Computer Gates Built From DNA Could Lead To Biocomputers We Can Inject Inside Us

Scientists are finding success recently in getting DNA to mimic non-biological circuits and form logic gates, the stuff from which all computers are made. DNA-based logic gates that could some day carry out calculations inside our bodies and can be programmed to target diseases as they arise. “The biocomputer would sense biomarkers and immediately react by releasing counter-agents for the disease,” says Itamar Willner of the Hebrew University of Jerusalem, Israel, who led the work.

The new logic gates are formed from short strands of DNA and their complementary strands, which in conjunction with some simple molecular machinery mimic their electronic equivalent. Two strands act as the input: each represents a 1 when present or a 0 when absent. The response to their presence or absence represents the output, which can also be a 1 or 0.

Take the “exclusive OR” or XOR logic gate. It produces an output when either of the two inputs is present but not when both are present or both are absent. To put the DNA version to the test, Willner and his team added molecules to both the complementary strands that caused them to fluoresce when each was present in isolation, representing a logical 1 as the output. But when both were present, the complementary strands combined and quenched the fluorescence, representing a 0 output.

One of DNA computing’s advantages is that it allows calculations to be carried out in parallel, if different types of logic gates are represented by different ingredients. The team tested this process by tossing the XOR ingredients into a test tube, along with those for two other gates, to produce the first few steps involved in binary addition and subtraction.

The team was also able to create logic gates that calculate in sequence. The trick here is to make the output from the first gate a new DNA string that can be used as the input for a second gate and so on. Such “cascading gates” allow for more complex calculations: the entire set of steps required for addition and subtraction, for example, or to deliver a multi-step drug treatment.

Previous DNA-based computers tended to slow down at each step as the DNA strands were used only once, and so became depleted with time. One significant advance claimed by Willner and his team is that their DNA strands reform after each step, allowing long sequences of calculations to be carried out easily for the first time.

Even a single logic gate could have useful medical applications, Willner says. His group built and tested a gate designed to reduce the activity of the blood-clotting enzyme thrombin, which can lead to brain damage following a head injury. The gate acts as a switch that is triggered by the presence of thrombin. Part of the gate consists of a DNA strand connected to a molecule that binds to thrombin. If thrombin is present, this molecule is released, otherwise it stays bound and inert. Such a smart drug could be injected into the bloodstream in advance and would only switch on when needed (Nature Nanotechnology, DOI: 10.1038/nnano.2010.88).

Another problem with earlier DNA computers is that they use enzymes to manipulate the DNA, and so function only in certain chemical environments that cannot easily be reproduced inside the body. Willner’s team use DNA-like molecules to do this job.

“Being enzyme-free, it has potential in future diagnostic and medical applications,” says Benny Gil of the Weizmann Institute of Science in Rehovot, Israel. He is impressed with the new gate system but recognises that it will take years of research and development to bring “smart drugs” to medicine.

Source: New Scientist.

Magnets And Nano-particles May One Day Grow Us A New Liver

Although scientists have been building artificial human organs for sometime now, researchers at Rice University and the MD Anderson Cancer Center in Houston have developed a simple way to make cells form 3-D structures using magnets and metal nano-particles. Building organs by tissue engineers has so far been limited to a 2D surface.

Being able to grow more realistic liver, heart, and other tissues in the lab could provide a new lease on life for patients waiting on the transplant list–and lead to more realistic systems for testing drugs. But tissue engineers have found that mimicking these complex, three-dimensional structures in the lab is difficult. Part of what’s holding them up are flat, two-dimensional tissue culture systems that grow cells in an environment very different from that inside the body.

Now researchers at Rice University and the MD Anderson Cancer Center in Houston have developed a simple way to make cells form 3-D structures. They developed a gel made up of a polymer, iron oxide nanoparticles, and engineered viruses called phage. When cells are added to this mixture, the phage cause them to absorb the magnetic particles. The Houston group showed that they could use a weak magnet to hold magnetized brain cancer cells in a 3-D suspension. Gene-expression studies showed that these suspended cells behave more naturally than a control group grown on a conventional flat surface: the cancer cells were producing a mix of proteins very similar to what they produce in the body. These results are described in Nature Nanotechnology this week.

The magnetizing gel has been licensed to a startup company, Nano3D Bioscience, which will run tests to compare the technology other methods for making 3-D tissues.

Source: 

http://thetechjournal.com

MIT Researcher Develops Technology To Make AI Smarter Than Ever

Artificial intelligence systems developed up until now are categorized into two types: logic-based or probability-based. But now a researcher at MIT has created a new language, Church, that combines the best aspects of the two categories and promises to make AI smarter than ever.

Artificial intelligence systems developed up until now are categorized into two types: logic-based or probability-based. But now a researcher at MIT has created a new language, Church, that Artificial intelligence researchers back in the 1950s thought of the human mind as a set of rules to be programmed and developed systems based on logical inferences, e.g., “if you know that birds can fly and are told that the waxwing is a bird, you can infer that waxwings can fly.”

But with rules-based AI, every exception had to be accounted for. The systems couldn’t figure out that there were types of birds that couldn’t fly; they had to be told so explicitly. Later AI models gave up these extensive rule sets and turned to probabilities: “a computer is fed lots of examples of something – like pictures of birds – and is left to infer, on its own, what those examples have in common.”

Church, a “grand unified theory of AI” developed by MIT researcher Noah Goodman, combines both systems, creating probability-based rules that are constantly revised as the system encounters new situations:

A Church program that has never encountered a flightless bird might, initially, set the probability that any bird can fly at 99.99 percent. But as it learns more about cassowaries – and penguins, and caged and broken-winged robins – it revises its probabilities accordingly. Ultimately, the probabilities represent all the conceptual distinctions that early AI researchers would have had to code by hand. But the system learns those distinctions itself, over time – much the way humans learn new concepts and revise old ones.

Researchers think that Church’s fluidity will help it surpass current AI models, and in a test in which the system was charged to make predictions based on a set of observations, it did a “significantly better job of modeling human thought than traditional artificial intelligence algorithms did.” Church is still rough around the edges, and while it’s effective at specific operations it’s too “computationally intensive” to tackle broader brain-simulation at this point. But Goodman will continue working on the new system, and in the mean time, it will only be getting smarter.

Source: MIT, Gizmodo