Poor Man's Sequencing?
Cheaper sequencing technologies are a high priority for many applications, including resequencing projects to study genomic variation. Shendure et al. (p. 1728, published online 4 August 2005; see the 5 August news story by Pennisi) bring the $1000 genome a step closer with a nonelectrophoretic approach, based on amplification of DNA fragments and enrichment followed by ligase-based sequencing on immobilized beads and imaging using an epifluorescence microscope. The procedure was roughly ninefold cheaper than conventional sequencing, with greater accuracy and speed. Other laboratories should be able to build their own equivalent sequencing system using off-the-shelf equipment.
Toward Magnetic Spintronics
At present, microelectronic technology relies on the flow and control of electron charge in lithographically fabricated circuits, but electrons also have a quantum-mechanical spin that could be exploited to create logic circuits. Many approaches to “spintronics” have focused on semiconducting materials, but others have investigated magnetic materials. Allwood et al. (p. 1688; see the cover) discuss a particular proposed architecture for magnetic logic circuits that harnesses the movement of magnetic domain walls, which are the boundaries between oppositely aligned magnetic regions. Basic logic functions and nonvolatility have been demonstrated with simple combinations of magnetic nanowires.
The primary mineral in Earth's lower mantle is perovskite (Fe,Mg)SiO3, but the amount of perovskite 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. (p. 1707, published online 28 July 2005) 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.
Long-range magnetic ordering that develops as a ferromagnet or antiferromagnet is cooled can be suppressed by introducing defects. Theoretical work has suggested that suppression could also occur on geometrically frustrated lattices in which the pairwise coupling of the spins cannot be met, such as on a triangular lattice. Nakatsuji et al. (p. 1697) now report on the realization of one such bulk triangular lattice, NiGa2S4, and present evidence that antiferromagnetic order can be completely suppressed, even to the lowest temperatures. The simple lattice structure could also be used to probe other cooperative phenomena, such as quantum criticality and second-order phase transitions.
Turning Its Stripes
Under conditions of vapor-solid growth at high temperatures, zinc oxide can form nanobelts, and the dipoles set up by the opposite charges of the two faces of these ultrathin ribbons can drive the form of spirals or even closed loops. Gao et al. (p. 1700; see the Perspective by Korgel) now report that prolonged annealing at very high temperatures (1400°C) in an inert atmosphere can cause the belts to widen and twist into long helices. High-resolution transmission electron microscopy shows that the nanobelts are converted into a superlattice of alternating stripes that run the length of the belt and that orient their c axes at right angles to one another. This change reduces the polarity difference between the two faces, and a small twist between adjacent stripes drives the formation of the helix.
More Makes More
The effect of increasing CO2 levels on forest soils has been studied by Heath et al. (p. 1711), who tracked the movement of carbon using stable carbon isotopes. High concentrations of CO2 stimulated increased photosynthesis and plant growth but also caused a decline in the amount of carbon sequestered in the soil that was not affected by addition of soil nutrients. Microbial respiration in soils could provide a large positive feedback on the rate of increase of the concentration of atmospheric CO2, and raise the possibility that the future rise in atmospheric CO2 concentrations could be higher than expected.
Puzzling Brain Genes
Mutations in the genes Microcephalin and ASPM (abnormal spindle-like microcephaly associated) in humans correlate with microcephaly. Although the affected brains are much reduced in size, the detailed architecture of the brain remains. A gene related to Microcephalin is under positive selection pressures in the evolution of primate lineages leading up to humans. Evans et al. (p. 1717) and Mekel-Bobrov et al. (p. 1720) have now analyzed the evolution of Microcephalin and ASPM genes in modern humans and find that both genes also respond as though under positive selection (see the news story by Balter). Thus, unknown advantages have encouraged the rapid spread of these gene variants throughout the human population.
The Message Is the Messenger
As the days lengthen in spring and summer, plants sense the hours of daylight in their leaves and respond by initiating flowering at the top of the plant, in the shoot apex. The identity of the signal that is transported from the leaf to the apex has been unclear (see Wigge et al., Abe et al., and the Perspective by Blázquez in the 12 August issue). Huang et al. (p. 1694, published online 11 August 2005) now show that local expression of the gene FT (FLOWERING LOCUS T) in a single leaf is sufficient to cause flowering by transfecting a heat-inducible form of FT into Arabidopsis plants. Within 6 hours of stimulating a single leaf, FT messenger RNA (mRNA) appears in the shoot apex, where it stimulates transcription of genes involved in flowering and of FT itself. Although other elements may be involved, FT mRNA is an important component of the floral stimulus that moves from leaf to shoot in response to increases in day length.
Patchwork Plant Life
The fynbos Mediterranean shrubland of the Cape Floristic Region of South Africa is one of the most species-rich plant habitats on Earth. Latimer et al. (p. 1722) find that the region's high plant diversity is associated with low migration rates and with speciation rates higher than those in the most diverse tropical forests such as Amazon rain forest. The local species abundance patterns in fynbos is a mosaic made up of centers of locally endemic plants, with little migration among them and relatively few universally rare species, unlike the well-mixed tree communities of Amazon upland rain forest.
Even highly rational people can be seduced by the prospect of getting something for nothing. Rome et al. (p. 1725; see the Perspective by Kuo) have devised a machine that recovers energy that is otherwise wasted. They have modified a backpack by introducing a vertically moveable weight that rises about 5 centimeters with each step and then turns a gear as it falls. This device can be used to recover some of the energy used in carrying supplies—a load of 38 kilograms produces up to 7 watts of electricity, compared with about 20 milliwatts from shoe-based devices. Although many refinements must be made, such an apparatus could generate power during journeys beyond the reach of power grids, reducing the need for heavy batteries.
The tumor suppressor protein p53 functions to promote cell death or apoptosis in response to stress. It acts by modulating gene expression in the nucleus and by interacting with regulatory proteins in the cytoplasm that control apoptosis. Chipuk et al. (p. 1732; see the Perspective by Vousden) provide evidence for a mechanism by which these actions of p53 may be coordinated. The product of one p53 target gene is a protein known as PUMA (p53 up-regulated modulator of apoptosis). In cells exposed to DNA-damaging agents, interaction of PUMA with the antiapoptotic protein Bcl-xL appears to cause release of p53 that was previously bound to Bcl-xL. The released p53 may then be free to activate the cytoplasmic events that lead to apoptosis.
Plague Targets Its Victims
So-called type III secretion machines are used by Yersinia 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. (p. 1739, published online 28 July 2005) 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.
Chemistry and Quantum Computation
One of the promises of quantum computation is that computational time will scale polynomially with the complexity of the problem, rather than exponentially. Aspuru-Guzik et al. (p. 1704) examined this issue for quantum chemistry by using a quantum computation simulator for calculating the ground-state energies of H2O with the minimal STO-3G basis set and for LiH with the larger 6-31G basis set. Because they used a recursive phase estimator algorithm in these simulations, only 4 qubits were needed to read out the answer. They recovered reasonably accurate energies with only 8 and 11 qubits, respectively, to represent the wave functions of these molecules, and show that the number of qubits that would be needed for quantum computation will scale linearly with molecule size.
Preindustrial Methane Emissions
The atmospheric concentration of methane, a powerful greenhouse gas, has risen from approximately 600 parts per billion (ppb) to more than 1700 ppb between 1750 and 2005 A.D., due mostly to a combination of biomass and fossil-fuel burning, land-use changes, and climate change. However, in the preindustrial past, human activity had a large impact on the global methane budget. Ferretti et al. (p. 1714) analyzed the isotopic composition of carbon in methane trapped in bubbles in a rapidly accumulating ice core from Antarctica. Large isotopic variations occurred between 1000 and 1700 A.D., despite the relatively stable atmospheric methane concentration during that time. They also found that the carbon-isotopic composition of preindustrial methane was much more depleted in the heavy isotope 13C than expected, especially during the period from 1 to 1000 A.D. They attribute these behaviors to changes in biomass burning emissions, driven by both climatic variation and human population dynamics.
Making and Breaking the Gradient
To combat infection, lymphocytes must first be “enticed” to leave their organ of residence and enter the circulation. The same is true for mature thymocytes that must exit the thymus in order to seed peripheral lymphoid organs. A dominant signal for lymphocyte egress comes from sphingosine 1-phosphate (S1P), although it remains to be established how this extracellular lipid mediator is itself regulated to control lymphocyte trafficking. Schwab et al. (p. 1735; see the Perspective by Hla) observe that a long-established inhibitor of thymocyte egress, the food colorant 2-acetyl-4-tetrahydroxybutylimidazole (THI), also inhibits lymphocyte migration and causes the accumulation of S1P in lymph nodes, which are otherwise low in S1P relative to the lymph and blood. This accumulation could be overcome with saturating levels of an essential cofactor for S1P lyase, an enzyme that degrades S1P, which suggests that THI works by preventing S1P breakdown. The maintenance of an S1P gradient between lymphoid tissues and the circulation by S1P lyase may provide a target for selective therapeutic immune suppression.