Descripción: Genomes contain the necessary information to ensure that genes are expressed in the right place, at the right time, and with the proper rate. Metazoan developmental genes often possess long stretches of DNA flanking their coding sequences and/or large introns which contain elements that influence gene expression. Most of these regulatory elements are relatively small and can be studied in isolation. For example, transcriptional enhancers, the elements that generate the expression pattern of a gene, have been traditionally studied with reporter constructs in transgenic animals. These studies have provided and will provide invaluable insights into enhancer evolution and function. However, this experimental approach has its limits; often, enhancer elements do not faithfully recapitulate native expression patterns. This fact suggests that additional information in cis-regulatory regions modulates the activity of enhancers and other regulatory elements. Indeed, recent studies have revealed novel functional aspects at the level of whole cis-regulatory regions. First, the discovery of "shadow enhancers." Second, the ubiquitous interactions between cis-regulatory elements. Third, the notion that some cis-regulatory regions may not function in a modular manner. Last, the effect of chromatin conformation on cis-regulatory activity. In this article, I describe these recent findings and discuss open questions in the field. © 2012 Wiley Periodicals, Inc.

Descripción: Using Advanced Composition Explorer (ACE) in situ data we identify and describe an interplanetary magnetic cloud (MC) observed near Earth on 13 April 2006. We also use multi-instrument and multi-wavelength observations from the Solar and Heliospheric Observatory (SOHO), the Transition Region and Coronal Explorer (TRACE) and ground-based solar observatories to determine the solar source of this magnetic cloud. A launch window for the MC between 9 and 11 April 2006 was estimated from the propagation time of the ejecta observed near Earth. A number of large active regions (ARs) were present on the Sun during this period, which were initially considered to be the most likely candidate source regions of the MC. However, it was determined that the solar source of the MC was a small, spotless active region observed in the Northern Hemisphere. Following an eruption from this region on 11 April 2006, the ACE spacecraft detected, 59 h later, the passage of the MC, preceded by the arrival of a weak, forward fast shock. The link between the eruption in this active region and the interplanetary MC is supported by several pieces of evidence, including the location of the solar source near to the disk centre and to the east of the central meridian (in agreement with the spacecraft trajectory through the western leg of the magnetic cloud), the propagation time of the ejecta, the agreement between the amount of flux in the magnetic cloud and in the active region, and the agreement between the signs of helicity of the magnetic cloud and the active region (which differs from the sign of helicity of each of the other active regions on the Sun at this time). In addition, the active region is located on the boundary of a coronal hole, and a high speed solar wind stream originating from this region is observed near Earth shortly after the passage of the magnetic cloud.

Descripción: We obtain a black hole solution in the Einstein-Gauss-Bonnet theory for the string cloud model in a five-dimensional spacetime. We analyze the event horizons and naked singularities. Later, we compute the Hawking temperature TH, the specific heat C, the entropy S, and the Helmholtz free energy F of the black hole. The entropy was computed using the Wald formulation. In addition, the quantum correction to the Wald's entropy is considered for the string cloud source. We mainly explore the thermodynamical global and local stability of the system with vanishing or non-vanishing cosmological constant. The global thermodynamic phase structure indicates that the Hawking-Page transition is achieved for this model. Further, we observe that there exist stable black holes with small radii and that these regions are enlarged when choosing small values of the string cloud density and of the Gauss-Bonnet parameter. Besides, the rate of evaporation for these black holes are studied, determining whether the evaporation time is finite or not. Then, we concentrate on the dynamical stability of the system, studying the effective potential for s-waves propagating on the string cloud background. © 2010 Elsevier B.V. All rights reserved.

Descripción: We study the coupling between the hot plasma confined in a coronal loop and the much colder chromospheric plasma at the footpoints. Considering the coronal heating rate as a control parameter, we find that the static equilibrium becomes unstable for heating rates below a critical value, giving rise to the appearance of a stable limit cycle. Starting from the hydrodynamic equations, we derive a model which generalizes the analysis of Kuin and Martens and consistently takes into account the condensation-evaporation process. In this paper, we linearize our equations in order to find the bifurcation point where the stability of the static equilibrium is lost. We also show that this model can provide a natural explanation for the excess widths of EUV spectral lines formed in the transition region. Moreover, we can predict the observed reduction in the broadening of these lines when they form in certain active regions, like quiescent prominences or sunspots.

Descripción: Using molecular dynamics experiments, we analyze equilibrium and dynamical characteristics related to the solvation of excess protons in water-acetone mixtures. Our approach is based on the implementation of an extended valence-bond Hamiltonian, which incorporates translocation of the excess charge between neighboring water molecules. Different mixtures have been analyzed, starting from the pure water case down to solutions with a water molar fraction x w 0.25. In all cases, we have verified that the structure of the first solvation shell of the H 3 O moiety remains practically unchanged, compared to the one observed in pure water. This shell is composed by three water molecules acting as hydrogen bond acceptors, with no evidence of hydrogen bond donor-like connectivity. Moreover, the increment in the acetone concentration leads to a gradual stabilization of Eigen-like [H 3O·(H 2O) 3] configurations, in detriment of Zundel-like [H·(H 2O) 2] ones. Rates of proton transfer and proton diffusion coefficients have been recorded at various water-acetone relative concentrations. In both cases, we have found a transition region, in the vicinity of x w ∼ 0.8, where the concentration dependences of the two magnitudes change at a quantitative level. A crude estimate shows that, at this tagged concentration, the volumes occupied by the two solvents become comparable. The origins of this transition separating water-rich from acetone-rich realms is rationalized in terms of modifications operated in the nearby, second solvation shell, which in the latter solutions, normally includes at least, one acetone molecule. Our results would suggest that one possible mechanism controlling the proton transfer in acetone-rich solutions is the exchange of one of these tagged acetone molecules, by nearby water ones. This exchange would give rise to Zundel-like structures, exhibiting a symmetric, first solvation shell composed exclusively by water molecules, and would facilitate the transfer between neighboring water molecules along the resonant complex. © 2012 American Institute of Physics.

Descripción: The thermohaline structure across the tidal fronts of the continental shelf off Patagonia is analyzed using historical and recent summer hydrographic sections. The near-summer tidal front location is determined on the basis of the magnitude of vertical stratification of the water column as measured by the Simpson parameter. Sea surface and air CO2 partial pressures based on data from eleven transects collected in summer and fall from 2000 to 2004 are used to estimate CO2 fluxes over the shelf. The near-shore waters are a source of CO2 to the atmosphere while the midshelf region is a CO2 sink. The transition between source and sink regions closely follows the location of tidal fronts, suggesting a link between vertical stratification of the water column and the regional CO2 balance. The highest surface values of Chl a are associated with the strongest CO2 sinks. The colocation of lowest CO2 partial pressure (pCO2) and highest Chl a suggests that phytoplankton blooms on the stratified side of the fronts draw the ocean's CO2 to very low levels. The mean shelf sea-air difference in pCO2 (ΔpCO2) is -24 μatm and rises to -29 μatm if the shelf break front is included. Peaks in ΔpCO2 of -110 μatm, among the highest observed in the global ocean, are observed. The estimated summer mean CO2 flux over the shelf is -4.4 mmol m-2 d-1 and rises to -5.7 mmol m-2 d-1 when the shelf break area is taken into account. Thus, during the warm season the shelf off Patagonia is a significant atmospheric CO2 sink. Copyright 2005 by the American Geophysical Union.

Descripción: Working within the domain of inviscid incompressible MHD theory, we found that a tangential discontinuity (TD) separating two uniform regions of different density, velocity and magnetic field may be Kelvin-Helmholtz (KH) stable and yet a study of a transition between the same constant regions given by a continuous velocity profile shows the presence of the instability with significant growth rates. Since the cause of the instability stems from the velocity gradient, and since a TD may be considered as the ultimate limit of such gradient, the statement comes as a surprise. In fact, a long wavelength (λ) boundary for the KH instability does not exist in ordinary liquids being instead a consequence of the presence of magnetic shear, a possibility that has passed unnoticed in the literature. It is shown that KH modes of a magnetic field configuration with constant direction do not have the long A boundary. A theoretical explanation of this feature and examples of the violation of the TD stability condition are given using a model that can be solved in closed form. Stability diagrams in the (kd, MA) plane are given (where kd = 2πd/λ, 2d is the velocity gradient length scale, and MA is the Alfvénic Mach number) that show both the well-known limit at small λs and the boundary for large but finite As noted here. Consequences of this issue are relevant for stability studies of the dayside magnetopause as the stability condition for a TD should be used with care in data analysis work.

Descripción: Background. Micro RNAs (miRs) constitute a large group of endogenous small RNAs that have crucial roles in many important plant functions. Virus infection and transgenic expression of viral proteins alter accumulation and activity of miRs and so far, most of the published evidence involves post-transcriptional regulations. Results. Using transgenic plants expressing a reporter gene under the promoter region of a characterized miR (P-miR164a), we monitored the reporter gene expression in different tissues and during Arabidopsis development. Strong expression was detected in both vascular tissues and hydathodes. P-miR164a activity was developmentally regulated in plants with a maximum expression at stages 1.12 to 5.1 (according to Boyes, 2001) along the transition from vegetative to reproductive growth. Upon quantification of P-miR164a-derived GUS activity after Tobacco mosaic virus Cg or Oilseed rape mosaic virus (ORMV) infection and after hormone treatments, we demonstrated that ORMV and gibberellic acid elevated P-miR164a activity. Accordingly, total mature miR164, precursor of miR164a and CUC1 mRNA (a miR164 target) levels increased after virus infection and interestingly the most severe virus (ORMV) produced the strongest promoter induction. Conclusion. This work shows for the first time that the alteration of miR pathways produced by viral infections possesses a transcriptional component. In addition, the degree of miR alteration correlates with virus severity since a more severe virus produces a stronger P-miR164a induction. © 2009 Bazzini et al; licensee BioMed Central Ltd.