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Programming language for novel biological circuits

MIT biological engineers have created a programming language that allows them to rapidly design complex, DNA-encoded circuits that give new functions to living cells.

Using this language, anyone can write a program for the function they want, such as detecting and responding to certain environmental conditions. They can then generate a DNA sequence that will achieve it.

"It is literally a programming language for bacteria," says Christopher Voigt, an MIT professor of biological engineering. "You use a text-based language, just like you're programming a computer. Then you take that text and you compile it and it turns it into a DNA sequence that you put into the cell, and the circuit runs inside the cell."

Voigt and colleagues at Boston University and the National Institute of Standards and Technology have used this language, which they describe in the April 1 issue of Science, to build circuits that can detect up to three inputs and respond in different ways. Future applications for this kind of programming include designing bacterial cells that can produce a cancer drug when they detect a tumor, or creating yeast cells that can halt their own fermentation process if too many toxic byproducts build up.

The researchers plan to make the user design interface available on the Web.

No experience needed

Over the past 15 years, biologists and engineers have designed many genetic parts, such as sensors, memory switches, and biological clocks, that can be combined to modify existing cell functions and add new ones.

However, designing each circuit is a laborious process that requires great expertise and often a lot of trial and error. "You have to have this really intimate knowledge of how those pieces are going to work and how they're going to come together," Voigt says.

Users of the new programming language, however, need no special knowledge of genetic engineering.

"You could be completely naive as to how any of it works. That's what's really different about this," Voigt says. "You could be a student in high school and go onto the Web-based server and type out the program you want, and it spits back the DNA sequence."

The language is based on Verilog, which is commonly used to program computer chips. To create a version of the language that would work for cells, the researchers designed computing elements such as logic gates and sensors that can be encoded in a bacterial cell's DNA. The sensors can detect different compounds, such as oxygen or glucose, as well as light, temperature, acidity, and other environmental conditions. Users can also add their own sensors. "It's very customizable," Voigt says.

The biggest challenge, he says, was designing the 14 logic gates used in the circuits so that they wouldn't interfere with each other once placed in the complex environment of a living cell.

In the current version of the programming language, these genetic parts are optimized for E. coli, but the researchers are working on expanding the language for other strains of bacteria, including Bacteroides, commonly found in the human gut, and Pseudomonas, which often lives in plant roots, as well as the yeast Saccharomyces cerevisiae. This would allow users to write a single program and then compile it for different organisms to get the right DNA sequence for each one.

Biological circuits

Using this language, the researchers programmed 60 circuits with different functions, and 45 of them worked correctly the first time they were tested. Many of the circuits were designed to measure one or more environmental conditions, such as oxygen level or glucose concentration, and respond accordingly. Another circuit was designed to rank three different inputs and then respond based on the priority of each one.

One of the new circuits is the largest biological circuit ever built, containing seven logic gates and about 12,000 base pairs of DNA.

Another advantage of this technique is its speed. Until now, "it would take years to build these types of circuits. Now you just hit the button and immediately get a DNA sequence to test," Voigt says.

His team plans to work on several different applications using this approach: bacteria that can be swallowed to aid in digestion of lactose; bacteria that can live on plant roots and produce insecticide if they sense the plant is under attack; and yeast that can be engineered to shut off when they are producing too many toxic byproducts in a fermentation reactor.

The lead author of the Science paper is MIT graduate student Alec Nielsen. Other authors are former MIT postdoc Bryan Der, MIT postdoc Jonghyeon Shin, Boston University graduate student Prashant Vaidyanathan, Boston University associate professor Douglas Densmore, and National Institute of Standards and Technology researchers Vanya Paralanov, Elizabeth Strychalski, and David Ross.

Story Source:

The above post is reprinted from materials provided by Massachusetts Institute of Technology. The original item was written by Anne Trafton. Note: Materials may be edited for content and length.

Source: https://www.sciencedaily.com/releases/2016/03/160331154001.htm

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Founded by Russian entrepreneur Dmitry Itskov in February 2011 with the participation of leading Russian specialists in the field of neural interfaces, robotics, artificial organs and systems.

The main goals of the 2045 Initiative: the creation and realization of a new strategy for the development of humanity which meets global civilization challenges; the creation of optimale conditions promoting the spiritual enlightenment of humanity; and the realization of a new futuristic reality based on 5 principles: high spirituality, high culture, high ethics, high science and high technologies. 

The main science mega-project of the 2045 Initiative aims to create technologies enabling the transfer of a individual’s personality to a more advanced non-biological carrier, and extending life, including to the point of immortality. We devote particular attention to enabling the fullest possible dialogue between the world’s major spiritual traditions, science and society.

A large-scale transformation of humanity, comparable to some of the major spiritual and sci-tech revolutions in history, will require a new strategy. We believe this to be necessary to overcome existing crises, which threaten our planetary habitat and the continued existence of humanity as a species. With the 2045 Initiative, we hope to realize a new strategy for humanity's development, and in so doing, create a more productive, fulfilling, and satisfying future.

The "2045" team is working towards creating an international research center where leading scientists will be engaged in research and development in the fields of anthropomorphic robotics, living systems modeling and brain and consciousness modeling with the goal of transferring one’s individual consciousness to an artificial carrier and achieving cybernetic immortality.

An annual congress "The Global Future 2045" is organized by the Initiative to give platform for discussing mankind's evolutionary strategy based on technologies of cybernetic immortality as well as the possible impact of such technologies on global society, politics and economies of the future.


Future prospects of "2045" Initiative for society


The emergence and widespread use of affordable android "avatars" controlled by a "brain-computer" interface. Coupled with related technologies “avatars’ will give people a number of new features: ability to work in dangerous environments, perform rescue operations, travel in extreme situations etc.
Avatar components will be used in medicine for the rehabilitation of fully or partially disabled patients giving them prosthetic limbs or recover lost senses.


Creation of an autonomous life-support system for the human brain linked to a robot, ‘avatar’, will save people whose body is completely worn out or irreversibly damaged. Any patient with an intact brain will be able to return to a fully functioning  bodily life. Such technologies will  greatly enlarge  the possibility of hybrid bio-electronic devices, thus creating a new IT revolution and will make  all  kinds of superimpositions of electronic and biological systems possible.


Creation of a computer model of the brain and human consciousness  with the subsequent development of means to transfer individual consciousness  onto an artificial carrier. This development will profoundly change the world, it will not only give everyone the possibility of  cybernetic immortality but will also create a friendly artificial intelligence,  expand human capabilities  and provide opportunities for ordinary people to restore or modify their own brain multiple times.  The final result  at this stage can be a real revolution in the understanding of human nature that will completely change the human and technical prospects for humanity.


This is the time when substance-independent minds will receive new bodies with capacities far exceeding those of ordinary humans. A new era for humanity will arrive!  Changes will occur in all spheres of human activity – energy generation, transportation, politics, medicine, psychology, sciences, and so on.

Today it is hard to imagine a future when bodies consisting of nanorobots  will become affordable  and capable of taking any form. It is also hard to imagine body holograms featuring controlled matter. One thing is clear however:  humanity, for the first time in its history, will make a fully managed evolutionary transition and eventually become a new species. Moreover,  prerequisites for a large-scale  expansion into outer space will be created as well.


Key elements of the project in the future

• International social movement
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• scientific research centre "Immortality"
• business incubator
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