Computing building blocks created from bacteria and DNA

ScienceDaily (Oct. 18, 2011) — Scientists have successfully demonstrated that they can build some of the basic components for digital devices out of bacteria and DNA, which could pave the way for a new generation of biological computing devices, in research published October 18 in the journal Nature Communications.

The researchers, from Imperial College London, have demonstrated that they can build logic gates, which are used for processing information in devices such as computers and microprocessors, out of harmless gut bacteria and DNA. These are the most advanced biological logic gates ever created by scientists.

Professor Richard Kitney, co-author of the paper from the Centre for Synthetic Biology and Innovation and the Department of Bioengineering at Imperial College London, says: "Logic gates are the fundamental building blocks in silicon circuitry that our entire digital age is based on. Without them, we could not process digital information. Now that we have demonstrated that we can replicate these parts using bacteria and DNA, we hope that our work could lead to a new generation of biological processors, whose applications in information processing could be as important as their electronic equivalents."

Although still a long way off, the team suggest that these biological logic gates could one day form the building blocks in microscopic biological computers. Devices may include sensors that swim inside arteries, detecting the build up of harmful plaque and rapidly delivering medications to the affected zone. Other applications may include sensors that detect and destroy cancer cells inside the body and pollution monitors that can be deployed in the environment, detecting and neutralising dangerous toxins such as arsenic.

Previous research only proved that biological logic gates could be made. The team say that the advantage of their biological logic gates over previous attempts is that they behave more like their electronic counterparts. The new biological gates are also modular, which means that they can be fitted together to make different types of logic gates, paving the way for more complex biological processors to be built in the future.

In the new study, the researchers demonstrated how these biological logic gates worked. In one experiment, they showed how biological logic gates can replicate the way that electronic logic gates process information by either switching "on" or "off."

The scientists constructed a type of logic gate called an "AND Gate" from bacteria called Escherichia coli (E.Coli), which is normally found in the lower intestine. The team altered the E.Coli with modified DNA, which reprogrammed it to perform the same switching on and off process as its electronic equivalent when stimulated by chemicals.

The researchers were also able to demonstrate that the biological logic gates could be connected together to form more complex components in a similar way that electronic components are made. In another experiment, the researchers created a "NOT gate" and combined it with the AND gate to produce the more complex "NAND gate."

The next stage of the research will see the team trying to develop more complex circuitry that comprises multiple logic gates. One of challenges faced by the team is finding a way to link multiple biological logic gates together, similar to the way in which electronic logic gates are linked together, to enable complex processing to be carried out.

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Journal Reference:

Baojun Wang, Richard I Kitney, Nicolas Joly, Martin Buck. Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology. Nature Communications, 2011; 2: 508 DOI: 10.1038/ncomms1516

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Building better catalysts

ScienceDaily (Sep. 30, 2011) — University of Utah chemists developed a method to design and test new catalysts, which are substances that speed chemical reactions and are crucial for producing energy, chemicals and industrial products. By using the new method, the chemists also made a discovery that will make it easier to design future catalysts.

The discovery: the sizes and electronic properties of catalysts interact to affect how well a catalyst performs, and are not independent factors as was thought previously. Chemistry Professor Matt Sigman and doctoral student Kaid Harper, report their findings in the Sept. 30, 2011, issue of the journal Science.

"It opens our eyes to how to design new catalysts that we wouldn't necessarily think about designing, for a broad range of reactions," Sigman says. "We're pretty excited."

Sigman believes the new technique for designing and testing catalysts "is going to be picked up pretty fast," first by academic and then by industrial chemists, who "will see it's a simple way to rapidly design better catalysts."

'Catalysts Make the World Go 'Round'

Catalysts speed chemical reactions without being consumed by those reactions. Their importance to society and the economy is tough to overstate. Products made with catalysts include medicines, fuels, foods and fertilizers.

Ninety percent of U.S. chemical manufacturing processes involve catalysts, which also are used to make more than one-fifth of all industrial products. Those processes consume much energy, so making catalytic reactions more efficient would both save energy and reduce emissions of climate-warming carbon dioxide gas.

"Catalysts make the world go 'round," says Sigman. "Catalysts are how we make molecules more efficiently and, more important, make molecules that can't be made using any other method."

The Utah researchers developed a new method for rapidly identifying and designing what are known as "asymmetric catalysts," which are catalyst molecules that are considered either left-handed or right-handed because they are physically asymmetrical. In chemistry, this property of handedness is known as chirality.

Chemists want new asymmetric catalysts because they impart handedness or chirality to the molecules they are used to make. For example, when a left-handed or right-handed catalyst is used to speed a chemical reaction, the chemical that results from that reaction can be either left-handed or right-handed.

"Handedness is an essential component of a drug's effectiveness," Sigman says.

Drugs generally work by latching onto proteins involved in a disease-causing process. The drug is like a key that fits into a protein lock, and chirality "is the direction the key goes" to fit properly and open the lock, says Sigman.

"However, developing asymmetric catalysts [to produce asymmetric drug molecules] can be a time-consuming and sometimes unsuccessful undertaking" because it usually is done by trial and error, he adds.

Sigman says the new study "is a step toward developing faster methods to identify optimal catalysts and insight into how to design them."

A Mathematical Approach to Catalyst Design

Harper and Sigman combined principles of data analysis with principles of catalyst design to create a "library" of nine related catalysts that they hypothesized would effectively catalyze a given reaction -- one that could be useful for making new pharmaceuticals. Essentially, they used math to find the optimal size and electronic properties of the candidate catalysts.

Then the chemists tested the nine catalysts -- known as "quinoline proline ligands" -- to determine how well their degree of handedness would be passed on to the chemical reaction products the catalysts were used to produce.

Sigman and Harper depicted results of the reactions using the different catalysts as a three-dimensional mathematical surface that bulges upward. The highest part of the bulge represents those among the nine catalysts that had the greatest degree of handedness.

This technique was used -- and can be used in the future -- to identify the optimal catalysts among a number of candidates. But it also revealed the unexpected link between the size and electronic properties of catalysts in determining their effectiveness in speeding reactions.

"This study shows quantitatively that the two factors are related," and knowing that will make it easier to design many future catalysts, Sigman says.

The new study was funded by the National Science Foundation.

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The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by University of Utah.

Journal Reference:

Matt Sigman and Kaid Harper. A Well-Behaved Catalyst. Science, 30 September 2011: 1797 DOI: 10.1126/science.333.6051.1797-f

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Building better catalysts

ScienceDaily (Sep. 30, 2011) — University of Utah chemists developed a method to design and test new catalysts, which are substances that speed chemical reactions and are crucial for producing energy, chemicals and industrial products. By using the new method, the chemists also made a discovery that will make it easier to design future catalysts.

The discovery: the sizes and electronic properties of catalysts interact to affect how well a catalyst performs, and are not independent factors as was thought previously. Chemistry Professor Matt Sigman and doctoral student Kaid Harper, report their findings in the Sept. 30, 2011, issue of the journal Science.

"It opens our eyes to how to design new catalysts that we wouldn't necessarily think about designing, for a broad range of reactions," Sigman says. "We're pretty excited."

Sigman believes the new technique for designing and testing catalysts "is going to be picked up pretty fast," first by academic and then by industrial chemists, who "will see it's a simple way to rapidly design better catalysts."

'Catalysts Make the World Go 'Round'

Catalysts speed chemical reactions without being consumed by those reactions. Their importance to society and the economy is tough to overstate. Products made with catalysts include medicines, fuels, foods and fertilizers.

Ninety percent of U.S. chemical manufacturing processes involve catalysts, which also are used to make more than one-fifth of all industrial products. Those processes consume much energy, so making catalytic reactions more efficient would both save energy and reduce emissions of climate-warming carbon dioxide gas.

"Catalysts make the world go 'round," says Sigman. "Catalysts are how we make molecules more efficiently and, more important, make molecules that can't be made using any other method."

The Utah researchers developed a new method for rapidly identifying and designing what are known as "asymmetric catalysts," which are catalyst molecules that are considered either left-handed or right-handed because they are physically asymmetrical. In chemistry, this property of handedness is known as chirality.

Chemists want new asymmetric catalysts because they impart handedness or chirality to the molecules they are used to make. For example, when a left-handed or right-handed catalyst is used to speed a chemical reaction, the chemical that results from that reaction can be either left-handed or right-handed.

"Handedness is an essential component of a drug's effectiveness," Sigman says.

Drugs generally work by latching onto proteins involved in a disease-causing process. The drug is like a key that fits into a protein lock, and chirality "is the direction the key goes" to fit properly and open the lock, says Sigman.

"However, developing asymmetric catalysts [to produce asymmetric drug molecules] can be a time-consuming and sometimes unsuccessful undertaking" because it usually is done by trial and error, he adds.

Sigman says the new study "is a step toward developing faster methods to identify optimal catalysts and insight into how to design them."

A Mathematical Approach to Catalyst Design

Harper and Sigman combined principles of data analysis with principles of catalyst design to create a "library" of nine related catalysts that they hypothesized would effectively catalyze a given reaction -- one that could be useful for making new pharmaceuticals. Essentially, they used math to find the optimal size and electronic properties of the candidate catalysts.

Then the chemists tested the nine catalysts -- known as "quinoline proline ligands" -- to determine how well their degree of handedness would be passed on to the chemical reaction products the catalysts were used to produce.

Sigman and Harper depicted results of the reactions using the different catalysts as a three-dimensional mathematical surface that bulges upward. The highest part of the bulge represents those among the nine catalysts that had the greatest degree of handedness.

This technique was used -- and can be used in the future -- to identify the optimal catalysts among a number of candidates. But it also revealed the unexpected link between the size and electronic properties of catalysts in determining their effectiveness in speeding reactions.

"This study shows quantitatively that the two factors are related," and knowing that will make it easier to design many future catalysts, Sigman says.

The new study was funded by the National Science Foundation.

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and Google +1:

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Story Source:

The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by University of Utah.

Journal Reference:

Matt Sigman and Kaid Harper. A Well-Behaved Catalyst. Science, 30 September 2011: 1797 DOI: 10.1126/science.333.6051.1797-f

Note: If no author is given, the source is cited instead.

Disclaimer: Views expressed in this article do not necessarily reflect those of ScienceDaily or its staff.

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New synchrotron technique could see hidden building blocks of life

ScienceDaily (May 30, 2011) — Scientists from Finland and France have developed a new synchrotron X-ray technique that may revolutionize the chemical analysis of rare materials like meteoric rock samples or fossils. The results have been published on 29 May 2011 in Nature Materials as an advance online publication.

Life, as we know it, is based on the chemistry of carbon and oxygen. The three-dimensional distribution of their abundance and chemical bonds has been difficult to study up to now in samples where these elements were embedded deep inside other materials. Examples are tiny inclusions of possible water or other chemicals inside martian rock samples, fossils buried inside a lava rock, or minerals and chemical compounds within meteorites.

X-ray tomography, which is widely used in medicine and material science, is sensitive to the shape and texture of a given sample but cannot reveal chemical states at the macroscopic scale. For instance graphite and diamond both consist of pure carbon, but they differ in the chemical bond between the carbon atoms. This is why their properties are so radically different. Imaging the variations in atomic bonding has been surprisingly difficult, and techniques for imaging of chemical bonds are highly desirable in many fields like engineering and research in physics, chemistry, biology, and geology.

Now an international team of scientists from the University of Helsinki, Finland, and the European Synchrotron Radiation Facility (ESRF), Grenoble, France, has developed a novel technique that is suitable exactly for this purpose. The researchers use extremely bright X-rays from a synchrotron light source to form images of the chemical bond distribution of different carbon forms embedded deep in an opaque material; an achievement previously thought to be impossible without destroying the sample.

"Now I would love to try this on Martian or moon rocks. Our new technique can see not only which elements are present in any inclusions but also what kind of molecule or crystal they belong to. If the inclusion contains oxygen, we can tell whether the oxygen belongs to a water molecule. If it contains carbon, we can tell whether it is graphite, diamond-like, or some other carbon form. Just imagine finding tiny inclusions of water or diamond inside martian rock samples hidden deep inside the rock," says Simo Huotari from the University of Helsinki.

The newly developed method will give insights into the molecular level structure of many other interesting materials ranging, for example, from novel functional nanomaterials to fuel cells and new types of batteries.

The research was funded by the European Synchrotron Radiation Facility (ESRF), the Academy of Finland, and the University of Helsinki.

Story Source:

The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by European Synchrotron Radiation Facility.

Journal Reference:

Simo Huotari, Tuomas Pylkkänen, Roberto Verbeni, Giulio Monaco, Keijo Hämäläinen. Direct tomography with chemical-bond contrast. Nature Materials, 2011; DOI: 10.1038/NMAT3031

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Gallery: Building the NPP Climate Satellite

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