Developmental constraints on vertebrate genome evolution

Constraints in embryonic development are thought to bias the direction of evolution by making some changes less likely, and others more likely, depending on their consequences on ontogeny. Here, we characterize the constraints acting on genome evolution in vertebrates. We used gene expression data from two vertebrates: zebrafish, using a microarray experiment spanning 14 stages of development, and mouse, using EST counts for 26 stages of development. We show that, in both species, genes expressed early in development (1) have a more dramatic effect of knock-out or mutation and (2) are more likely to revert to single copy after whole genome duplication, relative to genes expressed late. This supports high constraints on early stages of vertebrate development, making them less open to innovations (gene gain or gene loss). Results are robust to different sources of data-gene expression from microarrays, ESTs, or in situ hybridizations; and mutants from directed KO, transgenic insertions, point mutations, or morpholinos. We determine the pattern of these constraints, which differs from the model used to describe vertebrate morphological conservation ("hourglass" model). While morphological constraints reach a maximum at mid-development (the "phylotypic" stage), genomic constraints appear to decrease in a monotonous manner over developmental time

Simulation of neutrophil motion and deformation: influence of rheology and flow configuration

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Strain versus stress in a model granular material: a Devil's staircase

The series of equilibrium states reached by disordered packings of rigid, frictionless discs in two dimensions, under gradually varying stress, are studied by numerical simulations. Statistical properties of trajectories in configuration space are found to be independent of specific assumptions ruling granular dynamics, and determined by geometry only. A monotonic increase in some macroscopic loading parameter causes a discrete sequence of rearrangements. For a biaxial compression, we show that, due to the statistical importance of such events of large magnitudes, the dependence of the resulting strain on stress direction is a Levy flight in the thermodynamic limit.Comment: REVTeX, 4 pages, 5 included PostScript figures. New version altered throughout text, very close to published pape

Turbulent-like fluctuations in quasistatic flow of granular media

We analyze particle velocity fluctuations in a simulated granular system subjected to homogeneous quasistatic shearing. We show that these fluctuations share the following scaling characteristics of fluid turbulence in spite of their different physical origins: 1) Scale-dependent probability distribution with non-Guassian broadening at small time scales; 2) Power-law spectrum, reflecting long-range correlations and the self-affine nature of the fluctuations; 3) Superdiffusion with respect to the mean background flow

Dynamic glass transition: bridging the gap between mode-coupling theory and the replica approach

We clarify the relation between the ergodicity breaking transition predicted by mode-coupling theory and the so-called dynamic transition predicted by the static replica approach. Following Franz and Parisi [Phys. Rev. Lett. 79, 2486 (1997)], we consider a system of particles in a metastable state characterized by non-trivial correlations with a quenched configuration. We show that the assumption that in a metastable state particle currents vanish leads to an expression for the replica off-diagonal direct correlation function in terms of a replica off-diagonal static four-point correlation function. A factorization approximation for this function results in an approximate closure for the replica off-diagonal direct correlation function. The replica off-diagonal Ornstein-Zernicke equation combined with this closure coincides with the equation for the non-ergodicity parameter derived using the mode-coupling theory.Comment: revised version; to be published in EP

Internal avalanches in models of granular media

We study the phenomenon of internal avalanching within the context of recently introduced lattice models of granular media. The avalanche is produced by pulling out a grain at the base of the packing and studying how many grains have to rearrange before the packing is once more stable. We find that the avalanches are long-ranged, decaying as a power-law. We study the distriution of avalanches as a function of the density of the packing and find that the avalanche distribution is a very sensitive structural probe of the system.Comment: 12 pages including 9 eps figures, LaTeX. To appear in Fractal

Scattering by a toroidal coil

In this paper we consider the Schr\"odinger operator in ${\mathbb R}^3$ with a long-range magnetic potential associated to a magnetic field supported inside a torus ${\mathbb{T}}$. Using the scheme of smooth perturbations we construct stationary modified wave operators and the corresponding scattering matrix $S(\lambda)$. We prove that the essential spectrum of $S(\lambda)$ is an interval of the unit circle depending only on the magnetic flux $\phi$ across the section of $\mathbb{T}$. Additionally we show that, in contrast to the Aharonov-Bohm potential in ${\mathbb{R}}^2$, the total scattering cross-section is always finite. We also conjecture that the case treated here is a typical example in dimension 3.Comment: LaTeX2e 17 pages, 1 figur

Age-dependent gain of alternative splice forms and biased duplication explain the relation between splicing and duplication.

We analyze here the relation between alternative splicing and gene duplication in light of recent genomic data, with a focus on the human genome. We show that the previously reported negative correlation between level of alternative splicing and family size no longer holds true. We clarify this pattern and show that it is sufficiently explained by two factors. First, genes progressively gain new splice variants with time. The gain is consistent with a selectively relaxed regime, until purifying selection slows it down as aging genes accumulate a large number of variants. Second, we show that duplication does not lead to a loss of splice forms, but rather that genes with low levels of alternative splicing tend to duplicate more frequently. This leads us to reconsider the role of alternative splicing in duplicate retention

Equilibrium onions?

We demonstrate the possibility of a stable equilibrium multi-lamellar ("onion") phase in pure lamellar systems (no excess solvent) due to a sufficiently negative Gaussian curvature modulus. The onion phase is stabilized by non-linear elastic moduli coupled to a polydisperse size distribution (Apollonian packing) to allow space-filling without appreciable elastic distortion. This model is compared to experiments on copolymer-decorated lamellar surfactant systems, with reasonable qualitative agreement