motion of the robot itself.
“But the belts that drive the rollers wear out and need to be replaced,” said Michael Shomin, a Ph.D. student in robotics. “And when the belts are replaced, the system needs to be recalibrated.” He said the new motor’s solid-state system would eliminate that time-consuming process.
The rotor of the spherical induction motor is a precisely machined hollow iron ball with a copper shell. Current is induced in the ball with six laminated steel stators, each with three-phase wire windings. The stators are positioned just next to the ball and are oriented slightly off vertical.
The six stators generate travelling magnetic waves in the ball, causing the ball to move in the direction of the wave. The direction of the magnetic waves can be steered by altering the currents in the stators.
Hollis and Kumagai jointly designed the motor. Ankit Bhatia, a Ph.D. student in robotics, and Olaf Sassnick, a visiting scientist from Salzburg University of Applied Sciences, adapted it for use in ballbots.
Getting rid of the mechanical drive eliminates a lot of the friction of previous ballbot models, but virtually all friction could be eliminated by eventually installing an air bearing, Hollis said. The robot body would then be separated from the motor ball with a cushion of air, rather than passive rollers.
“Even without optimizing the motor’s performance, SIMbot has demonstrated impressive performance,” Hollis said. “We expect SIMbot technology will make ballbots more accessible and more practical for wide adoption.”
The National Science Foundation and, in Japan, Grants-in-Aid for Scientific Research (KAKENHI) supported this research. A report on the work was presented at the May IEEE International Conference on Robotics and Automation in Stockholm, Sweden.

Video by: Carnegie Mellon University
About Carnegie Mellon University: Carnegie Mellon (www.cmu.edu) is a private, internationally ranked research university with programs in areas ranging from science, technology and business, to public policy, the humanities and the arts. More than 13,000 students in the university’s seven schools and colleges benefit from a small student-to-faculty ratio and an education characterized by its focus on creating and implementing solutions for real problems, interdisciplinary collaboration and innovation.

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#427791 Robot Operating System (ROS) continues ...

Today by far the most commonly used robotics software is ROS, which stands for Robot Operating System. This is an open source software, and the most number of developers and robotics users are involved with this program with an ever increasing rate. It contains set of libraries, algorithms, developer tools and drivers for developing robotics projects. The first release of ROS was in 2010, and as of end of 2016, ROS has reached its 10th official release, which is called “ROS Kinetic Kame”. There are translations to 11 languages other than English, which are: German, Spanish, French, Italian, Japanese, Turkish, Korean, Portuguese, Russian, Thai and Chinese. It currently has 2000+ software libraries, which keeps increasing every year.
Many robots use ROS now, including but not limited to hobby robots, drones, educational or advanced humanoid robots, domestic robots including cleaning robot vacuums, cooking robots or telepresence robots and more, robot arms, farming robots, industrial robots, even Robonaut of NASA in space or the four legged military robots in development. A list of robots which use ROS can be found here: http://wiki.ros.org/Robots.
We were checking the Alexa.Com ranking of ROS since few years, in order to track the increase in usage, and we believe it is time to share it now, as we have enough data. The numbers on the left are dates we looked and the numbers on the right indicate the ranking of Ros.Org website from top, among all websites in the world:
May 2011: 189,000 th in the world, from top, among all other websites
April 2012: 187,900 th
January 2014: 107,821
May 2014: 112,236
September 2014: 83,875 (7219 in Canada, the country where it is most accessed)
January 2015: 83,556 (4,258 in Canada)
February 2015 : 75,680 (33185 in USA)
April 2015: 59,200 (31,334 in USA)
August 2015: 65,754 (50,132 in USA)
September 2016: 30,201 (China 5073)
This chart shows the increasing rank of ros.org among other websites in the world, which is a good indicator of its growth. The numbers on the left represent the site’s ranking from the top, among all other sites in the world. Chart Copyright: Robokingdom LLC.

As can be seen here, in May 2011, when we first checked this ranking, ROS.org was at 189,000 th place in the world from the top among all other websites in terms of unique visitors that visit the site, and it almost continuously increased its ranking. As of September 2016, it is now the 30,201st most reached website in the world, with mostly being accessed in China (5073 from top in China). Let’s not forget that even if it’s position remained the same, let alone going up, it would still mean the traffic of the site was going up, as every year there are more websites in the world which means the same ranking means better place and more traffic. The ranking of 30,201 means ROS.org is a very high traffic website in the world right now, being accessed probably by at least hundreds of thousands of people every day, with no indication of slowing down its rise yet.
The most important result of all of this, is that the use of robots is increasing, both in terms of number and type (when you look at the type of robots that use ros, as it also increases in variety all the time).
From Alexa, we were also able to see, from publicly available information, that the percentage of reach among countries for ROS.org is as follows:
China 47.5%
USA 11.5%
Japan 8.7%
South Korea 3.5%
Germany 3.4%
This also shows us that in China, a lot of things are going on for robotics development right now, as it gets most of its traffic from there with 47.5%. USA then follows with 11.5% and Japan is third with 8.7%.
With ROS, any type of sensors can be controlled, including 1d/2d range sensors, 3d range finders and cameras, audio/speech recognition sensors, cameras, environmental sensors, force/torque/touch sensors, motion capture, pose estimation, power supply, RFID, and sensor interfaces.
In ros.org site, in addition to all packages, there are also extensive tutorials and a discussion board that one can ask questions and share knowledge.
ROS also has an industrial section, the version of software modified for industrial applications. It is called ROS industrial, and can be reached at: http://rosindustrial.org/. Although we see domestic robots with new abilities or advanced research projects that aim to develop capabilities of robotics every year, according to the results of a study that is shown on http://rosindustrial.org/the-challenge/ website, the abilities of industrial robots are not progressing and the abilities are restricted to welding, material handling, dispensing, coating (although we know that they do additional tasks such as packaging, inspection, labeling etc…). ROS Industrial aims to solve this challenge by providing a common skeleton to all developers, with its extensive and stronger software architecture, than other individual robotics programs.
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