From Brookhaven Lab: “Researchers Find Surprising Similarities Between Genetic and Computer Codes”

Brookhaven Lab

March 28, 2013
Contacts: Chelsea Whyte, (631) 344-8671 or Peter Genzer, (631) 344-3174

“The term ‘survival of the fittest’ refers to natural selection in biological systems, but Darwin’s theory may apply more broadly than that. New research from the U.S. Department of Energy’s Brookhaven National Laboratory shows that this evolutionary theory also applies to technological systems.

Sergei Maslov

Computational biologist Sergei Maslov of Brookhaven National Laboratory worked with graduate student Tin Yau Pang from Stony Brook University to compare the frequency with which components ‘survive’ in two complex systems: bacterial genomes and operating systems on Linux computers. Their work is published in the Proceedings of the National Academy of Sciences.

Linux Mascot Tux

Maslov and Pang set out to determine not only why some specialized genes or computer programs are very common while others are fairly rare, but to see how many components in any system are so important that they can’t be eliminated. ‘If a bacteria genome doesn’t have a particular gene, it will be dead on arrival,’ Maslov said. ‘How many of those genes are there? The same goes for large software systems. They have multiple components that work together and the systems require just the right components working together to thrive.’

Using data from the massive sequencing of bacterial genomes, now a part of the DOE Systems Biology Knowledgebase (KBase), Maslov and Pang examined the frequency of usage of crucial bits of genetic code in the metabolic processes of 500 bacterial species and found a surprising similarity with the frequency of installation of 200,000 Linux packages on more than 2 million individual computers. Linux is an open source software collaboration that allows designers to modify source code to create programs for public use.

The most frequently used components in both the biological and computer systems are those that allow for the most descendants. That is, the more a component is relied upon by others, the more likely it is to be required for full functionality of a system.

It may seem logical, but the surprising part of this finding is how universal it is. ‘It is almost expected that the frequency of usage of any component is correlated with how many other components depend on it,’ said Maslov. ‘But we found that we can determine the number of crucial components – those without which other components couldn’t function – by a simple calculation that holds true both in biological systems and computer systems.’”

See the full article here.

One of ten national laboratories overseen and primarily funded by the Office of Science of the U.S. Department of Energy (DOE), Brookhaven National Laboratory conducts research in the physical, biomedical, and environmental sciences, as well as in energy technologies and national security. Brookhaven Lab also builds and operates major scientific facilities available to university, industry and government researchers. The Laboratory’s almost 3,000 scientists, engineers, and support staff are joined each year by more than 5,000 visiting researchers from around the world.Brookhaven is operated and managed for DOE’s Office of Science by Brookhaven Science Associates, a limited-liability company founded by Stony Brook University, the largest academic user of Laboratory facilities, and Battelle, a nonprofit, applied science and technology organization.

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From Berkeley Lab: “Programmable DNA Scissors Found for Bacterial Immune System”

Berkeley Lab

Discovery Could Lead to Editing Tool for Genomes

June 28, 2012
Lynn Yarris

“Genetic engineers and genomics researchers should welcome the news from the Lawrence Berkeley National Laboratory (Berkeley Lab) where an international team of scientists has discovered a new and possibly more effective means of editing genomes. This discovery holds potentially big implications for advanced biofuels and therapeutic drugs, as genetically modified microorganisms, such as bacteria and fungi, are expected to play a key role in the green chemistry production of these and other valuable chemical products.

Programmable DNA scissors: A double-RNA structure in the bacterial immune system has been discovered that directs Cas9 protein to cleave and destroy invading DNA at specific nucleotide sequences. This same dual RNA structure should be programmable for genome editing. (Image by H. Adam Steinberg, artforscience.com)

Jennifer Doudna, a biochemist with Berkeley Lab’s Physical Biosciences Division and professor at the University of California (UC) Berkeley, helped lead the team that identified a double-RNA structure responsible for directing a bacterial protein to cleave foreign DNA at specific nucleotide sequences. Furthermore, the research team found that it is possible to program the protein with a single RNA to enable cleavage of essentially any DNA sequence.

‘We’ve discovered the mechanism behind the RNA-guided cleavage of double-stranded DNA that is central to the bacterial acquired immunity system,’ says Doudna, who holds appointments with UC Berkeley’s Department of Molecular and Cell Biology and Department of Chemistry, and is an investigator with the Howard Hughes Medical Institute (HHMI).

See the full article here.

A U.S. Department of Energy National Laboratory Operated by the University of California

From Berkeley Lab: “Berkeley Lab Researchers Create First of Its Kind Gene Map of Sulfate-reducing Bacterium:”

Berkeley Lab

“Work Holds Implications for Future Bioremediation Efforts

Lynn Yarris
November 09, 2011

Critical genetic secrets of a bacterium that holds potential for removing toxic and radioactive waste from the environment have been revealed in a study by researchers with the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab). The researchers have provided the first ever map of the genes that determine how these bacteria interact with their surrounding environment.

‘Knowing how bacteria respond to environmental changes is crucial to our understanding of how their physiology tracks with consequences that are both good, such as bioremediation, and bad, such as biofouling,’ says Aindrila Mukhopadhyay, a chemist with Berkeley Lab’s Physical Biosciences Division, who led this research. ‘We have reported the first systematic mapping of the genes in a sulfate-reducing bacterium – Desulfovibrio vulgaris – that regulate the mechanisms by which the bacteria perceive and respond to environmental signals.’”

Desulfovibrio vulgaris is an anaerobic sulfate-eating microbe that can also consume toxic and radioactive waste, making it a prime candidate for bioremediation of contaminated environments. (Photo courtesy of Berkeley Lab)

A first-of-its-kind gene map of the Desulfovibrio vulgaris bacterium could play an important role in future clean-ups of a wide range of contaminated environments. (Image courtesy of Berkeley Lab)

See the full very important article here.

A U.S. Department of Energy National Laboratory Operated by the University of California

From Berkeley Lab: “Genome-scale Network of Rice Genes to Speed the Development of Biofuel Crops”

Berkeley Lab

Joint BioEnergy Institute Researchers Create RiceNet for Predicting Genetic Functions in Rice

“The first genome-scale model for predicting the functions of genes and gene networks in a grass species has been developed by an international team of researches that includes scientists with the U.S. Department of Energy (DOE)’s Joint BioEnergy Institute (JBEI), a multi-institutional partnership led by Lawrence Berkeley National Laboratory (Berkeley Lab). Called RiceNet, this systems-level model of rice gene interactions should help speed the development of new crops for the production of advanced biofuels, as well as help boost the production and improve the quality of one of the world’s most important food staples.

‘With RiceNet, instead of working on one gene at a time based on data from a single experimental set, we can predict the function of entire networks of genes, as well as entire genetic pathways that regulate a particular biological process,’ says Pamela Ronald, a plant geneticist who holds joint appointments with JBEI, where she directs the grass genetics program, and with the University of California (UC) Davis, where she is a professor in the Department of Plant Pathology and at The Genome Center. “RiceNet represents a systems biology approach that draws from diverse and large datasets for rice and other organisms.”

This graphic is a full-size view of a RiceNet layout, color-coded to indicate the likelihood of network links; red for higher and blue for lower likelihood scores. (Image from Ronald, et. al)

See the full article here.

This is not the first attempt by the scientific community to bring the world better rice. A project atWorld Community Grid , Nutritious Rice for the World was concerned with this subject, but not for biofuels. Rather, it was an attempt to find varieties of rice which did a better job of improving the diet of a large portion of the world’s population.

A U.S. Department of Energy National Laboratory Operated by the University of California