University of Wisconsin–Madison

A geologist questions a grand theory.

Atmospheric oxygen concentrations are falling. Breathing is difficult. Those that can't cope are collapsing and dying with symptoms akin to altitude sickness.

This may read like the first page of a Hollywood script, but, according to the oxygen-stress hypothesis, a similar scene occurred 251 million years ago at the end-Permian mass extinction, when up to 95% of all animal species died out. Like all good prevailing hypotheses, this one makes predictions that can be tested, if only the right rocks can be found.

Enter Tyler Beatty of the University of Calgary in Alberta, Canada, and his colleagues. They recently set up camp in the remote reaches of northwestern Canada, where rocks spanning the end-Permian extinction show a shift from Permian sandy carbonates to Triassic sand and mud. They found that fossils of entire creatures are not common at the boundary, preventing taxonomic analyses, but that fossils documenting sediment disturbance by animals are (T. W. Beatty et al. Geology 36, 771–774; 2008). This is fortuitous because such disturbance in marine sediments is linked to oxygen concentration. So these rocks may preserve a 'smoking gun' for an oxygen-stressed world.

However, the shallow marine sediments of the Early Triassic were pervasively burrowed by diverse organisms of the period, including large, oxygen-demanding arthropods. Only deeper-water sediments, deposited below wave-mixed surface waters, had the expected oxygen-stressed fossil traces.

This complicates the oxygen-stress story for the end-Permian mass extinction. Beatty et al. stop short of asking whether the end-Permian mass extinction was really caused by a massive reduction in atmospheric oxygen. But in light of their results, I am not holding my breath.

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Northwestern University, Evanston, Illinois

A physical chemist is pleased to learn that 'microscale' swimming isn't that hard after all.

Even if small organisms perfectly mimicked gold medallist Michael Phelps's technique, they wouldn't win a microswimming Olympics. The viscosity of water is so high that these little fellows have had to develop some unusual swimming styles. In 1977, E. M. Purcell formally expressed this idea with his famous 'scallop theorem'. He showed that swimming forwards cannot be achieved at the micrometre-scale with 'time-reversible' motions such as the back-and-forth wiggling of a rigid tail. Instead, tiny organisms must use complex, asymmetrical strokes.

But this is not always the case, according to engineers at the Massachusetts Institute of Technology in Cambridge and the University of California, San Diego. In July, they proved that time-reversible tail-wiggling or wing-flapping can be a viable mode of propulsion through a fluid, provided it is done next to a deformable interface such as a soft membrane (R. Trouilloud et al. Phys. Rev. Lett. 101, 048102; 2008). The reversible motions of the swimmer couple in a nonlinear way to the deformations of the interface, producing additional flows and forces that are sufficient for locomotion.

One of the most exciting extensions of this result might be in creating 'nanosubmarines' — a much-criticized dream of nanotechnologists to have devices navigate blood vessels, finding and fixing damaged organs as they go. The idea has so far seemed implausible because such machines would need elaborate nanopropellers — which are prohibitively difficult to build — to sculpt asymmetrical swimming motions. But what about using a simpler propulsion mechanism and relying on the deformations of blood-vessel walls to move nanosubmarines along? Is there a nanoshipyard out there somewhere to put this idea to the test?

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Laboratory of Crystallography, ETH Zurich, Switzerland

A crystallographer celebrates a method with niche applications.

In 2004, Oszlányi and Sü introduced a new way to determine crystal structures from diffraction data. To many crystallographers, including myself, this was a remarkable development. Although most of us had assumed that the trend of incremental but significant improvements to existing methods would continue, we had not expected a completely different approach to be discovered. The algorithm is an elegant one, based on a very simple perturbation (called charge flipping) of electron-density maps that are generated during the structure solution process.

Initially, the algorithm was viewed as a curiosity. After all, existing methods for solving structures work very well about 95% of the time, so a new technique was not really needed. However, the algorithm caught the attention of some inquisitive crystallographers, who tested it on their favourite problem cases. The result is that, just 4 years after its development, the approach has found niches in areas in which traditional methods flounder (Acta Cryst. A64, 123–134; 2008).

Scientists studying aperiodic materials (modulated structures and quasicrystals, whose structures are best described in more than three dimensions) were among the first to recognize the possibilities offered by the algorithm, because it could be easily adapted to work in higher dimensions. Charge flipping has enjoyed great success with such structures, and is now considered the method of choice by this community.

The algorithm has also proved effective in solving the structures of polycrystalline materials, mainly because complementary information from other sources (such as chemical analysis and electron microscopy) can be easily included. Now small protein structures and neutron- and electron-diffraction data are being explored — no doubt further niches will be found.

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University of Massachusetts Medical School, Worcester

A molecular biologist considers the corollary of misbehaving ion channels

More than half a century ago, Hodgkin and Huxley hypothesized that pore-forming proteins found in a cell membrane could regulate the flow of ions across that membrane. These days, we classify ion channels according to the ions they allow through and the nature of the pore-forming protein. The crucial part of a pore is the protein's alpha subunit, which lines the pore. Auxiliary subunits, denoted by other letters of the Greek alphabet, merely tweak a channel's characteristics.

The basics infer an assumption: that different channels can interact with each other, but that subunits buried within a channel are 'married' to that channel 'for life'. A voltage-activated calcium channel can, for instance, form a pair with a large-conductance calcium-activated potassium channel. But a beta subunit of the calcium channel can associate only with the calcium channel's main alpha subunit, and a beta subunit of the potassium channel remains 'faithful' to the alpha subunit that surrounds the potassium pore.

However, assumptions should always be tested. In this case, Shengwei Zou and his colleagues at the University of Houston in Texas have taken the potassium channel in this example and shown that it is bound by an auxiliary beta-1 subunit of an L-type calcium channel (Cav1). When this subunit interacts with the potassium pore, it alters both the pore's kinetics and calcium sensitivity (S. Zou et al. Mol. Pharmacol. 73, 369–378; 2008).

I view this finding as part of an emerging theme, the ramifications of which could be profound. Ion channels may, in general, be much more dynamic structures than is currently recognized. This means that when researchers monitor a channel's activity they may not be recording exactly what they think they are — and that targeting ion channels with new drugs could produce unexpected side effects.

Posted by Anna Petherick at 05:07 PM | Permalink | Comments (0) | TrackBacks (0)