Perovskite Preservation

The primary mineral in Earth's lower mantle is perovskite, (Fe,Mg)SiO₃, but the amount of pervoskite will depend on the overall composition. For example, subducted oceanic crust may be predominantly perovskite. The remixing or homogenization of these regions is affected greatly by the diffusion of major cations--Fe, Mg, and Si--at the high temperatures of Earth's mantle. Holzapfel et al. have now measured the interdiffusion of Fe and Mg in perovskite in experiments at high temperature and pressure. Diffusion is so slow that homogenization, even on very small scales, is not possible on time scales as long as the age of the Earth. Thus, disparate regions in Earth's mantle will be preserved unless they are mixed mechanically.

Predator Diversity in the Oceans

The diversity of large ocean predators will vary in relation to temperature and ocean productivity. Worm et al. used extensive data sets from fisheries records to determine how the diversity of large predatory species (tuna and billfishes) varies throughout the world's oceans. Overall, there has been a decline in diversity during the past 50 years. The detailed analysis reveals peaks in diversity at intermediate latitudes. Temperature and dissolved oxygen were the primary environmental factors that correlate with (and may be the cause of) the peaks in diversity. The abundance of zooplankton is highest in these "hot spots," which suggests that diversity peaks may be similar for organisms throughout the marine food chain. The observed patterns are largely consistent across the world's oceans and will help to inform and guide international efforts to establish marine parks.

Plague Targets Its Victims

So-called type III secretion machines are used by yersiniae and other Gram-negative bacteria to inject proteins directly into target cells. The injected effector substrates are essential factors for the pathogenesis of infectious disease. Marketon et al. now show that Yersinia pestis, the agent responsible for plague, selects macrophages, dendritic cells, and neutrophils for type III injection; B and T lymphocytes are rarely selected as targets. During plague, type III injection leads to the rapid depletion of immune cells from the spleen with a concomitant increase in the relative amount of injected cells. The selection of host cells with innate immune functions disables the immune system and leads to rapid progression of this invariably fatal illness.

A Backup Gene for Yeast Longevity

Calorie restriction can extend the life span of certain organisms, even the replicative life span of yeast, but it has been unclear whether the effect in yeast is entirely dependent on Sir2, a histone deacetylase of the sirtuin family. Sir2 is thought to reduce genome instability by suppressing recombination of ribosomal RNA. Lamming et al. have identified another Sir2-related gene in yeast called homologue of Sir 2 (Hst2) that also mediates the calorie restriction signal, even in the absence of Sir2.

Singlet-Triplet States in the Mix

One candidate for quantum information processing is based on manipulating the electron spins in quantum dots. The coupling of spins between adjacent quantum dots can form the basis of a quantum logic gate. However, recent work has shown that dots grown on GaAs also experience a large and random background field caused by the nuclear spins in the substrate, which leads to the spins losing their memory and mixing between spin-singlet and spin-triplet states. Koppens et al. provide a comprehensive study of the extent of this effect and show how decoherence can be mitigated to some degree by tuning the coupling strength between the dots and/or polarizing the background nuclear spins.

Why Large Size Increases Extinction Risk

A statistical analysis of extinction risk patterns for about 4000 mammal species by Cardillo et al. (see the news story by Stokstad) has provided an explanation for why species of large body size suffer the highest risk of extinction. Sensitivity to a variety of risk-promoting factors, such as low reproductive rate and low population density, increases sharply above a threshold of around 3 kilograms. For species below this threshold, extinction risk reflects simply where species live; above it, extinction risk also reflects biological traits, so that larger species are more likely to be predisposed to decline. The disproportionate disadvantages of large size might accelerate the loss of large mammal biodiversity in the face of environmental threats.

Controlled Mobilization

Tissue stem cells have the capacity to self-renew and generate differentiated cells that replace lost cells as an organism ages. Quiescent stem cells typically reside in specific microenvironments or "niches." When needed, they begin proliferating and exit the niche, a process thought to be controlled by extracellular cues from the niche and by intrinsic genetic programs. Studying mouse models, Flores et al. now show that epidermal stem cell mobilization is regulated by telomeres, the nucleoprotein structures at the ends of chromosomes. Short telomeres impaired mobilization, whereas overexpression of telomerase, the enzyme that synthesizes telomeres, promoted mobilization. The effect of telomeres on stem cell function could potentially explain, at least in part, their role in aging and cancer.

Snapshots in Solution

X-ray diffraction has long permitted chemists to map out the molecular structure of solids. Recently, short and intense x-ray pulses from synchrotrons have produced time-resolved pictures of structural rearrangements, but the samples, such as proteins, first had to be immobilized. Ihee et al. have used intense 100-picosecond x-ray pulses to probe a reaction in solution. They take advantage of the sensitivity of x-rays for heavy atoms by following an iodine atom in the photoinduced decomposition of diiodoethane to I₂ and C₂H₄. Over a large solvent background, the data offer direct structural evidence for a long-hypothesized I-bridged C₂H₄I intermediate. Thermal expansion of the solvent shell was monitored as well.

Host Factors Required for Microbial Residence

Certain microbes take up residence within host cells, and while much effort has gone into defining microbial virulence factors, the characteristics of the host cells that allow for microbial invasion and residence are less clear. Using a genome-wide screening approach, Philips et al. identified host factors required for infection by Mycobacterium fortuitum, a microbe that divides within host cell vacuoles. Factors fell into two main categories: those that generally affect phagocytosis (the process by which cells engulf extracellular particles), and those that cause a specific defect in mycobacterial uptake or growth. A Drosophila member of the CD36 family of scavenger receptors was specifically required for the uptake of mycobacteria. Using a similar approach, Agaisse et al. identified host factors that affect intracellular infection by Listeria monocytogenes, a bacterial pathogen that escapes from phagocytic vacuoles and replicates within the cytosol of host cells. Several phenotypes were observed, including decreases in the percentage of host cells infected, alterations of intracellular growth rates, and changes in subcellular location of bacteria. The identified host factors spanned a wide range of cellular functions. Comparing the two studies revealed host factors that specifically affect access to the cytosol by L. monocytogenes and host pathways that are differentially required for intracellular infection by a cytosolic versus a vacuolar intracellular bacterial pathogen.

Eukaryotic Potassium Channel Structure

Potassium channels regulate the flow of K⁺ ions out of cells; they repolarize the cell membrane after action potentials and determine the excitability of neurons. Voltage-gated K⁺ channels open in response to cell depolarization, reacting to the change in potential by movement of four charged arginine residues, which opens the pore and allows only K⁺ ions to exit the cell. X-ray crystallographic structures of bacterial channels have revealed the basis of the K⁺ selectivity. Forming crystals of the larger, multisubunit eukaryotic K⁺ channels has been more challenging, but Long et al. now present in two papers a 2.9-angstrom-resolution crystal structure and a mechanistic analysis for eukaryotic Kv1.2 channels from the Shaker family. The crystals, which were formed by adding lipids during crystallization, include the oxido-reductase β subunit and are probably in a native, open state. The β subunits are positioned directly below the intracellular opening to the pore but far enough away to allow the K⁺ ions access to the pore through four large side portals. The voltage-sensor domains act as almost independent regions positioned within the membrane beside the cylindrical pore, with at least one of the charge-sensing arginines in direct contact with lipid. Movement of the voltage sensor causes pore opening through the S4-S5 linker helix, which constricts and dilates the S6 "inner" helices around the pore. This structure explains many apparently contradictory results reported to date on K⁺ channel structure and function.

In Brevia: Migrating Bird Flu

On May 4th, a few bar-headed geese were reported sick and dying on Lake Qinghaihu in central China. By the end of the month, hundreds of thousands of birds were dead, including geese and two species of gull. This site is a major breeding center for birds migrating within Asia. Liu et al. (see the news story by Normile) collected dying birds, and postmortem serology and histology revealed the characteristic pathology of highly pathogenic H5N1 influenza virus. Sequencing confirmed the hallmarks of this strain, which was further verified by experimental infection in mice and chicks. H5N1 has clear potential to disseminate throughout Asia and beyond in migrant birds.

Tracking a Proton Propeller

Discovery of superacids revealed that, with a weak enough counterion, even a molecule as inert as methane could bind an extra proton. The product when methane is acidified, the CH₅⁺ ion, has long puzzled theorists and spectroscopists alike. The hydrogen atoms seem to change places with one another too rapidly to assign the geometry and bonding mode reliably. Asvany et al. have now measured the vibrational spectrum of CH₅⁺ by detecting its infrared-induced reaction with CO₂. Comparison with simulations supports a structure in which a CH₃ tripod binds an H₂ fragment through a three-centered, two-electron bond, with a barrier for exchange between these different sites of 0.3 kilocalorie per mole.

Jumping Ahead on Melting

It is relatively easy to look for nucleation sites in a material that is crystallizing, but it is much harder to spot the gradual loss of order as a crystal melts. At temperatures below the bulk melt temperature, premelting can occur at the crystal surface, but this phenomenon has not been observed in the bulk. Alsayed et al. study the melting of colloidal crystals that are composed of microgel particles that undergo large volume changes with small changes in temperature. Premelting can occur in the bulk at grain boundaries and dislocations and depends on the interfacial free energy associated with each type of defect.

Resolving Resolvase Structure and Function

The site-specific serine recombinase, resolvase, catalyzes recombination between two sites on negatively supercoiled DNA. This process requires double-strand cleavage at each site, strand exchange between the two sites, and religation. Li et al. provide insight into how this occurs by reporting a 3.4 angstrom resolution crystal structure of a synaptic intermediate of resolvase linked to two cleaved duplex DNAs. The DNA duplexes lie on opposite sides of a tetramer of resolvase. The tetramer structure differs from a presynaptic complex between dimeric resolvase and DNA and places the catalytic serine close to the scissile phosphate. The structure supports a subunit rotation hypothesis that posits a 180° rotation of two resolvase subunits to accomplish strand exchange. A flat interface in the tetramer makes such a rotation feasible.

Flex and Rise

Earth models that have attempted to simulate the sea level rise that resulted from the melting of ice sheets after the Last Glacial Maximum have failed reproduce the changes recorded at the so-called "far-field" sites, such as Tahiti and the Sunda Shelf. This discrepancy has led to suggestions that either the models are incomplete, or the far-field data are inaccurate. Bassett et al. now show that by using a model that combines a high-viscosity lower mantle and a significant contribution from the Antarctic ice sheet to meltwater formation, the reconstructed record and the data agree well. These results also provide another line of evidence that Antarctic ice was responsible for more of the deglacial sea level rise than was thought until recently.

Avoiding Too Much of a Good Thing

Certain plants carry genes that provide them with the ability to resist infection by specific pathogens--each resistance (R) gene variant matches a particular pathogen's virulence factor. However, too much or too little of the R protein can send the plant's immune response haywire. Holt et al. now provide a genetic analysis of some of the factors that keep the immune response in Arabidopsis primed for a rapid deployment but not running rampant. One component, RAR1, somehow promotes the accumulation of the R proteins, and another, SGT1, interacts with RAR1, antagonizing its activity. SGT1 does double-duty in infected plants by regulating the cell death response that limits the damage done by some pathogens.