Temporal precision in the neural code and the timescales of natural vision

The timing of action potentials relative to sensory stimuli can be precise down to milliseconds in the visual system, even though the relevant timescales of natural vision are much slower. The existence of such precision contributes to a fundamental debate over the basis of the neural code and, specifically, what timescales are important for neural computation. Using recordings in the lateral geniculate nucleus, here we demonstrate that the relevant timescale of neuronal spike trains depends on the frequency content of the visual stimulus, and that 'relative', not absolute, precision is maintained both during spatially uniform white-noise visual stimuli and naturalistic movies. Using information-theoretic techniques, we demonstrate a clear role of relative precision, and show that the experimentally observed temporal structure in the neuronal response is necessary to represent accurately the more slowly changing visual world. By establishing a functional role of precision, we link visual neuron function on slow timescales to temporal structure in the response at faster timescales, and uncover a straightforward purpose of fine-timescale features of neuronal spike trains.     

Persistence of soil organic matter as an ecosystem property

Globally, soil organic matter (SOM) contains more than three times as much carbon as either the atmosphere or terrestrial vegetation. Yet it remains largely unknown why some SOM persists for millennia whereas other SOM decomposes readily--and this limits our ability to predict how soils will respond to climate change. Recent analytical and experimental advances have demonstrated that molecular structure alone does not control SOM stability: in fact, environmental and biological controls predominate. Here we propose ways to include this understanding in a new generation of experiments and soil carbon models, thereby improving predictions of the SOM response to global warming.     

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.     

HIV preferentially infects HIV-specific CD4+ T cells

HIV infection is associated with the progressive loss of CD4(+) T cells through their destruction or decreased production. A central, yet unresolved issue of HIV disease is the mechanism for this loss, and in particular whether HIV-specific CD4(+) T cells are preferentially affected. Here we show that HIV-specific memory CD4(+) T cells in infected individuals contain more HIV viral DNA than other memory CD4(+) T cells, at all stages of HIV disease. Additionally, following viral rebound during interruption of antiretroviral therapy, the frequency of HIV viral DNA in the HIV-specific pool of memory CD4(+) T cells increases to a greater extent than in memory CD4(+) T cells of other specificities. These findings show that HIV-specific CD4(+) T cells are preferentially infected by HIV in vivo. This provides a potential mechanism to explain the loss of HIV-specific CD4(+) T-cell responses, and consequently the loss of immunological control of HIV replication. Furthermore, the phenomenon of HIV specifically infecting the very cells that respond to it adds a cautionary note to the practice of structured therapy interruption.     

Towards sustainability in world fisheries

Fisheries have rarely been 'sustainable'. Rather, fishing has induced serial depletions, long masked by improved technology, geographic expansion and exploitation of previously spurned species lower in the food web. With global catches declining since the late 1980s, continuation of present trends will lead to supply shortfall, for which aquaculture cannot be expected to compensate, and may well exacerbate. Reducing fishing capacity to appropriate levels will require strong reductions of subsidies. Zoning the oceans into unfished marine reserves and areas with limited levels of fishing effort would allow sustainable fisheries, based on resources embedded in functional, diverse ecosystems.     

What is narrative possibility?

In this paper I offer a new account of narrative possibility that I call the “ecological approach.” I situate it relative to alternative “metaphysical” and “epistemological” approaches, and argue that it has advantages in comparison. It saves some of the important insights from each, but serves the purposes of narrative explanation better than either, specifically because it delimits the explanatory modal space of narrative explanation correctly, whereas the others do not.     

Comparison of classifications using measures intermediate between metric dissimilarity and consensus similarity

Two fundamental approaches to the comparison of classifications (e g, partitions on the same finite set of objects) can be distinguished One approach is based upon measures of metric dissimilarity while the other is based upon measures of similarity, or consensus These approaches are not necessarily simple complements of each other Instead, each captures different, limited views of comparison of two classifications The properties of these measures are clarified by their relationships to Day's complexity models and to association measures of numerical taxonomy The two approaches to comparison are equated with the use of separation and minimum value sensitive measures, suggesting the potential application of an intermediate sensitive measure to the problem of comparison of classifications Such a measure is a linear combination of separation sensitive and minimum value sensitive components The application of these intermediate measures is contrasted with the two extremes The intermediate measure for the comparison of classifications is applied to a problem of character weighting arising in the analysis of Australian stream basinsWe thank Bill Day, Mike Austin, Peter Minchin and two anonymous referees for many helpful comments We also thank P Arabie for useful discussion of consensus methods and character weighting     

The lunar and Paschal tables of De ratione paschali attributed to Anatolius of Laodicea

Summary of conclusions The seven MS lunar and Paschal tables of De ratione paschali fall into two distinct groups which we have classified as Sirmond-type and Padua-type respectively, and from these we have restored the tables of their archetype. The Sirmond-type tables preserve a unique lunar year, which we term the Anatolian lunar year, and they first emerge in the context of a larger computus which was assembled in southern Ireland c. 658, a copy of which Wilfrid had evidently obtained by the time of the Synod of Whitby. The weight of circumstantial evidence supports the hypothesis that it was he who then instigated the corruption of both the tables and the patristic authorities of De ratione paschali, a copy of which subsequently passed to Bede and thence to the Sirmond group of MSS. The Padua-type tables on the other hand are represented only by the Padua MS, and they appear to have originated from within Insular circles on the Continent. These too were crudely corrupted, first by changing their lunar year from Anatolian to Roman and moving their ferial data from January to December and changing some Paschal data, and then secondly by collation with Sirmond-type tables. In the case of both types the objective was clearly to weaken the relationship between the lunar and Paschal tables and to try and obscure the Paschal principles that they preserve and thereby undermine the position of those followers of the Insular latercus who relied on the authority of De ratione paschali for their Pasch. These conclusions naturally give a rather different colour to the events of Whitby from that given by Bede, who places them completely in a theological context. However in material terms what was really at stake at Whitby was the transfer of the patronage of the entire kingdom of Northumbria from the Celtic to the Roman church. Here then was sufficient motivation to justify the most ruthless of expedients.     

Microtubule targeting agents: from biophysics to proteomics

This review explores various aspects of the interaction between microtubule targeting agents and tubulin, including binding site, affinity, and drug resistance. Starting with the basics of tubulin polymerization and microtubule targeting agent binding, we then highlight how the three-dimensional structures of drug–tubulin complexes obtained on stabilized tubulin are seeded by precise biological and biophysical data. New avenues opened by thermodynamics analysis, high throughput screening, and proteomics for the molecular pharmacology of these drugs are presented. The amount of data generated by biophysical, proteomic and cellular techniques shed more light onto the microtubule–tubulin equilibrium and tubulin–drug interaction. Combining these approaches provides new insight into the mechanism of action of known microtubule interacting agents and rapid in-depth characterization of next generation molecules targeting the interaction between microtubules and associated modulators of their dynamics. This will facilitate the design of improved and/or alternative chemotherapies targeting the microtubule cytoskeleton.