12,213 research outputs found
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
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
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
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
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 with
a long-range magnetic potential associated to a magnetic field supported inside
a torus . Using the scheme of smooth perturbations we construct
stationary modified wave operators and the corresponding scattering matrix
. We prove that the essential spectrum of is an
interval of the unit circle depending only on the magnetic flux across
the section of . Additionally we show that, in contrast to the
Aharonov-Bohm potential in , 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
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
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
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