Letters in 2008

A plume of water vapour escapes from fissures crossing the south polar region of Saturn's moon, Enceladus. This study reports observations of an occultation of a star by the plume on 24 October 2007, which revealed four high-density gas jets at positions that coincide with those of the previously seen dust jets. The amount of water seen does not agree with earlier predictions.

Gibberellin is an important plant hormone that regulates several development processes. This paper presents the struccture of gibberellin bound to its receptor.

The direct detection and exploitation of optical forces in an integrated silicon photonic circuit that contains a nanomechanical resonator is reported. This nanomechanical device, which is a freestanding, vibrating waveguide, is driven by a laser diode and its motion can be read-out through evanescent coupling of the light through the waveguide to the dielectric substrate. This demonstration uncovers a new optical force that enables all-optical operation of nanomechanical systems on a CMOS compatible platform.

The association of particular major histocompatibility complex (MHC) polymorphisms with susceptibility to a number of autoimmune disease has been a puzzling phenomenon. This paper proposes a mechanism that might account in part for the onset of coeliac disease. Transaminase-mediated deamination of glutamine residues in gluten peptides may cause them to bind more tightly to disease-associated MHC alleles, activating heteroclitic gluten-peptide specific T-cell autoreactivity in the gut.

Crenarchaeota, which comprise the most abundant clade of organisms on Earth, are believed to be responsible for the majority of ammonia oxidation in terrestrial and marine environments. But recent studies have suggested that not all species are autotrophic. Using a comprehensive dataset, it is now shown that a significant proportion of marine crenarchaeota lack the genes required for ammonia oxidation, suggesting that they are heterotrophs.

This paper shows that specific genetic disruption of the Ncor–HdaC3 interaction in mice causes aberrant regulation of clock genes and results in abnormal circadian behaviour. These mice are also leaner and more insulin sensitive due to increased energy expenditure. Loss of a functional Ncor–HdaC3 complex in vivo changes the oscillatory patterns of several metabolic genes, demonstrating that circadian regulation of metabolism is critical for normal energy balance.

The PU.1-related transcription factor Spi-C controls the development of a tissue macrophage subset in the spleen involved in the removal of red blood cells. Spi-C deficient mice fail to phagocytose trapped red blood cells.

Natural or artificial oceanic iron supplementation induces blooms that are dominated by pennate diatoms. It is shown that these diatoms contain the iron storage protein ferritin, which may explain their success in iron-limited waters.

Phylogeny-driven reconstructions of ancestral protein sequences have predicted that the last universal common ancestor (LUCA) was a thermophile, but analyses of ribosomal RNA sequences suggested that LUCA preferred a cooler environment. rRNA and protein sequences are used to show that thermotolerance initially increased from a mesophilic LUCA to thermophilic ancestors of Bacteria and Archaea–Eukaryota, and then subsequently decreased.

Both strands of DNA are replicated simultaneously, but they have opposite polarities. A trombone model has been proposed to explain how replication machinery that moves in one direction can accomplish this feat. In this model, the lagging strand forms a loop that allows it to enter the replication machinery in the same direction as the leading strand. This study uses single molecule techniques to examine this process in real time, and it finds that this loop is reinitiated with the priming of every Okazaki fragment, and released when the previous fragment is encountered by the replisome.

This paper presents a general thermodynamic model that accurately captures the relationship between a gene promoter sequence, including weak, stastically undetectable regulatory sites, and its expression output. The work implies a relatively minor role of chromatin and will facilitate rational genetic design in biotechnology and synthetic biology.

During gastrulation in Drosophila embryo, there is apical constriction of ventral cells, which results in formation of a ventral furrow and invagination of the mesoderm. This study reports a mechanism for this process and shows that apical constriction of ventral cells is pulsed. These pulses are powered by the actin–myosin contractions and are dependent on the expression of a transcription factor, Snail, whereas the constricted state is stabilized by the transcription factor Twist.

Polploidy is a common feature of many plants, and in addition some plants exist as intra- and interspecific hybrinds. Such plants display growth vigour, and genes involved in metabolism and energy, photosynthesis and starch accumulation are upregulated compared to the parents. This study examines the mechanistic basis of increased growth, and reports that epigenetic modifications of circadian clock regulators mediates the expression of genes in photosynthetic and metabolic pathways.

In this paper, the crystal structure and stacking fault density of semiconducting nanowires composed of the same material are controlled by doping, leading to twinning superlattices. Periodic arrays of rotational dislocations lead to crystal heterostructures in indium phosphide and gallium phosphide nanowires.

In most superconductors, the pairing-up of electrons responsible for resistance-less conduction is driven by vibrations of the solid's crystal lattice. But other materials exist in which the attractive interaction responsible for binding electrons is believed to have a very different origin: quantum fluctuations of spin or charge. This paper identifies an unusually 'violent' generalization of such pairing mechanisms, in which these spin and charge instabilities combine forces.

This study presents optical geodetic observations to constrain the sources responsible for long-period volcanic earthquakes, which are coincident with frequent explosive eruptions at Santiaguito Volcano, Guatemala. It is found that acceleration in deformation of the volcanic dome, extracted from the high-resolution optical image processing, is coincident with recorded long-period seismic sources. On the basis of these observations, abrupt mass shift of solidified domes, conduit magma or magma pads seem to be part of the mechanism responsible for generating long-period earthquakes at silicic volcanic systems.

The 2.4 Å structure of the Ca²⁺-bound calpain 2 heterodimer bound to one of the four inhibitory domains of calpastatin. Calpastatin seems to inhibit calpain by occupying both the primed and unprimed sides of the active site cleft. This crystal structure also reveals the conformational changes that calpain undergoes upon binding calcium, which include opening of the active site cleft and movement of the domains relative to each other to produce a more compact enzyme.

This paper reports an excess of galactic cosmic-ray electrons at energies of ∼300-800 GeV, which indicates a nearby source of energetic electrons. Such a source could be an unseen astrophysical object that accelerates electrons to those energies, or the electrons could arise from the annihilation of dark matter.

This paper presents simulations with a coupled model of glacial climate and biogeochemical cycles, forced only with changes in the Atlantic meridional overturning circulation. It is found that variations in atmospheric carbon dioxide levels on millennial time scales are dominated by slow changes in the deep ocean inventory of biologically-sequestered carbon and are correlated to Antarctic temperature and Southern Ocean stratification. The results suggest that ocean circulation changes were the primary mechanism that drove glacial fluctuations in carbon dioxide and nitrous oxide fluctuations on millennial time scales.