Controlled DNA compaction within chromatin: the tail-bridging effect

We study the mechanism underlying the attraction between nucleosomes, the fundamental packaging units of DNA inside the chromatin complex. We introduce a simple model of the nucleosome, the eight-tail colloid, consisting of a charged sphere with eight oppositely charged, flexible, grafted chains that represent the terminal histone tails. We demonstrate that our complexes are attracted via the formation of chain bridges and that this attraction can be tuned by changing the fraction of charged monomers on the tails. This suggests a physical mechanism of chromatin compaction where the degree of DNA condensation can be controlled via biochemical means, namely the acetylation and deacetylation of lysines in the histone tails.Comment: 4 pages, 5 figures, submitte

Rate- and State-Dependent Friction Law and Statistical Properties of Earthquakes

In order to clarify how the statistical properties of earthquakes depend on the constitutive law characterizing the stick-slip dynamics, we make an extensive numerical simulation of the one-dimensional spring-block model with the rate- and state-dependent friction law. Both the magnitude distribution and the recurrence-time distribution are studied with varying the constitutive parameters characterizing the model. While a continuous spectrum of seismic events from smaller to larger magnitudes is obtained, earthquakes described by this model turn out to possess pronounced ``characteristic'' features.Comment: Minor revisions are made in the text and in the figures. Accepted for publication in Europhys. Letter

Crystal-like high frequency phonons in the amorphous phases of solid water

The high frequency dynamics of low- (LDA) and high-density amorphous-ice (HDA) and of cubic ice (I_c) has been measured by inelastic X-ray Scattering (IXS) in the 1-15 nm^{-1} momentum transfer (Q) range. Sharp phonon-like excitations are observed, and the longitudinal acoustic branch is identified up to Q = 8nm^{-1} in LDA and I_c and up to 5nm^{-1} in HDA. The narrow width of these excitations is in sharp contrast with the broad features observed in all amorphous systems studied so far. The "crystal-like" behavior of amorphous ices, therefore, implies a considerable reduction in the number of decay channels available to sound-like excitations which is assimilated to low local disorder.Comment: 4 pages, 3 figure

A combined XAS and XRD Study of the High-Pressure Behaviour of GaAsO4 Berlinite

Combined X-ray absorption spectroscopy (XAS) and X-ray diffraction (XRD) experiments have been carried out on GaAsO4 (berlinite structure) at high pressure and room temperature. XAS measurements indicate four-fold to six-fold coordination changes for both cations. The two local coordination transformations occur at different rates but appear to be coupled. A reversible transition to a high pressure crystalline form occurs around 8 GPa. At a pressure of about 12 GPa, the system mainly consists of octahedral gallium atoms and a mixture of arsenic in four-fold and six-fold coordinations. A second transition to a highly disordered material with both cations in six-fold coordination occurs at higher pressures and is irreversible.Comment: 8 pages, 5 figures, LaTeX2

Mitochondrial peroxiredoxin functions as crucial chaperone reservoir in Leishmania infantum

Cytosolic eukaryotic 2-Cys-peroxiredoxins have been widely reported to act as dual-function proteins, either detoxifying reactive oxygen species or acting as chaperones to prevent protein aggregation. Several stimuli, including peroxide-mediated sulfinic acid formation at the active site cysteine, have been proposed to trigger the chaperone activity. However, the mechanism underlying this activation and the extent to which the chaperone function is crucial under physiological conditions in vivo remained unknown. Here we demonstrate that in the vector-borne protozoan parasite Leishmania infantum, mitochondrial peroxiredoxin (Prx) exerts intrinsic ATP-independent chaperone activity, protecting a wide variety of different proteins against heat stress-mediated unfolding in vitro and in vivo. Activation of the chaperone function appears to be induced by temperature-mediated restructuring of the reduced decamers, promoting binding of unfolding client proteins in the center of Prx's ringlike structure. Client proteins are maintained in a folding-competent conformation until restoration of nonstress conditions, upon which they are released and transferred to ATP-dependent chaperones for refolding. Interference with client binding impairs parasite infectivity, providing compelling evidence for the in vivo importance of Prx's chaperone function. Our results suggest that reduced Prx provides a mitochondrial chaperone reservoir, which allows L. infantum to deal successfully with protein unfolding conditions during the transition from insect to the mammalian hosts and to generate viable parasites capable of perpetuating infection.We thank Frederico Silva for help with size-exclusion chromatography experiments, and Ana G. Gomes-Alves and Ricardo Silva for constructing the pSSU-PHLEO-infantum-MTS.His.THR-mTXNPx plasmid. This work was supported by National Institutes of Health Grant GM065318 (to U.J.) and Project "NORTE-07-0124-FEDER-000002-Host-Pathogen Interactions" cofunded by Programa Operacional Regional do Norte under the Quadro de Referencia Estrategico Nacional, through Fundo Europeu de Desenvolvimento Regional, and by the Portuguese Foundation for Science and Technology (FCT) (A.M.T.). F.T. and H.C. were supported by Portuguese FCT Fellowships SFRH/BD/70438/2010 and SFRH/BPD/80836/2011, respectively

Rap1-mediated nuclear factor-kappaB (NF-κB) activity regulates the paracrine capacity of mesenchymal stem cells in heart repair following infarction

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