Technion scientists create biological computer

By
June 8, 2013 23:11

New Worlds: Scientists at the Technion-Israel Institute of Technology have developed and built a molecular transducer.




Computer technology

Computer technology. (photo credit:Pepe Fainberg)

Scientists at the Technion-Israel Institute of Technology have developed and built a molecular transducer – an advanced computing machine solely out of biomolecules like DNA and enzymes that can manipulate genetic codes. This “unprecedented device,” they said, can compute using the output as a new input for subsequent computations (called an iterative computation).

In addition, it produces outputs in the form of biologically meaningful phenomena, such as resistance of bacteria to various antibiotics. The researchers showed that their transducer can perform a long division of binary numbers by the number 3 and preformed an iterative computation.

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Prof. Ehud Keinan, postdoctoral chemistry fellows Dr. Tamar Ratner and Dr. Ron Piran and Dr. Natasha Jonoska of the department of Mathematics at the University of South Florida published their work recently in the prestigious journal Chemistry & Biology of the Cell. Their work may open up interesting opportunities in biotechnology, including individual gene therapy and cloning.

“The ever-increasing interest in biomolecular computing devices has not arisen from the hope that such machines could ever compete with their electronic counterparts by offering greater computation speed, fidelity and power or performance in traditional computing tasks,” said Keinan. “The main advantages of biomolecular computing devices over the electronic computers arise from other properties. As shown in this work and other projects carried out in our lab, these systems can interact directly with biological systems and even with living organisms.

No interface is required since all components of molecular computers, including hardware, software, input and output, are molecules that interact in solution along a cascade of programmable chemical events.

“All biological systems, and even entire living organisms, are natural molecular computers. Every one of us is a biomolecular computer, that is, a machine in which all components are molecules ‘talking’ to one another in a logical manner. The hardware and software are complex biological molecules that activate one another to carry out some predetermined chemical tasks. The input is a molecule that undergoes specific, programmed changes, following a specific set of rules (software) and the output of this chemical computation process is another well-defined molecule.

“Our results are significant because they demonstrate for the first time a synthetic, designed computing machine that not only computes iteratively, but also produces biologically relevant results. Although this transducer was employed to solve a specific problem, the general methodology shows that similar devices could be applied for other computational problems.

In addition to its enhanced computation power, this DNA-based transducer offers multiple benefits, such as the ability to read and transform genetic information, miniaturization to the molecular scale and the aptitude to produce computational results which interact directly with living organisms. Therefore, its implementation on a genetic material may not just evaluate and detect specific sequences, but it can also alter and algorithmically process the genetic code.

TRYING TO REDUCE FRICTION Prof. Jacob Klein, of the Weizmann Institute of Science’s department of materials and interfaces, has been awarded the Gold Medal in Tribology from British Ambassador Matthew Gould. The prize is the highest award of the Tribology Trust Fund, a fund administered by the Institution of Mechanical Engineers in London.

Tribology? It isn’t a misspelling of biology, and doesn’t have anything to do with tribes. Tribology is the study of surfaces rubbing against each other; it attempts to understand friction, lubrication and wear to avoid their negative qualities and make use of their positive ones.

The prize was given in recognition of Klein’s innovative research, published in the journal Nature, on mimicking the lubrication of joints. In the body, bones in joints are covered with cartilage. Long molecules protrude from the cartilage into the fluid between the bones. This system reduces friction and allows the body to move, walk and bend.

Klein’s artificial materials mimic the body’s system. He uses ceramic surfaces in place of bones and cartilage and polyelectrolytes in place of long molecules to produce a system which is very resistant to friction.

Klein’s lubricant is up to a thousand times more effective than standard lubricants and opens the possibility of myriad uses from larger hard disks for computers, to better, longer lasting hip joint implants, as well as treatment of dry-eye syndrome.

When awarding the gold medal, Gould said: “I am proud to award this medal to Prof. Klein. In the UK, this award is presented to the winner by a member of the British royalty. My residence may not be Buckingham Palace, but because I am a diplomat, I am always anxious to reduce friction.

Therefore, I would like to consider myself a tribologist as well.”

A ROSE IS A ROSE...

Why do rose petals have rounded ends while their leaves are more pointed? If this phenomenon has been worrying you lately, you’re be relieved to hear that British researchers have found the answer.

Scientists from the University of East Anglia have published a study in the open-access journal PLOS Biology that found the shape of petals is controlled by a hidden map located within the plant’s growing buds.

Leaves and petals perform different functions related to their shape.

Leaves acquire sugars for a plant via photosynthesis, which can then be transported throughout the plant.

Petals develop later in the life cycle and help attract pollinators. In earlier work, this team discovered that leaves in the plant Arabidopsis contain a hidden map that orients growth in a pattern that converges towards the tip of the bud, giving leaves their characteristic pointed tips.

In the new study, the researchers discover that Arabidopsis petals contain a similar, hidden map that orients growth in the flower’s bud. However, the pattern of growth is different to that in leaves – in the petal growth is oriented towards the edge, giving a more rounded shape – accounting for the different shapes of leaves and petals.

The researchers discovered that molecules called PIN proteins are involved in this oriented growth, which are located toward the ends of each cell.

“The discovery of these hidden polarity maps was a real surprise and provides a simple explanation for how different shapes can be generated,” said senior study author Prof. Enrico Coen.

The team of researchers confirmed their ideas by using computer simulations to test which maps could predict the correct petal shape. They then confirmed experimentally that PIN proteins located at the right sites are involved in oriented growth, and identified another protein, called JAGGED, that is involved in promoting growth toward the edge of petals and in establishing the hidden map that determines petal growth and shape.

Unlike animal cells, plant cells are unable to move and migrate to form structures of a particular shape, and so these findings help to explain how plants create differently shaped organs – by controlling rates and orientations of cell growth. From an evolutionary perspective, this system creates the flexibility needed for plant organs to adapt to their environment and to develop different functions, Coen said.


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