Genome sequencing in microfabricated high-density picolitre reactors

The proliferation of large-scale DNA-sequencing projects in recent years has driven a search for alternative methods to reduce time and cost. Here we describe a scalable, highly parallel sequencing system with raw throughput significantly greater than that of state-of-the-art capillary electrophoresis instruments. The apparatus uses a novel fibre-optic slide of individual wells and is able to sequence 25 million bases, at 99% or better accuracy, in one four-hour run. To achieve an approximately 100-fold increase in throughput over current Sanger sequencing technology, we have developed an emulsion method for DNA amplification and an instrument for sequencing by synthesis using a pyrosequencing protocol optimized for solid support and picolitre-scale volumes. Here we show the utility, throughput, accuracy and robustness of this system by shotgun sequencing and de novo assembly of the Mycoplasma genitalium genome with 96% coverage at 99.96% accuracy in one run of the machine.     

The bipolar mitotic kinesin Eg5 moves on both microtubules that it crosslinks

During cell division, mitotic spindles are assembled by microtubule-based motor proteins. The bipolar organization of spindles is essential for proper segregation of chromosomes, and requires plus-end-directed homotetrameric motor proteins of the widely conserved kinesin-5 (BimC) family. Hypotheses for bipolar spindle formation include the 'push-pull mitotic muscle' model, in which kinesin-5 and opposing motor proteins act between overlapping microtubules. However, the precise roles of kinesin-5 during this process are unknown. Here we show that the vertebrate kinesin-5 Eg5 drives the sliding of microtubules depending on their relative orientation. We found in controlled in vitro assays that Eg5 has the remarkable capability of simultaneously moving at approximately 20 nm s(-1) towards the plus-ends of each of the two microtubules it crosslinks. For anti-parallel microtubules, this results in relative sliding at approximately 40 nm s(-1), comparable to spindle pole separation rates in vivo. Furthermore, we found that Eg5 can tether microtubule plus-ends, suggesting an additional microtubule-binding mode for Eg5. Our results demonstrate how members of the kinesin-5 family are likely to function in mitosis, pushing apart interpolar microtubules as well as recruiting microtubules into bundles that are subsequently polarized by relative sliding.     

Morphological differences between Saturn's ultraviolet aurorae and those of Earth and Jupiter

It has often been stated that Saturn's magnetosphere and aurorae are intermediate between those of Earth, where the dominant processes are solar wind driven, and those of Jupiter, where processes are driven by a large source of internal plasma. But this view is based on information about Saturn that is far inferior to what is now available. Here we report ultraviolet images of Saturn, which, when combined with simultaneous Cassini measurements of the solar wind and Saturn kilometric radio emission, demonstrate that its aurorae differ morphologically from those of both Earth and Jupiter. Saturn's auroral emissions vary slowly; some features appear in partial corotation whereas others are fixed to the solar wind direction; the auroral oval shifts quickly in latitude; and the aurora is often not centred on the magnetic pole nor closed on itself. In response to a large increase in solar wind dynamic pressure Saturn's aurora brightened dramatically, the brightest auroral emissions moved to higher latitudes, and the dawn side polar regions were filled with intense emissions. The brightening is reminiscent of terrestrial aurorae, but the other two variations are not. Rather than being intermediate between the Earth and Jupiter, Saturn's auroral emissions behave fundamentally differently from those at the other planets.     

Voltage-sensor activation with a tarantula toxin as cargo

The opening and closing of voltage-activated Na+, Ca2+ and K+ (Kv) channels underlies electrical and chemical signalling throughout biology, yet the structural basis of voltage sensing is unknown. Hanatoxin is a tarantula toxin that inhibits Kv channels by binding to voltage-sensor paddles, crucial helix-turn-helix motifs within the voltage-sensing domains that are composed of S3b and S4 helices. The active surface of the toxin is amphipathic, and related toxins have been shown to partition into membranes, raising the possibility that the toxin is concentrated in the membrane and interacts only weakly and transiently with the voltage sensors. Here we examine the kinetics and state dependence of the toxin-channel interaction and the physical location of the toxin in the membrane. We find that hanatoxin forms a strong and stable complex with the voltage sensors, far outlasting fluctuations of the voltage sensors between resting (closed) conformations at negative voltages and activated (open) conformations at positive voltages. Toxin affinity is reduced by voltage-sensor activation, explaining why the toxin stabilizes the resting conformation. We also find that when hanatoxin partitions into membranes it is localized to an interfacial region, with Trp 30 positioned about 8.5 A from the centre of the bilayer. These results demonstrate that voltage-sensor paddles activate with a toxin as cargo, and suggest that the paddles traverse no more than the outer half of the bilayer during activation.     

Tuning clathrate hydrates for hydrogen storage

The storage of large quantities of hydrogen at safe pressures is a key factor in establishing a hydrogen-based economy. Previous strategies--where hydrogen has been bound chemically, adsorbed in materials with permanent void space or stored in hybrid materials that combine these elements--have problems arising from either technical considerations or materials cost. A recently reported clathrate hydrate of hydrogen exhibiting two different-sized cages does seem to meet the necessary storage requirements; however, the extreme pressures (approximately 2 kbar) required to produce the material make it impractical. The synthesis pressure can be decreased by filling the larger cavity with tetrahydrofuran (THF) to stabilize the material, but the potential storage capacity of the material is compromised with this approach. Here we report that hydrogen storage capacities in THF-containing binary-clathrate hydrates can be increased to approximately 4 wt% at modest pressures by tuning their composition to allow the hydrogen guests to enter both the larger and the smaller cages, while retaining low-pressure stability. The tuning mechanism is quite general and convenient, using water-soluble hydrate promoters and various small gaseous guests.     

The genome sequence of the rice blast fungus Magnaporthe grisea

Magnaporthe grisea is the most destructive pathogen of rice worldwide and the principal model organism for elucidating the molecular basis of fungal disease of plants. Here, we report the draft sequence of the M. grisea genome. Analysis of the gene set provides an insight into the adaptations required by a fungus to cause disease. The genome encodes a large and diverse set of secreted proteins, including those defined by unusual carbohydrate-binding domains. This fungus also possesses an expanded family of G-protein-coupled receptors, several new virulence-associated genes and large suites of enzymes involved in secondary metabolism. Consistent with a role in fungal pathogenesis, the expression of several of these genes is upregulated during the early stages of infection-related development. The M. grisea genome has been subject to invasion and proliferation of active transposable elements, reflecting the clonal nature of this fungus imposed by widespread rice cultivation.