Nature \ 430, 78 - 81 (01 July 2004); doi:10.1038/nature02663 Nature AOP, published online 6 June 2004
Local sleep and learning
Human sleep is a global state whose functions remain unclear. During much of sleep, cortical neurons undergo slow oscillations in membrane potential, which appear in electroencephalograms as slow wave activity (SWA) of <4 Hz. The amount of SWA is homeostatically regulated, increasing after wakefulness and returning to baseline during sleep. It has been suggested that SWA homeostasis may reflect synaptic changes underlying a cellular need for sleep. If this were so, inducing local synaptic changes should induce local SWA changes, and these should benefit neural function. Here we show that sleep homeostasis indeed has a local component, which can be triggered by a learning task involving specific brain regions. Furthermore, we show that the local increase in SWA after learning correlates with improved performance of the task after sleep. Thus, sleep homeostasis can be induced on a local level and can benefit performance.
Nature 430, 35 - 44 (01 July 2004); doi:10.1038/nature02579
Genome evolution in yeasts
Identifying the mechanisms of eukaryotic genome evolution by comparative genomics is often complicated by the multiplicity of events that have taken place throughout the history of individual lineages, leaving only distorted and superimposed traces in the genome of each living organism. The hemiascomycete yeasts, with their compact genomes, similar lifestyle and distinct sexual and physiological properties, provide a unique opportunity to explore such mechanisms. We present here the complete, assembled genome sequences of four yeast species, selected to represent a broad evolutionary range within a single eukaryotic phylum, that after analysis proved to be molecularly as diverse as the entire phylum of chordates. A total of approximately 24,200 novel genes were identified, the translation products of which were classified together with Saccharomyces cerevisiae proteins into about 4,700 families, forming the basis for interspecific comparisons. Analysis of chromosome maps and genome redundancies reveal that the different yeast lineages have evolved through a marked interplay between several distinct molecular mechanisms, including tandem gene repeat formation, segmental duplication, a massive genome duplication and extensive gene loss.
Nature 430, 51 - 53 (01 July 2004); doi:10.1038/nature02671
No stellar p-mode oscillations in space-based photometry of Procyon
Pressure-driven (p-mode) oscillations at the surface of the Sun, resulting from sound waves travelling through the solar interior, are a powerful probe of solar structure, just as seismology can reveal details about the interior of the Earth. Astronomers have hoped to exploit p-mode asteroseismology in Sun-like stars to test detailed models of stellar structure and evolution, but the observations are extremely difficult. The bright star Procyon has been considered one of the best candidates for asteroseismology, on the basis of models and previous reports of p-modes detected in ground-based spectroscopy. Here we present a search for p-modes in 32 days of nearly continuous photometric satellite-based observations of Procyon. If there are p-modes in Procyon, they must have lifetimes less than 2–3 days and/or peak amplitudes <15 parts per million, which defy expectations from the Sun's oscillations and previous theoretical predictions. Target selection for future planned asteroseismology space missions may need to be reconsidered, as will the theory of stellar oscillations.
Nature 430, 58 - 61 (01 July 2004); doi:10.1038/nature02682
Cyclotron frequency shifts arising from polarization forces
The cyclotron frequency of a charged particle in a uniform magnetic field B is related to its mass m and charge q by the relationship c = qB/m. This simple relationship forms the basis for sensitive mass comparisons using ion cyclotron resonance mass spectroscopy, with applications ranging from the identification of biomolecules and the study of chemical reaction rates to determinations of the fine structure constant of atomic spectra. Here we report the observation of a deviation from the cyclotron frequency relationship for polarizable particles: in high-accuracy measurements of a single CO+ ion, a dipole induced in the orbiting ion shifts the measured cyclotron frequency. We use this cyclotron frequency shift to measure non-destructively the quantum state of the CO+ ion. The effect also provides a means to determine to a few per cent the body-frame dipole moment of CO+, thus establishing a method for measuring dipole moments of molecular ions for which few comparably accurate measurements exist. The general perturbation that we describe here affects the most precise mass comparisons attainable today, with applications including direct tests of Einstein's mass–energy relationship and charge-parity-time reversal symmetry, and possibly the weighing of chemical bonds.
Nature 430, 61 - 65 (01 July 2004); doi:10.1038/nature02674
Single-crystal metallic nanowires and metal/semiconductor nanowire heterostructures
Substantial effort has been placed on developing semiconducting carbon nanotubes and nanowires as building blocks for electronic devices—such as field-effect transistors—that could replace conventional silicon transistors in hybrid electronics or lead to stand-alone nanosystems. Attaching electric contacts to individual devices is a first step towards integration, and this step has been addressed using lithographically defined metal electrodes. Yet, these metal contacts define a size scale that is much larger than the nanometre-scale building blocks, thus limiting many potential advantages. Here we report an integrated contact and interconnection solution that overcomes this size constraint through selective transformation of silicon nanowires into metallic nickel silicide (NiSi) nanowires. Electrical measurements show that the single crystal nickel silicide nanowires have ideal resistivities of about 10 µ cm and remarkably high failure-current densities, >108 A cm-2. In addition, we demonstrate the fabrication of nickel silicide/silicon (NiSi/Si) nanowire heterostructures with atomically sharp metal–semiconductor interfaces. We produce field-effect transistors based on those heterostructures in which the source–drain contacts are defined by the metallic NiSi nanowire regions. Our approach is fully compatible with conventional planar silicon electronics and extendable to the 10-nm scale using a crossed-nanowire architecture.
Nature 430, 68 - 71 (01 July 2004); doi:10.1038/nature02638
Role of metal-reducing bacteria in arsenic release from Bengal delta sediments
The contamination of ground waters, abstracted for drinking and irrigation, by sediment-derived arsenic threatens the health of tens of millions of people worldwide, most notably in Bangladesh and West Bengal. Despite the calamitous effects on human health arising from the extensive use of arsenic-enriched ground waters in these regions, the mechanisms of arsenic release from sediments remain poorly characterized and are topics of intense international debate. We use a microscosm-based approach to investigate these mechanisms: techniques of microbiology and molecular ecology are used in combination with aqueous and solid phase speciation analysis of arsenic. Here we show that anaerobic metal-reducing bacteria can play a key role in the mobilization of arsenic in sediments collected from a contaminated aquifer in West Bengal. We also show that, for the sediments in this study, arsenic release took place after Fe(III) reduction, rather than occurring simultaneously. Identification of the critical factors controlling the biogeochemical cycling of arsenic is one important contribution to fully informing the development of effective strategies to manage these and other similar arsenic-rich ground waters worldwide.
Nature 430, 71 - 75 (01 July 2004); doi:10.1038/nature02708
Why large-scale climate indices seem to predict ecological processes better than local weather
Large-scale climatic indices such as the North Atlantic Oscillation are associated with population dynamics, variation in demographic rates and values of phenotypic traits in many species. Paradoxically, these large-scale indices can seem to be better predictors of ecological processes than local climate. Using detailed data from a population of Soay sheep, we show that high rainfall, high winds or low temperatures at any time during a 3-month period can cause mortality either immediately or lagged by a few days. Most measures of local climate used by ecologists fail to capture such complex associations between weather and ecological process, and this may help to explain why large-scale, seasonal indices of climate spanning several months can outperform local climatic factors. Furthermore, we show why an understanding of the mechanism by which climate influences population ecology is important. Through simulation we demonstrate that the timing of bad weather within a period of mortality can have an important modifying influence on intraspecific competition for food, revealing an interaction between climate and density dependence that the use of large-scale climatic indices or inappropriate local weather variables might obscure.
Nature 430, 81 - 85 (01 July 2004); doi:10.1038/nature02533
Resilient circadian oscillator revealed in individual cyanobacteria
Circadian oscillators, which provide internal daily periodicity, are found in a variety of living organisms, including mammals, insects, plants, fungi and cyanobacteria. Remarkably, these biochemical oscillators are resilient to external and internal modifications, such as temperature and cell division cycles. They have to be 'fluctuation (noise) resistant' because relative fluctuations in the number of messenger RNA and protein molecules forming the intracellular oscillators are likely to be large. In multicellular organisms, the strong temporal stability of circadian clocks, despite molecular fluctuations, can easily be explained by intercellular interactions. Here we study circadian rhythms and their stability in unicellular cyanobacteria Synechoccocus elongatus. Low-light-level microscopy has allowed us to measure gene expression under circadian control in single bacteria, showing that the circadian clock is indeed a property of individual cells. Our measurements show that the oscillators have a strong temporal stability with a correlation time of several months. In contrast to many circadian clocks in multicellular organisms, this stability seems to be ensured by the intracellular biochemical network, because the interactions between oscillators seem to be negligible.
Nature 430, 75 - 78 (01 July 2004); doi:10.1038/nature02654
Microbialite resurgence after the Late Ordovician extinction
Microbialites, including biogenic stromatolites, thrombolites and dendrolites, were formed by various microbial mats that trapped and bound sediments or formed the locus of mineral precipitation. Microbialites were common and diverse during the Proterozoic, but declined in abundance and morphological diversity when multicellular life diversified during the Cambrian Radiation. A second decline occurred during the Ordovician Radiation of marine animals, and from then until the present microbialites have been confined largely to high-stress environments where multicellular organisms are rare. The microbialite declines in the Phanerozoic are attributed to disruption of the mats by animals. A resurgence of stromatolite abundance and size during reduced animal diversity after the Permian extinction has been documented anecdotally. Here we show, with statistical support, that a microbialite resurgence also occurred after the Late Ordovician extinction event in western North America. The resurgences were associated with loss of mat-inhibiting animals, providing insights into shallow-water community structures after extinction events.
Nature 430, 98 - 101 (01 July 2004); doi:10.1038/nature02635
Nitrification by plants that also fix nitrogen
Nitrification is a key stage in the nitrogen cycle; it enables the transformation of nitrogen into an oxidized, inorganic state. The availability of nitrates produced by this process often limits primary productivity and is an important determinant in plant community ecology and biodiversity. Chemoautotrophic prokaryotes are recognized as the main facilitators of this process, although heterotrophic nitrification by fungi may be significant under certain conditions. However, there has been neither biochemical nor ecological evidence to support nitrification by photoautotrophic plants. Here we show how certain legumes that accumulate the toxin, 3-nitropropionic acid, generate oxidized inorganic nitrogen in their shoots, which is returned to the soil in their litter. In nitrogen-fixing populations this 'new' nitrate and nitrite can be derived from the assimilation of nitrogen gas. Normally, the transformation of elemental nitrogen from the atmosphere into a fixed oxidized form (as nitrate) is represented in the nitrogen cycle as a multiphasic process involving several different organisms. We show how this can occur in a single photoautotrophic organism, representing a previously undescribed feature of this biogeochemical cycle.
