Community structure and metabolism through reconstruction of microbial genomes from the environment

Microbial communities are vital in the functioning of all ecosystems; however, most microorganisms are uncultivated, and their roles in natural systems are unclear. Here, using random shotgun sequencing of DNA from a natural acidophilic biofilm, we report reconstruction of near-complete genomes of Leptospirillum group II and Ferroplasma type II, and partial recovery of three other genomes. This was possible because the biofilm was dominated by a small number of species populations and the frequency of genomic rearrangements and gene insertions or deletions was relatively low. Because each sequence read came from a different individual, we could determine that single-nucleotide polymorphisms are the predominant form of heterogeneity at the strain level. The Leptospirillum group II genome had remarkably few nucleotide polymorphisms, despite the existence of low-abundance variants. The Ferroplasma type II genome seems to be a composite from three ancestral strains that have undergone homologous recombination to form a large population of mosaic genomes. Analysis of the gene complement for each organism revealed the pathways for carbon and nitrogen fixation and energy generation, and provided insights into survival strategies in an extreme environment.     

Comparison of transfer ribonucleic acid aminoacylation by various regions of chicken brain

Summary Aminoacylation of tRNA with valine was greater in the cerebrum of chicken than the cerebellum or optic lobes. This greater aminoacylation was due to both the activity of the cerebral valyl-tRNA synthetases and the accepting activity of the cerebral tRNA^val.     

Synthetic chromosome arms function in yeast and generate phenotypic diversity by design

Recent advances in DNA synthesis technology have enabled the construction of novel genetic pathways and genomic elements, furthering our understanding of system-level phenomena. The ability to synthesize large segments of DNA allows the engineering of pathways and genomes according to arbitrary sets of design principles. Here we describe a synthetic yeast genome project, Sc2.0, and the first partially synthetic eukaryotic chromosomes, Saccharomyces cerevisiae chromosome synIXR, and semi-synVIL. We defined three design principles for a synthetic genome as follows: first, it should result in a (near) wild-type phenotype and fitness; second, it should lack destabilizing elements such as tRNA genes or transposons; and third, it should have genetic flexibility to facilitate future studies. The synthetic genome features several systemic modifications complying with the design principles, including an inducible evolution system, SCRaMbLE (synthetic chromosome rearrangement and modification by loxP-mediated evolution). We show the utility of SCRaMbLE as a novel method of combinatorial mutagenesis, capable of generating complex genotypes and a broad variety of phenotypes. When complete, the fully synthetic genome will allow massive restructuring of the yeast genome, and may open the door to a new type of combinatorial genetics based entirely on variations in gene content and copy number.     

Magnetic fields at the solar wind termination shock

A transition between the supersonic solar wind and the subsonic heliosheath was observed by Voyager 1, but the expected termination shock was not seen owing to a gap in the telemetry. Here we report observations of the magnetic field structure and dynamics of the termination shock, made by Voyager 2 on 31 August-1 September 2007 at a distance of 83.7 au from the Sun (1 au is the Earth-Sun distance). A single crossing of the shock was expected, with a boundary that was stable on a timescale of several days. But the data reveal a complex, rippled, quasi-perpendicular supercritical magnetohydrodynamic shock of moderate strength undergoing reformation on a scale of a few hours. The observed structure suggests the importance of ionized interstellar atoms ('pickup protons') at the shock.     

100-metre-diameter moonlets in Saturn's A ring from observations of 'propeller' structures

Saturn's main rings are composed predominantly of water-ice particles ranging between about 1 centimetre and 10 metres in radius. Above this size range, the number of particles drops sharply, according to the interpretation of spacecraft and stellar occultations. Other than the gap moons Pan and Daphnis (the provisional name of S/2005 S1), which have sizes of several kilometres, no individual bodies in the rings have been directly observed, and the population of ring particles larger than ten metres has been essentially unknown. Here we report the observation of four longitudinal double-streaks in an otherwise bland part of the mid-A ring. We infer that these 'propeller'-shaped perturbations arise from the effects of embedded moonlets approximately 40 to 120 m in diameter. Direct observation of this phenomenon validates models of proto-planetary disks in which similar processes are posited. A population of moonlets, as implied by the size distribution that we find, could help explain gaps in the more tenuous regions of the Cassini division and the C ring. The existence of such large embedded moonlets is most naturally compatible with a ring originating in the break-up of a larger body, but accretion from a circumplanetary disk is also plausible if subsequent growth onto large particles occurs after the primary accretion phase has concluded.     

Teaching in tandem-running ants

The ant Temnothorax albipennis uses a technique known as tandem running to lead another ant from the nest to food--with signals between the two ants controlling both the speed and course of the run. Here we analyse the results of this communication and show that tandem running is an example of teaching, to our knowledge the first in a non-human animal, that involves bidirectional feedback between teacher and pupil. This behaviour indicates that it could be the value of information, rather than the constraint of brain size, that has influenced the evolution of teaching.     

Directly measured mid-depth circulation in the northeastern North Atlantic Ocean

The circulation of water masses in the northeastern North Atlantic Ocean has a strong influence on global climate owing to the northward transport of warm subtropical water to high latitudes. But the ocean circulation at depths below the reach of satellite observations is difficult to measure, and only recently have comprehensive, direct observations of whole ocean basins been possible. Here we present quantitative maps of the absolute velocities at two levels in the northeastern North Atlantic as obtained from acoustically tracked floats. We find that most of the mean flow transported northward by the Gulf Stream system at the thermocline level (about 600 m depth) remains within the subpolar region, and only relatively little enters the Rockall trough or the Nordic seas. Contrary to previous work, our data indicate that warm, saline water from the Mediterranean Sea reaches the high latitudes through a combination of narrow slope currents and mixing processes. At both depths under investigation, currents cross the Mid-Atlantic Ridge preferentially over deep gaps in the ridge, demonstrating that sea-floor topography can constrain even upper-ocean circulation patterns.     

Impact of climate change on marine pelagic phenology and trophic mismatch

Phenology, the study of annually recurring life cycle events such as the timing of migrations and flowering, can provide particularly sensitive indicators of climate change. Changes in phenology may be important to ecosystem function because the level of response to climate change may vary across functional groups and multiple trophic levels. The decoupling of phenological relationships will have important ramifications for trophic interactions, altering food-web structures and leading to eventual ecosystem-level changes. Temperate marine environments may be particularly vulnerable to these changes because the recruitment success of higher trophic levels is highly dependent on synchronization with pulsed planktonic production. Using long-term data of 66 plankton taxa during the period from 1958 to 2002, we investigated whether climate warming signals are emergent across all trophic levels and functional groups within an ecological community. Here we show that not only is the marine pelagic community responding to climate changes, but also that the level of response differs throughout the community and the seasonal cycle, leading to a mismatch between trophic levels and functional groups.