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The Laboratory
in the News

Inactive genes may cause bubonic plague
An international team led by researchers at Livermore’s Biology and Biotechnology Research Program Directorate has found that the virulence of bubonic plague—whose bacterium is perhaps the most infectious in humans—may be caused by the inactivation of several hundred genes as the bacterium evolved over time. The plague has long been considered a prime candidate for bioterrorism because of its virulence and potential to be spread.
To study the plague bacterium, Yersinia pestis, researchers first sequenced the complete genome of Y. pseudotuberculosis. This bacterium has an almost identical DNA sequence to Y. pestis. However, Y. pseudotuberculosis produces distinct and less acute symptoms than Y. pestis and, thus, is rarely fatal. Researchers compared the DNA sequences of two Y. pestis strains with the Y. pseudotuberculosis genome. Although the comparison revealed several genes in the plague bacterium that are not present in its relative, researchers also found that as many as 13 percent of Y. pestis genes are inactive.
The research, conducted in conjunction with the Yersinia Research Unit of the Institut Pasteur in Paris and several other organizations, was reported in the September 21, 2004, issue of the Proceedings of the National Academy of Sciences. The study suggests that natural selection may have led to the inactivation of genes that tend to suppress the lethality of Y. pestis.
Sequencing of the Y. pseudotuberculosis genome was part of an initiative funded by the Department of Energy’s Chemical and Biological Nonproliferation Program, which is now part of the Department of Homeland Security’s Science and Technology Directorate.
Contacts: Emilio Garcia (925) 422-8002 (garcia12@llnl.gov) and Patrick Chain (925) 424-5492 (chain2@llnl.gov).

Earth’s mantle may provide energy
Researchers have discovered that untapped methane reserves may exist well below Earth’s surface and could provide a virtually inexhaustible source of energy for future generations. A team from Lawrence Livermore, Carnegie Institution’s Geophysical Laboratory, Harvard University, Argonne National Laboratory, and Indiana University at South Bend reported their findings in the September 28, 2004, issue of the Proceedings of the National Academy of Science.
The scientists used a series of experiments and theoretical calculations to demonstrate that methane—the main component of natural gas—forms under the temperatures and pressures that occur in Earth’s upper mantle when carbon in calcite combines with hydrogen in water.
Although methane is the most plentiful hydrocarbon in Earth’s crust, oil and gas wells are typically drilled only 5 to 10 kilometers beneath the surface. At these depths, the pressure is only a few thousand times the pressure at Earth’s surface—not high enough to transform the subsurface materials. Using a diamond anvil cell, the scientists squeezed materials common at Earth’s surface—iron oxide, calcite, and water—to pressures from 50,000 to 110,000 atmospheres (5 to 11 gigapascals) and temperatures to above 1,300°C, creating conditions similar to those found deep within Earth. In these experiments, methane was produced over a range of temperatures and pressures. Production was most favorable at 480°C and 70,000 atmospheres of pressure. Above 1,200°C, the carbon in calcite formed carbon dioxide instead of methane.
These experiments indicate that hydrocarbons may be created from nonbiological reactions between water and rock, not just from the decomposition of living organisms. Because calculations show that methane is thermodynamically stable under conditions typical of Earth’s mantle, scientists believe methane reserves could potentially exist for millions of years.
Contact: Larry Fried (925) 422-7796 (fried1@llnl.gov).

Simulations point to unexpected physics in hydrogen
Livermore scientists have used quantum simulations to compute the melting temperature of hydrogen as a function of pressure. Their results indicate that the melting curve of hydrogen has a maximum, which opens up the interesting possibility of finding a low-temperature metallic fluid at about 4 million atmospheres of pressure (400 gigapascals). Such a fluid is expected to have unusual properties and would likely represent an entirely new state of matter.
In addition to predicting the melting curve, the simulations provide a microscopic model showing the physical origin of the maximum melting temperature in hydrogen. Contrary to previous expectations, the researchers have discovered that the hydrogen melting temperature is strongly influenced by subtle changes in intermolecular interactions that occur in the fluid phase at ultrahigh pressure.
Numerous experiments have attempted to measure the high-pressure phases of hydrogen. However, until now, the phase boundary that separates the solid and liquid phases has remained relatively unknown. With this new understanding of the physical process involved in the melting of hydrogen, the Livermore researchers have proposed experiments to measure the solid–liquid phase boundary. Results from the team’s research appeared in the October 7, 2004, issue of Nature.
Contact: Stanimir Bonev (925) 422-8391 (bonev@llnl.gov).

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UCRL-52000-04-12 | December 7, 2004