9,508 research outputs found
Differential expression of pattern recognition receptors during the development of foetal sheep
Spin and orbital Hall effects for diffracting optical beams in gradient-index media
We examine the evolution of paraxial beams carrying intrinsic spin and
orbital angular momenta (AM) in gradient-index media. A parabolic-type equation
is derived which describes the beam diffraction in curvilinear coordinates
accompanying the central ray. The center of gravity of the beam experiences
transverse AM-dependent deflections -- the spin and orbital Hall effects. The
spin Hall effect generates a transverse translation of the beam as a whole, in
precise agreement with recent geometrical optics predictions. At the same time,
the orbital Hall effect is significantly affected by the diffraction in the
inhomogeneous medium and is accompanied by changes in the intrinsic orbital AM
and deformations of the beam.Comment: 4 pages, 2 figures, to appear in Phys. Rev.
Coexistence in a One-Dimensional Cyclic Dominance Process
Cyclic (rock-paper-scissors-type) population models serve to mimic complex
species interactions. Focusing on a paradigmatic three-species model with
mutations in one dimension, we observe an interplay between equilibrium and
non-equilibrium processes in the stationary state. We exploit these insights to
obtain asymptotically exact descriptions of the emerging reactive steady state
in the regimes of high and low mutation rates. The results are compared to
stochastic lattice simulations. Our methods and findings are potentially
relevant for the spatio-temporal evolution of other non-equilibrium stochastic
processes.Comment: 4 pages, 4 figures and 2 pages of Supplementary Material. To appear
in Physical Review
Spatial fluctuations of a surviving particle in the trapping reaction
We consider the trapping reaction, , where and particles
have a diffusive dynamics characterized by diffusion constants and .
The interaction with particles can be formally incorporated in an effective
dynamics for one particle as was recently shown by Bray {\it et al}. [Phys.
Rev. E {\bf 67}, 060102 (2003)]. We use this method to compute, in space
dimension , the asymptotic behaviour of the spatial fluctuation,
, for a surviving particle in the perturbative regime,
, for the case of an initially uniform distribution of
particles. We show that, for , with
. By contrast, the fluctuations of paths constrained to return to
their starting point at time grow with the larger exponent 1/3. Numerical
tests are consistent with these predictions.Comment: 10 pages, 5 figure
Survival probabilities in the double trapping reaction A +B -> B, B + C -> C
We consider the double trapping reaction A + B -> B, B + C -> C in one
dimension. The survival probability of a given A particle is calculated under
various conditions on the diffusion constants of the reactants, and on the
ratio of initial B and C particle densities. The results are of more general
form than those obtained in previous work on the problem.Comment: 5 page
DNA-encoded nucleosome occupancy is associated with transcription levels in the human malaria parasite Plasmodium falciparum.
BackgroundIn eukaryotic organisms, packaging of DNA into nucleosomes controls gene expression by regulating access of the promoter to transcription factors. The human malaria parasite Plasmodium falciparum encodes relatively few transcription factors, while extensive nucleosome remodeling occurs during its replicative cycle in red blood cells. These observations point towards an important role of the nucleosome landscape in regulating gene expression. However, the relation between nucleosome positioning and transcriptional activity has thus far not been explored in detail in the parasite.ResultsHere, we analyzed nucleosome positioning in the asexual and sexual stages of the parasite's erythrocytic cycle using chromatin immunoprecipitation of MNase-digested chromatin, followed by next-generation sequencing. We observed a relatively open chromatin structure at the trophozoite and gametocyte stages, consistent with high levels of transcriptional activity in these stages. Nucleosome occupancy of genes and promoter regions were subsequently compared to steady-state mRNA expression levels. Transcript abundance showed a strong inverse correlation with nucleosome occupancy levels in promoter regions. In addition, AT-repeat sequences were strongly unfavorable for nucleosome binding in P. falciparum, and were overrepresented in promoters of highly expressed genes.ConclusionsThe connection between chromatin structure and gene expression in P. falciparum shares similarities with other eukaryotes. However, the remarkable nucleosome dynamics during the erythrocytic stages and the absence of a large variety of transcription factors may indicate that nucleosome binding and remodeling are critical regulators of transcript levels. Moreover, the strong dependency between chromatin structure and DNA sequence suggests that the P. falciparum genome may have been shaped by nucleosome binding preferences. Nucleosome remodeling mechanisms in this deadly parasite could thus provide potent novel anti-malarial targets
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