Protein Mobility in the Cytoplasm of Escherichia coli

The rate of protein diffusion in bacterial cytoplasm may constrain a variety of cellular functions and limit the rates of many biochemical reactions in vivo. In this paper, we report noninvasive measurements of the apparent diffusion coefficient of green fluorescent protein (GFP) in the cytoplasm of Escherichia coli. These measurements were made in two ways: by photobleaching of GFP fluorescence and by photoactivation of a red-emitting fluorescent state of GFP (M. B. Elowitz, M. G. Surette, P. E. Wolf, J. Stock, and S. Leibler, Curr. Biol. 7:809-812, 1997). The apparent diffusion coefficient, Da, of GFP in E. coli DH5alpha was found to be 7.7 ± 2.5 µm^2/s. A 72-kDa fusion protein composed of GFP and a cytoplasmically localized maltose binding protein domain moves more slowly, with Da of 2.5 ± 0.6 µm^2/s. In addition, GFP mobility can depend strongly on at least two factors: first, Da is reduced to 3.6 ± 0.7 µm^2/s at high levels of GFP expression; second, the addition to GFP of a small tag consisting of six histidine residues reduces Da to 4.0 ± 2.0 µm^2/s. Thus, a single effective cytoplasmic viscosity cannot explain all values of Da reported here. These measurements have implications for the understanding of intracellular biochemical networks

Non-stationary patterns of isolation-by-distance: inferring measures of local genetic differentiation with Bayesian kriging

Patterns of isolation-by-distance arise when population differentiation increases with increasing geographic distances. Patterns of isolation-by-distance are usually caused by local spatial dispersal, which explains why differences of allele frequencies between populations accumulate with distance. However, spatial variations of demographic parameters such as migration rate or population density can generate non-stationary patterns of isolation-by-distance where the rate at which genetic differentiation accumulates varies across space. To characterize non-stationary patterns of isolation-by-distance, we infer local genetic differentiation based on Bayesian kriging. Local genetic differentiation for a sampled population is defined as the average genetic differentiation between the sampled population and fictive neighboring populations. To avoid defining populations in advance, the method can also be applied at the scale of individuals making it relevant for landscape genetics. Inference of local genetic differentiation relies on a matrix of pairwise similarity or dissimilarity between populations or individuals such as matrices of FST between pairs of populations. Simulation studies show that maps of local genetic differentiation can reveal barriers to gene flow but also other patterns such as continuous variations of gene flow across habitat. The potential of the method is illustrated with 2 data sets: genome-wide SNP data for human Swedish populations and AFLP markers for alpine plant species. The software LocalDiff implementing the method is available at http://membres-timc.imag.fr/Michael.Blum/LocalDiff.htmlComment: In press, Evolution 201

The mean, variance and limiting distribution of two statistics sensitive to phylogenetic tree balance

For two decades, the Colless index has been the most frequently used statistic for assessing the balance of phylogenetic trees. In this article, this statistic is studied under the Yule and uniform model of phylogenetic trees. The main tool of analysis is a coupling argument with another well-known index called the Sackin statistic. Asymptotics for the mean, variance and covariance of these two statistics are obtained, as well as their limiting joint distribution for large phylogenies. Under the Yule model, the limiting distribution arises as a solution of a functional fixed point equation. Under the uniform model, the limiting distribution is the Airy distribution. The cornerstone of this study is the fact that the probabilistic models for phylogenetic trees are strongly related to the random permutation and the Catalan models for binary search trees.Comment: Published at http://dx.doi.org/10.1214/105051606000000547 in the Annals of Applied Probability (http://www.imstat.org/aap/) by the Institute of Mathematical Statistics (http://www.imstat.org

Modular properties of two-loop maximal supergravity and connections with string theory

The low-momentum expansion of the two-loop four-graviton scattering amplitude in eleven-dimensional supergravity compactified on a circle and a two-torus is considered up to terms of order S^6R^4 (where S is a Mandelstam invariant and R is the linearized Weyl curvature). In the case of the toroidal compactification the coefficient of each term in the low energy expansion is generically a sum of a number of SL(2,Z)-invariant functions of the complex structure of the torus. Each such function satisfies a separate Poisson equation on moduli space with particular source terms that are bilinear in coefficients of lower order terms, consistent with qualitative arguments based on supersymmetry. Comparison is made with the low-energy expansion of type II string theories in ten and nine dimensions. Although the detailed behaviour of the string amplitude is not generally expected to be reproduced by supergravity perturbation theory to all orders, for the terms considered here we find agreement with direct results from string perturbation theory. These results point to a fascinating pattern of interrelated Poisson equations for the IIB coefficients at higher orders in the momentum expansion which may have a significance beyond the particular methods by which they were motivated.Comment: 79 pages, 4 figures. Latex format. v2: Small corrections made, version to appear in JHE

Government Solvency: Revisiting some EMU Countries

Corsetti and Roubini (1991) reported that the government finances of Greece, Ireland, Italy and the Netherlands (now all EMU countries) did not satisfy the intertemporal budget constraint (IBC). We re-examine this issue by utilizing a new empirical approach and extended data set. Structural shifts, an issue which Corsetti and Roubini were unable to address due to the lack of suitable econometric methods, are tackled. We find that: (i) multiple structural shifts, most of which correspond to important policy changes, did occur in the fiscal path of these countries; (ii) the effect of the majority of structural shifts has been to strengthen the evidence supporting IBC; and (iii) government finances of all four countries satisfy the IBC and this finding is robust to different time horizons. We also find a clear positive Maastricht effect on IBC for all countries.intertemporal budget constraints, strong and weak form sustainability, structural breaks