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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Thalamocortical synchronization and cognition: implications for schizophrenia?

Cognitive deficits are a core dysfunction in schizophrenia. In this issue of Neuron, Parnaudeau et al. (2013) investigated synchronization in thalamocortical pathways in an animal model to address the disconnection between brain regions as a mechanism for working memory impairments in the disorder.implicated dysfunctional neural oscillations in the explanation of cognitive deficits and certain clinical symptoms of schizophrenia. Specifically, we will focus on findings that have examined neural oscillations during 1) perceptual processing, 2) working memory and executive processes and 3) spontaneous activity. The importance of the development of paradigms suitable for human and animal models is discussed as well as the search for mechanistic explanation for oscillatory dysfunctions

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

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

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

Two-photon optics of Bessel-Gaussian modes

In this paper we consider geometrical two-photon optics of Bessel-Gaussian modes generated in spontaneous parametric down-conversion of a Gaussian pump beam. We provide a general theoretical expression for the orbital angular momentum (OAM) spectrum and Schmidt number in this basis and show how this may be varied by control over the radial degree of freedom, a continuous parameter in Bessel-Gaussian modes. As a test we first implement a back-projection technique to classically predict, by experiment, the quantum correlations for Bessel-Gaussian modes produced by three holographic masks, a blazed axicon, binary axicon and a binary Bessel function. We then proceed to test the theory on the down-converted photons using the binary Bessel mask. We experimentally quantify the number of usable OAM modes and confirm the theoretical prediction of a flattening in the OAM spectrum and a concomitant increase in the OAM bandwidth. The results have implications for the control of dimensionality in quantum states.Comment: 8 pages, 10 figure

The ecology, biogeography, history and future of two globally important weeds : Cardiospermum halicacabum Linn. and C. grandiflorum Sw.

Members of the balloon vine genus, Cardiospermum, have been extensively moved around the globe as medicinal and horticultural species, two of which are now widespread invasive species; C. grandiflorum and C. halicacabum. A third species, C. corindum, may also have significant invasion potential. However, in some regions the native status of these species is not clear, hampering management. For example, in South Africa it is unknown whether C. halicacabum and C. corindum are native, and this is a major constraint to on-going biological control programmes against invasive C. grandiflorum. We review the geography, biology and ecology of selected members of the genus with an emphasis on the two most widespread invaders, C. halicacabum and C. grandiflorum. Specifically, we use molecular data to reconstruct a phylogeny of the group in order to shed light on the native ranges of C. halicacabum and C. corindum in southern Africa. Phylogenetic analyses indicate that southern African accessions of these species are closely related to South American taxa indicating human-mediated introduction and/or natural long distance dispersal. Then, on a global scale we use species distribution modelling to predict potential suitable climate regions where these species are currently absent. Native range data were used to test the accuracy with which bioclimatic modelling can identify the known invasive ranges of these species. Results show that Cardiospermum species have potential to spread further in already invaded or introduced regions in Australia, Africa and Asia, underlining the importance of resolving taxonomic uncertainties for future management efforts. Bioclimatic modelling predicts Australia to have highly favourable environmental conditions for C. corindum and therefore vigilance against this species should be high. Species distribution modelling showed that native range data over fit predicted suitable ranges, and that factors other than climate influence establishment potential. This review opens the door to better understand the global biogeography of the genus Cardiospermum, with direct implications for management, while also highlighting gaps in current research