Induced folding in RNA recognition by Arabidopsis thaliana DCL1

DCL1 is the ribonuclease that carries out miRNA biogenesis in plants. The enzyme has two tandem double stranded RNA binding domains (dsRBDs) in its C-terminus. Here we show that the first of these domains binds precursor RNA fragments when isolated and cooperates with the second domain in the recognition of substrate RNA. Remarkably, despite showing RNA binding activity, this domain is intrinsically disordered. We found that it acquires a folded conformation when bound to its substrate, being the first report of a complete dsRBD folding upon binding. The free unfolded form shows tendency to adopt folded conformations, and goes through an unfolded bound state prior to the folding event. The significance of these results is discussed by comparison with the behavior of other dsRBDs.Fil: Suarez, Irina Paula. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Burdisso, Paula. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Benoit Matthieu P. M. H.. Institut de Biologie Structurale Jean Pierre Ebel; FranciaFil: Boisbouvier, Jerome. Institut de Biologie Structurale Jean Pierre Ebel; FranciaFil: Rasia, Rodolfo Maximiliano. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; Argentin

Cell division: a source of active stress in cellular monolayers

We introduce the notion of cell division-induced activity and show that the cell division generates extensile forces and drives dynamical patterns in cell assemblies. Extending the hydrodynamic models of lyotropic active nematics we describe turbulent-like velocity fields that are generated by the cell division in a confluent monolayer of cells. We show that the experimentally measured flow field of dividing Madin-Darby Canine Kidney (MDCK) cells is reproduced by our modeling approach. Division-induced activity acts together with intrinsic activity of the cells in extensile and contractile cell assemblies to change the flow and director patterns and the density of topological defects. Finally we model the evolution of the boundary of a cellular colony and compare the fingering instabilities induced by cell division to experimental observations on the expansion of MDCK cell cultures.Comment: Accepted Manuscript for Celebrating Soft Matter's 10th Anniversar

Axially symmetric membranes with polar tethers

Axially symmetric equilibrium configurations of the conformally invariant Willmore energy are shown to satisfy an equation that is two orders lower in derivatives of the embedding functions than the equilibrium shape equation, not one as would be expected on the basis of axial symmetry. Modulo a translation along the axis, this equation involves a single free parameter c.If c\ne 0, a geometry with spherical topology will possess curvature singularities at its poles. The physical origin of the singularity is identified by examining the Noether charge associated with the translational invariance of the energy; it is consistent with an external axial force acting at the poles. A one-parameter family of exact solutions displaying a discocyte to stomatocyte transition is described.Comment: 13 pages, extended and revised version of Non-local sine-Gordon equation for the shape of axi-symmetric membrane

Infinite Kinematic Self-Similarity and Perfect Fluid Spacetimes

Perfect fluid spacetimes admitting a kinematic self-similarity of infinite type are investigated. In the case of plane, spherically or hyperbolically symmetric space-times the field equations reduce to a system of autonomous ordinary differential equations. The qualitative properties of solutions of this system of equations, and in particular their asymptotic behavior, are studied. Special cases, including some of the invariant sets and the geodesic case, are examined in detail and the exact solutions are provided. The class of solutions exhibiting physical self-similarity are found to play an important role in describing the asymptotic behavior of the infinite kinematic self-similar models.Comment: 38 pages, 6 figures. Accepted for publication in General Relativity & Gravitatio

Ultra-shallow-marine anoxia in an Early Triassic shallow-marine clastic ramp (Spitsbergen) and the suppression of benthic radiation

Lower Triassic marine strata in Spitsbergen accumulated on a mid-to-high latitude ramp in which high-energy foreshore and shoreface facies passed offshore into sheet sandstones of probable hyperpycnite origin. More distal facies include siltstones, shales and dolomitic limestones. Carbon isotope chemostratigraphy comparison allows improved age dating of the Boreal sections and shows a significant hiatus in the upper Spathian. Two major deepening events, in earliest Griesbachian and late Smithian time, are separated by shallowing-upwards trends that culminated in the Dienerian and Spathian substages. The redox record, revealed by changes in bioturbation, palaeoecology, pyrite framboid content and trace metal concentrations, shows anoxic phases alternating with intervals of better ventilation. Only Dienerian–early Smithian time witnessed persistent oxygenation that was sufficient to support a diverse benthic community. The most intensely anoxic, usually euxinic, conditions are best developed in offshore settings, but at times euxinia also developed in upper offshore settings where it is even recorded in hyperpycnite and storm-origin sandstone beds: an extraordinary facet of Spitsbergen's record. The euxinic phases do not track relative water depth changes. For example, the continuous shallowing upwards from the Griesbachian to lower Dienerian was witness to several euxinic phases separated by intervals of more oxic, bioturbated sediments. It is likely that the euxinia was controlled by climatic oscillations rather than intra-basinal factors. It remains to be seen if all the anoxic phases found in Spitsbergen are seen elsewhere, although the wide spread of anoxic facies in the Smithian/Spathian boundary interval is clearly a global event

An abrupt extinction in the Middle Permian (Capitanian) of the Boreal Realm (Spitsbergen) and its link to anoxia and acidification

The controversial Capitanian (Middle Permian, 262 Ma) extinction event is only known from equatorial latitudes, and consequently its global extent is poorly resolved. We demonstrate that there were two, severe extinctions amongst brachiopods in northern Boreal latitudes (Spitsbergen) in the Middle to Late Permian, separated by a recovery phase. New age dating of the Spitsbergen strata (belonging to the Kapp Starostin Formation), using strontium isotopes and d13C trends and comparison with better-dated sections in Greenland, suggests that the first crisis occurred in the Capitanian. This age assignment indicates that this Middle Permian extinction is manifested at higher latitudes. Redox proxies (pyrite framboids and trace metals) show that the Boreal crisis coincided with an intensification of oxygen depletion, implicating anoxia in the extinction scenario. The widespread and near-total loss of carbonates across the Boreal Realm also suggests a role for acidification in the crisis. The recovery interval saw the appearance of new brachiopod and bivalve taxa alongside survivors, and an increased mollusk dominance, resulting in an assemblage reminiscent of younger Mesozoic assemblages. The subsequent end-Permian mass extinction terminated this Late Permian radiation

Geometrical Frustration and Static Correlations in Hard-Sphere Glass Formers

We analytically and numerically characterize the structure of hard-sphere fluids in order to review various geometrical frustration scenarios of the glass transition. We find generalized polytetrahedral order to be correlated with increasing fluid packing fraction, but to become increasingly irrelevant with increasing dimension. We also find the growth in structural correlations to be modest in the dynamical regime accessible to computer simulations.Comment: 21 pages; part of the "Special Topic Issue on the Glass Transition

Observations of the Sunyaev-Zel'dovich effect at high angular resolution towards the galaxy clusters A665, A2163 and CL0016+16

We report on the first observation of the Sunyaev-Zel'dovich effect with the Diabolo experiment at the IRAM 30 metre telescope. A significant brightness decrement is detected in the direction of three clusters (Abell 665, Abell 2163 and CL0016+16). With a 30 arcsecond beam and 3 arcminute beamthrow, this is the highest angular resolution observation to date of the SZ effect.Comment: 23 pages, 8 figures, 6 tables, accepted to New Astronom

Signature of small rings in the Raman spectra of normal and compressed amorphous silica: A combined classical and ab initio study

We calculate the parallel (VV) and perpendicular (VH) polarized Raman spectra of amorphous silica. Model SiO2 glasses, uncompressed and compressed, were generated by a combination of classical and ab initio molecular-dynamics simulations and their dynamical matrices were computed within the framework of the density functional theory. The Raman scattering intensities were determined using the bond-polarizability model and a good agreement with experimental spectra was found. We confirm that the modes associated to the fourfold and threefold rings produce most of the Raman intensity of the D1 and D2 peaks, respectively, in the VV Raman spectra. Modifications of the Raman spectra upon compression are found to be in agreement with experimental data. We show that the modes associated to the fourfold rings still exist upon compression but do not produce a strong Raman intensity, whereas the ones associated to the threefold rings do. This result strongly suggests that the area under the D1 and D2 peaks is not directly proportional to the concentration of small rings in amorphous SiO2.Comment: 21 pages, 8 figures. Phys. Rev. B, in pres