Life Built With Toxic Chemical: First Known Microbe on Earth Able to Thrive and Reproduce Using Arsenic

NASA-funded astrobiology research has changed the fundamental knowledge about what comprises all known life on Earth.Researchers conducting tests in the harsh environment of Mono Lake in California have discovered the first known microorganism on Earth able to thrive and reproduce using the toxic chemical arsenic. The microorganism substitutes arsenic for phosphorus in its cell components.

"The definition of life has just expanded," said Ed Weiler, NASA's associate administrator for the Science Mission Directorate at the agency's Headquarters in Washington. "As we pursue our efforts to seek signs of life in the solar system, we have to think more broadly, more diversely and consider life as we do not know it."

This finding of an alternative biochemistry makeup will alter biology textbooks and expand the scope of the search for life beyond Earth. The research is published in this week's edition of Science Express.

Carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur are the six basic building blocks of all known forms of life on Earth. Phosphorus is part of the chemical backbone of DNA and RNA, the structures that carry genetic instructions for life, and is considered an essential element for all living cells.

Phosphorus is a central component of the energy-carrying molecule in all cells (adenosine triphosphate) and also the phospholipids that form all cell membranes. Arsenic, which is chemically similar to phosphorus, is poisonous for most life on Earth. Arsenic disrupts metabolic pathways because chemically it behaves similarly to phosphate.

"We know that some microbes can breathe arsenic, but what we've found is a microbe doing something new -- building parts of itself out of arsenic," said Felisa Wolfe-Simon, a NASA Astrobiology Research Fellow in residence at the U.S. Geological Survey in Menlo Park, Calif., and the research team's lead scientist. "If something here on Earth can do something so unexpected, what else can life do that we haven't seen yet?"

The newly discovered microbe, strain GFAJ-1, is a member of a common group of bacteria, the Gammaproteobacteria. In the laboratory, the researchers successfully grew microbes from the lake on a diet that was very lean on phosphorus, but included generous helpings of arsenic. When researchers removed the phosphorus and replaced it with arsenic the microbes continued to grow. Subsequent analyses indicated that the arsenic was being used to produce the building blocks of new GFAJ-1 cells.

The key issue the researchers investigated was when the microbe was grown on arsenic did the arsenic actually became incorporated into the organisms' vital biochemical machinery, such as DNA, proteins and the cell membranes. A variety of sophisticated laboratory techniques was used to determine where the arsenic was incorporated.

The team chose to explore Mono Lake because of its unusual chemistry, especially its high salinity, high alkalinity, and high levels of arsenic. This chemistry is in part a result of Mono Lake's isolation from its sources of fresh water for 50 years.

The results of this study will inform ongoing research in many areas, including the study of Earth's evolution, organic chemistry, biogeochemical cycles, disease mitigation and Earth system research. These findings also will open up new frontiers in microbiology and other areas of research.

"The idea of alternative biochemistries for life is common in science fiction," said Carl Pilcher, director of the NASA Astrobiology Institute at the agency's Ames Research Center in Moffett Field, Calif. "Until now a life form using arsenic as a building block was only theoretical, but now we know such life exists in Mono Lake."

The research team included scientists from the U.S. Geological Survey, Arizona State University in Tempe, Ariz., Lawrence Livermore National Laboratory in Livermore, Calif., Duquesne University in Pittsburgh, Penn., and the Stanford Synchroton Radiation Lightsource in Menlo Park, Calif.

NASA's Astrobiology Program in Washington contributed funding for the research through its Exobiology and Evolutionary Biology program and the NASA Astrobiology Institute. NASA's Astrobiology Program supports research into the origin, evolution, distribution, and future of life on Earth.

For more information about the finding and a complete list of researchers, visit: http://astrobiology.nasa.gov

Breakthrough Chip Technology Lights Path to Exascale Computing: Optical Signals Connect Chips Together Faster and With Lower Power

IBM scientists have unveiled a new chip technology that integrates electrical and optical devices on the same piece of silicon, enabling computer chips to communicate using pulses of light (instead of electrical signals), resulting in smaller, faster and more power-efficient chips than is possible with conventional technologies.
The new technology, called CMOS Integrated Silicon Nanophotonics, is the result of a decade of development at IBM's global research laboratories. The patented technology will change and improve the way computer chips communicate -- by integrating optical devices and functions directly onto a silicon chip, enabling over 10X improvement in integration density than is feasible with current manufacturing techniques.

IBM anticipates that Silicon Nanophotonics will dramatically increase the speed and performance between chips, and further the company's ambitious exascale computing program, which is aimed at developing a supercomputer that can perform one million trillion calculations -- or an exaflop -- in a single second. An exascale supercomputer will be approximately one thousand times faster than the fastest machine today.

"The development of the Silicon Nanophotonics technology brings the vision of on-chip optical interconnections much closer to reality," said Dr. T.C. Chen, vice president, Science and Technology, IBM Research. "With optical communications embedded into the processor chips, the prospect of building power-efficient computer systems with performance at the exaflop level is one step closer to reality."

In addition to combining electrical and optical devices on a single chip, the new IBM technology can be produced on the front-end of a standard CMOS manufacturing line and requires no new or special tooling. With this approach, silicon transistors can share the same silicon layer with silicon nanophotonics devices. To make this approach possible, IBM researchers have developed a suite of integrated ultra-compact active and passive silicon nanophotonics devices that are all scaled down to the diffraction limit -- the smallest size that dielectric optics can afford.

"Our CMOS Integrated Nanophotonics breakthrough promises unprecedented increases in silicon chip function and performance via ubiquitous low-power optical communications between racks, modules, chips or even within a single chip itself," said Dr. Yurii A. Vlasov, Manager of the Silicon Nanophotonics Department at IBM Research. "The next step in this advancement is to establishing manufacturability of this process in a commercial foundry using IBM deeply scaled CMOS processes."

By adding just a few more processing modules to a standard CMOS fabrication flow, the technology enables a variety of silicon nanophotonics components, such as: modulators, germanium photodetectors and ultra-compact wavelength-division multiplexers to be integrated with high-performance analog and digital CMOS circuitry. As a result, single-chip optical communications transceivers can now be manufactured in a standard CMOS foundry, rather than assembled from multiple parts made with expensive compound semiconductor technology.

The density of optical and electrical integration demonstrated by IBM's new technology is unprecedented -- a single transceiver channel with all accompanying optical and electrical circuitry occupies only 0.5mm2 -- 10 times smaller than previously announced by others. The technology is amenable for building single-chip transceivers with area as small as 4x4mm2 that can receive and transmit over Terabits per second that is over a trillion bits per second.

The development of CMOS Integrated Silicon Nanophotonics is the culmination of a series of related advancements by IBM Research that resulted in the development of deeply scaled front-end integrated Nanophotonics components for optical communications. These milestones include:

* March 2010, IBM announced a Germanium Avalanche Photodetector working at unprecedented 40Gb/s with CMOS compatible voltages as low as 1.5V. This was the last piece of the puzzle that completes the prior development of the "nanophotonics toolbox" of devices necessary to build the on-chip interconnects.
* March 2008, IBM scientists announced the world's tiniest nanophotonic switch for "directing traffic" in on-chip optical communications, ensuring that optical messages can be efficiently routed.
* December 2007, IBM scientists announced the development of an ultra-compact silicon electro-optic modulator, which converts electrical signals into the light pulses, a prerequisite for enabling on-chip optical communications.
* December 2006, IBM scientists demonstrated silicon nanophotonic delay line that was used to buffer over a byte of information encoded in optical pulses -- a requirement for building optical buffers for on-chip optical communications.

The details and results of this research effort was reported in a presentation delivered by Dr. Yurii Vlasov at the major international semiconductor industry conference SEMICON held in Tokyo on Dec. 1, 2010. The talk is entitled "CMOS Integrated Silicon Nanophotonics: Enabling Technology for Exascale Computational Systems," co-authored by William Green, Solomon Assefa, Alexander Rylyakov, Clint Schow, Folkert Horst, and Yurii Vlasov of IBM's T.J. Watson Research Center in Yorktown Heights, N.Y. and IBM Zurich Research Lab in Rueschlikon, Switzerland.

Longevity Breakthrough: Scientists 'Activate' Life Extension in Worm, Discover Mitochondria's Metabolic State Controls Life Span

If you think life's too short, then you're not alone. A team of scientists set out to find what it would take to live a very long life and they made important discoveries that bring longer life spans much closer to reality. A new research report featured on the cover of The FASEB Journal, describes how scientists "activated" life extension in the roundworm C. elegans, and in the process discovered a new metabolic state correlating with long life.

The discovery was reported by lead author Jeffrey A. Butler and corresponding author Shane L. Rea, of the Barshop Institute for Longevity and Aging Studies and the Department of Physiology at the University of Texas Health Science Center at San Antonio, in collaboration with Natascia Ventura, of the Department of Experimental Medicine and Biochemical Sciences, University of Rome Tor Vergata, and Thomas E. Johnson, of the Department of Integrative Physiology, Institute for Behavioral Genetics, University of Colorado.

To make this discovery, scientists compared one class of long-lived C. elegans, called the Mit mutants (which have disrupted mitochondrial electron transport chain functionality), with non-mutant wild type C. elegans. Their comparison showed significant metabolism changes, suggesting that their cellular engines had been reconfigured to run on new fuels and to make new waste products, leading to increased lifespans.

To determine the cause of these metabolism changes, scientists created a new method for collecting cellular waste and studied it to identify the specific chemical reactions. They found that that the worms achieved long life through changes in how their cells extracted energy (metabolic state). Although C. elegans often is used as an animal model for human biology, more research is needed to determine if an equivalent metabolic state could be created in humans with the same results.

"C. elegans has provided a useful animal model for human biology," said Gerald Weissmann, M.D., Editor-in-Chief of The FASEB Journal, "because of their relative simplicity and our understanding of the genes that control their metabolism. Helping these worms to live longer is a proof of concept; indeed much of what we now know about human aging was first worked out in these worms."

"This research on worms shows that the secret to a long life comes from how we extract energy from our food," commented Weissmann. "With any luck, we'll be able to change human life in the same direction: onward and upward!"

Physicists Create Supernova in a Jar

A team of physicists from the University of Toronto and Rutgers University has mimicked a supernova -- an explosion of a star -- in miniature.
In a certain type of supernova, the detonation starts with a flame ball buried deep inside a white dwarf. The flame ball is much lighter than its surroundings, so it rises rapidly making a plume topped with an accelerating smoke ring.

"We created a smaller version of this process by triggering a special chemical reaction in a closed container that generates similar plumes and vortex rings," says Stephen Morris, a University of Toronto physics professor.

Autocatalytic chemical reactions release heat and change the composition of a solution, which can create buoyancy forces that can stir the liquid, leading to more reaction and a runaway explosive process. "A supernova is a dramatic example of this kind of self-sustaining explosion in which gravity and buoyancy forces are important effects. We wanted to see what the liquid motion would look like in such a self-stirred chemical reaction," says Michael Rogers, who led the experiment as part of his PhD research, under the supervision of Morris.

"It is extremely difficult to observe the inside of a real exploding star light years away so this experiment is an important window into the complex fluid motions that accompany such an event," Morris explains. "The study of such explosions in stars is crucial to understanding the size and evolution of the universe."

The research will appear in Physics Review E in the next few weeks. In addition to Morris and Rogers, the research team included Abdelfattah Zebib from Rutgers. The work was funded by the Natural Sciences and Engineering Research Council of Canada.

Distribution of Gravitational Wave Sources Predicted

A pair of neutron stars spiraling toward each other until they merge in a violent explosion should produce detectable gravitational waves. A new study led by an undergraduate at the University of California, Santa Cruz, predicts for the first time where such mergers are likely to occur in the local galactic neighborhood.

According to Enrico Ramirez-Ruiz, associate professor of astronomy and astrophysics at UC Santa Cruz, the results provide valuable information for researchers at gravitational-wave detectors, such as the Laser Interferometry Gravitational-Wave Observatory (LIGO) in Louisiana and Washington. "This is a very important result, as it is likely to significantly alter how gravitational-wave observatories currently operate," Ramirez-Ruiz said.

Luke Zoltan Kelley, a UCSC undergraduate working with Ramirez-Ruiz, is first author of a paper describing the new findings, to be published in the December 10 issue of Astrophysical Journal Letters and currently available online.

A key prediction of Einstein's general theory of relativity, gravitational waves are ripples in the fabric of space-time caused by the motions of massive objects. Scientists have yet to detect gravitational waves directly because they are so weak and decay rapidly, but a planned upgrade for LIGO (called Advanced LIGO) is expected to greatly increase its sensitivity. Compact binaries--which can consist of two neutron stars, two black holes, or one of each--are among the best candidates for emitting gravitational waves that could be detected by LIGO or other current experiments.

Kelley investigated the implications of a key observation about compact binaries: The two objects are not only moving in orbit around each other, they are also typically speeding through space together, their center of mass moving with a velocity that can be well above 200 kilometers per second.

"By the time the two objects merge, they are likely to be located far away from the galaxy where they were born," Kelley said.

This has implications for efforts to observe mergers that emit gravitational waves. Scientists hope to match a detection at a gravitational-wave observatory with telescope observations of the corresponding merger event. The new study suggests that astronomers might not want to look in the nearest galaxies for these "optical counterparts" of gravitational waves.

"Our predictions show that the proposed use of galaxy catalogs for follow-up from possible gravity-wave detections will need to account for the possibility of mergers away from the observed galaxies," Ramirez-Ruiz said.

The "kick" that sends compact binaries sailing out of their home galaxies comes from a slight asymmetry in the supernova explosions that give birth to neutron stars and black holes. When a massive star explodes, its core collapses to form either a neutron star (a rapidly rotating ball of densely packed neutrons) or a black hole. According to Kelley, a one-percent asymmetry in the supernova explosion would result in a recoil velocity of about 1,000 kilometers per second (about 2 million miles per hour).

"That is around the maximum velocity observed for lone neutron stars and pulsars," he said. "In binary systems, the net kick velocity to the center of mass is noticeably less, and still fairly uncertain, but is around 200 kilometers per second."

The researchers used a standard cosmological simulation of dark matter and the formation of structure in the universe to study how different kick velocities would affect the distribution of merging compact binaries. The simulation, run on a supercomputer at UCSC, showed the formation of halos of dark matter whose gravitational pull is thought to drive the formation of galaxies. The researchers populated the more massive halos with tracer particles representing compact binary systems. On separate runs, they gave the binaries different velocities.

After running the model for a simulated 13.8 billion years (the current age of the universe), Kelley found a region that looked like our local universe, with a galaxy the size of the Milky Way surrounded by a comparable set of neighboring galaxies. He then generated an image of the sky as it would appear to astronomers in the simulated universe, showing the locations of compact binaries and local galaxies.

The results showed that variations in kick velocity lead to marked differences in the distribution of compact binaries. If the merger of a compact binary occurs away from the bright background of a galaxy, it could be detected by a survey telescope such as the planned Large Synoptic Survey Telescope (LSST). The operators of gravitational-wave observatories would then know when and where to look in their data for a gravitational-wave signal, Ramirez-Ruiz said.

He and colleagues at UCSC, including theoretical astrophysicist Stan Woosley and graduate student Luke Roberts, are currently trying to work out what the optical signal of a compact-binary merger should look like. "Detecting the optical counterparts of gravitational-wave detections will be a lot easier if they are not within galaxies," Ramirez-Ruiz said.

Kelley is currently finishing up his senior thesis at UCSC, helping Ramirez-Ruiz teach an astrophysics class, and deciding where he will go to graduate school.

In addition to Kelley and Ramirez-Ruiz, the coauthors of the paper include Marcel Zemp of the University of Michigan, Ann Arbor; Jürg Diemand of the Institute for Theoretical Physics at the University of Zurich; and Ilya Mandel of the Kavli Institute at the Massachusetts Institute of Technology. This research was supported by NASA, the David and Lucile Packard Foundation, the U.S. National Science Foundation, and the Swiss National Science Foundation.

The Future of Metabolic Engineering: Designer Molecules, Cells and Microorganisms

Will we one day design and create molecules, cells and microorganisms that produce specific chemical products from simple, readily-available, inexpensive starting materials? Will the synthetic organic chemistry now used to produce pharmaceutical drugs, plastics and a host of other products eventually be surpassed by metabolic engineering as the mainstay of our chemical industries? Yes, according to Jay Keasling, chemical engineer and one of the world's foremost practitioners of metabolic engineering.
In a paper published in the journal Science Keasling discusses the potential of metabolic engineering -- one of the principal techniques of modern biotechnology -- for the microbial production of many of the chemicals that are currently derived from non-renewable resources or limited natural resources. Examples include, among a great many other possibilities, the replacement of gasoline and other transportation fuels with clean, green and renewable biofuels.

"Continued development of the tools of metabolic engineering will be necessary to expand the range of products that can be produced using biological systems, Keasling says. "However, when more of these tools are available, metabolic engineering should be just as powerful as synthetic organic chemistry, and together the two disciplines can greatly expand the number of chemical products available from renewable resources."

Keasling is the chief executive officer for the Joint BioEnergy Institute, a U.S. Department of Energy (DOE) bioenergy research center. He also holds joint appointments with the Lawrence Berkeley National Laboratory (Berkeley Lab), where he oversees that institute's biosciences research programs, and the University of California (UC), Berkeley, where he serves as director of the Synthetic Biology Engineering Research Center, and is the Hubbard Howe Jr. Distinguished Professor of Biochemical Engineering.

Metabolic engineering is the practice of altering genes and metabolic pathways within a cell or microorganism to increase its production of a specific substance. Keasling led one of the most successful efforts to date in the application of metabolic engineering, when he combined it with synthetic organic chemistry techniques to develop a microbial-based means of producing artemisinin, the most potent of all anti-malaria drugs. He and his research group at JBEI are now applying that same combination to the synthesis of liquid transportation fuels from lignocellulosic biomass. In all cases, the goal is to engineer microbes to perform as much of the chemistry required to produce a desired final product as possible.

"To date, microbial production of natural chemical products has been achieved by transferring product-specific enzymes or entire metabolic pathways from rare or genetically intractable organisms to those that can be readily engineered," Keasling says. "Production of non-natural specialty chemicals, bulk chemicals, and fuels has been enabled by combining enzymes or pathways from different hosts into a single microorganism, and by engineering enzymes to have new function."

These efforts have utilized well-known, industrial microorganisms, but future efforts, he says, may include designer molecules and cells that are tailor-made for the desired chemical and production process.

"In any future, metabolic engineering will soon rival and potentially eclipse synthetic organic chemistry," Keasling says.

Keasling cites the production of active pharmaceutical ingredients as one area where metabolic engineering enjoys a distinct advantage over synthetic organic chemistry. This includes three specific classes of chemicals -- alkaloids, which are primarily derived from plants; polyketides and non-ribosomal peptides, which are produced by various bacteria and fungi; and isoprenoids, which also are typically produced by microbes.

"Many of these natural products are too complex to be chemically synthesized and yet have a value that justifies the cost of developing a genetically engineered microorganism," Keasling says. "The cost of starting materials is generally a small fraction of the complete cost of these products, and relatively little starting material is necessary so availability is not an issue."

Keasling also says that metabolic engineering could provide a valuable alternative means of producing variations of terpenes, the hydrocarbon compounds common to the resins of conifers, in a form that could yield pharmaceuticals that are more effective for the treatment of human disease than the forms that nature has provided.

Perhaps the ripest targets of opportunity for future metabolic engineering efforts are petroleum-based bulk chemical products, including gasoline and other fuels, polymers and solvents. Because such products can be inexpensively catalyzed from petroleum, microbial production has until now been rare, but with fluctuating oil prices, dwindling resources and other considerations, the situation, Keasling says, has changed.

"It is now possible to consider production of these inexpensive bulk chemicals from low-cost starting materials, such as starch, sucrose, or cellulosic biomass with a microbial catalyst," he says. "The key to producing these bulk chemicals in metabolically-engineered cells will be our ability to make the exact molecule needed for existing products rather than something 'similar but green' that will require extensive product testing before it can be used."

In his Science paper, Keasling discusses the formidable roadblocks that stand in the way of a future in which microorganisms and molecules can be tailor-made through metabolic engineering, including the need for "debugging routines" that can find and fix errors in engineered cells. However, he is convinced these roadblocks can and will be overcome.

"One can even envision a day when cell manufacturing is done by different companies, each specializing in certain aspects of the synthesis, with one company constructing the chromosome, one company building the membrane and cell wall bag, and one company filling this bag with the basic molecules needed to boot up the cell."

The Joint BioEnergy Institute (JBEI) is one of three Bioenergy Research Centers funded by the U.S. Department of Energy to advance the development of the next generation of biofuels. It is a scientific partnership led by Berkeley Lab and including the Sandia National Laboratories, the University of California campuses of Berkeley and Davis, the Carnegie Institution for Science, and the Lawrence Livermore National Laboratory.

The Synthetic Biology Engineering Research Center (SynBERC) is a multi-institution partnership, funded by the National Science Foundation, that is aimed at "making biology easier to engineer." The SynBERC partnership is led by UC Berkeley and includes UC San Francisco, Harvard, MIT, Stanford, and Prairie View A&M University.

Dark Matter Could Transfer Energy in the Sun

Researchers from the Institute for Corpuscular Physics (IFIC) and other European groups have studied the effects of the presence of dark matter in the Sun. According to their calculations, low mass dark matter particles could be transferring energy from the core to the external parts of the Sun, which would affect the quantity of neutrinos that reach Earth.
"We assume that the dark matter particles interact weakly with the Sun's atoms, and what we have done is calculate at what level these interactions can occur, in order to better describe the structure and evolution of the Sun," Marco Taoso, researcher at the IFIC, a combined centre of the Spanish National Research Council and the University of Valencia, explains.

The astrophysical observations suggest that our galaxy is situated in a halo of dark matter particles. According to the models, some of these particles, the WIMPs (Weakly Interacting Massive Particles) interact weakly with other normal ones, such as atoms, and could be building up on the inside of stars. The study, recently published in the journal Physical Review D, carries out an in-depth study of the case of the Sun in particular.

"When the WIMPs pass through the Sun they can break up the atoms of our star and lose energy. This prevents them from escaping the gravitational force of the Sun which captures them, and they become trapped, orbiting inside it, with no way of escaping," the researcher points out.

The dark matter cools down the Sun's core

Scientists believe that the majority of the dark matter particles gather together in the centre of the Sun, but in their elliptic orbits they also travel to the outer part, interacting and exchanging with the solar atoms. In this way, the WIMPs transport the energy from the burning central core to the cooler peripheral parts.

"This effect produces a cooling down of the core, the region from where the neutrinos originate due to the nuclear reactions of the Sun," Taoso points out. "And this corresponds to a reduction in the flux of solar neutrinos, since these depend greatly on the temperature of the core."

The neutrinos that reach Earth can be measured by means of different techniques. These data can be used to detect the modifications of the solar temperature caused by the WIMPs. The transport of energy by these particles depends on the likelihood of them interacting with the atoms, and the "size" of these interactions is related to the reduction in the neutrino flux.

"As a result, current data about solar neutrinos can be used to put limits on the extent of the interactions between dark matter and atoms, and using numerical codes we have proved that certain values correspond to a reduction in the flux of solar neutrinos and clash with the measurements," the scientist reveals.

The team has applied their calculations to better understand the effects of low mass dark matter particles (between 4 and 10 gigaelectronvolts). At this level we find models that attempt to explain the results of experiments such as DAMA (beneath an Italian mountain) or CoGent (in a mine in the USA), which look for dark material using "scintillators" or WIMP detectors.

Debate about WIMP and solar composition

This year another study by scientists from Oxford University (United Kingdom) also appeared. It states that WIMPs not only reduce the fluxes of solar neutrinos, but also, furthermore, modify the structure of the Sun and can explain its composition.

"Our calculations, however, show that the modifications of the star's structure are too small to support this claim and that the WIMPs cannot explain the problem of the composition of the sun," Taoso concludes.