Genome sequence of the biocontrol strain Pseudomonas fluorescens F113

Pseudomonas fluorescens F113 is a plant growth-promoting rhizobacterium (PGPR) that has biocontrol activity against fungal plant pathogens and is a model for rhizosphere colonization. Here, we present its complete genome sequence, which shows that besides a core genome very similar to those of other strains sequenced within this species, F113 possesses a wide array of genes encoding specialized functions for thriving in the rhizosphere and interacting with eukaryotic organisms.     

The depletion attraction: an underappreciated force driving cellular organization

Cellular structures are shaped by hydrogen and ionic bonds, plus van der Waals and hydrophobic forces. In cells crowded with macromolecules, a little-known and distinct force-the "depletion attraction"-also acts. We review evidence that this force assists in the assembly of a wide range of cellular structures, ranging from the cytoskeleton to chromatin loops and whole chromosomes.     

An estimate of population sizes of burrowing seabirds at the Diego Ramirez archipelago, Chile, using distance sampling and burrow-scoping

The Diego Ramirez Islands lie 60 nautical miles southwest of Cape Horn and are the breeding site for three species of burrowing seabirds: blue petrels (Halobaena caerulea), common diving petrels (Pelecanoides urinatrix) and sooty shearwater (Puffinus griseus). Burrowing seabirds are highly vulnerable to predation by introduced vertebrate pests, and Diego Ramirez is an important breeding site because it is one of a few remaining subantarctic island groups with no introduced predators. Diego Ramirez is the only known breeding site for blue petrels in the southeast Pacific region, holding about 80% of the global population of that species, and with a population ten times larger than any other population in the world. We estimated the population size in 2002, using a novel application of the distance sampling technique to determine burrow density, and a burrow-scope with excavations to determine occupying species. We found that density was correlated with slope angle and soil wetness. Burrow densities in flatter terrain with drier soils were 2.03 burrows/m² (95% confidence intervals: 1.82–2.27) and 1.11 burrows/m² (0.84–1.48) in steeper terrain with wetter soils. The occupation rate of burrows were significantly different between habitat types (t=2.74, d.f. 11, P<0.05); in flatter drier habitats the proportion of burrows that led to a nest was 0.85 (0.74–0.96), in steeper wetter habitats this decreased to 0.64 (0.50–0.78). We used a digital elevation model to calculate true area rather than planar area for the two habitat types on the main island of Bartolome, and charts to calculate planar area for the remainder of the archipelago. There were 1.35 (1.15–1.54) million pairs of blue petrels and 99,000 (65,000–134,000) pairs of common diving petrels on the archipelago. These are similar figures to those from the only previous estimate, made in 1980. We found breeding sooty shearwaters for the first time, and estimated a population of several thousand pairs. We emphasise the facility of distance sampling as an unbiased technique with practical advantages over commonly used area search methods for monitoring populations of burrowing seabirds. These advantages include increased survey efficiency allowing a larger sample size for a given effort and a correspondingly tighter estimation of density.     

Capturing the essence of a metabolic network: A flux balance analysis approach

As genome-scale metabolic reconstructions emerge, tools to manage their size and complexity will be increasingly important. Flux balance analysis (FBA) is a constraint-based approach widely used to study the metabolic capabilities of cellular or subcellular systems. FBA problems are highly underdetermined and many different phenotypes can satisfy any set of constraints through which the metabolic system is represented.Two of the main concerns in FBA are exploring the space of solutions for a given metabolic network and finding a specific phenotype which is representative for a given task such as maximal growth rate. Here, we introduce a recursive algorithm suitable for overcoming both of these concerns. The method proposed is able to find the alternate optimal patterns of active reactions of an FBA problem and identify the minimal subnetwork able to perform a specific task as optimally as the whole.Our method represents an alternative to and an extension of other approaches conceived for exploring the space of solutions of an FBA problem. It may also be particularly helpful in defining a scaffold of reactions upon which to build up a dynamic model, when the important pathways of the system have not yet been well-defined.     

Why are (the best) women so good at chess? Participation rates and gender differences in intellectual domains

A popular explanation for the small number of women at the top level of intellectually demanding activities from chess to science appeals to biological differences in the intellectual abilities of men and women. An alternative explanation is that the extreme values in a large sample are likely to be greater than those in a small one. Although the performance of the 100 best German male chess players is better than that of the 100 best German women, we show that 96 per cent of the observed difference would be expected given the much greater number of men who play chess. There is little left for biological or cultural explanations to account for. In science, where there are many more male than female participants, this statistical sampling explanation, rather than differences in intellectual ability, may also be the main reason why women are under-represented at the top end.