Description: Bromodeoxyuridine (5-bromo-2'-deoxyuridine, BrdU) is a halogenated nucleotide of low toxicity commonly used to monitor DNA replication. It is considered a valuable tool for in vitro and in vivo studies, including the detection of the small population of neural stem cells (NSC) in the mammalian brain. Here, we show that NSC grown in self-renewing conditions in vitro , when exposed to BrdU, lose the expression of stem cell markers like Nestin, Sox2 and Pax6 and undergo glial differentiation, strongly up-regulating the astrocytic marker GFAP. The onset of GFAP expression in BrdU exposed NSC was paralleled by a reduced expression of key DNA methyltransferases (DNMT) and a rapid loss of global DNA CpG methylation, as we determined by our specially developed analytic assay. Remarkably, a known DNA demethylating compound, 5-aza-2'-deoxycytidine (Decitabine), had similar effect on demethylation and differentiation of NSC. Since our key findings apply also to NSC derived from murine forebrain, our observations strongly suggest more caution in BrdU uses in stem cells research. We also propose that BrdU and its related substances may also open new opportunities for differentiation therapy in oncology.

Description: In Escherichia coli , the SeqA protein binds specifically to GATC sequences which are methylated on the A of the old strand but not on the new strand. Such hemimethylated DNA is produced by progression of the replication forks and lasts until Dam methyltransferase methylates the new strand. It is therefore believed that a region of hemimethylated DNA covered by SeqA follows the replication fork. We show that this is, indeed, the case by using global ChIP on Chip analysis of SeqA in cells synchronized regarding DNA replication. To assess hemimethylation, we developed the first genome-wide method for methylation analysis in bacteria. Since loss of the SeqA protein affects growth rate only during rapid growth when cells contain multiple replication forks, a comparison of rapid and slow growth was performed. In cells with six replication forks per chromosome, the two old forks were found to bind surprisingly little SeqA protein. Cell cycle analysis showed that loss of SeqA from the old forks did not occur at initiation of the new forks, but instead occurs at a time point coinciding with the end of SeqA-dependent origin sequestration. The finding suggests simultaneous origin de-sequestration and loss of SeqA from old replication forks.

Description: The intrusion mechanism and internal structure of sills are still under debate. We present a detailed magnetic study, including anisotropy of magnetic susceptibility and rock magnetic analyses of a Cretaceous (94 Ma), 7-m-thick sill from the Lusitanian Basin in Portugal, the Foz da Fonte sill. The results, from both the top surface and a vertical profile, allow us to propose a model for the magmatic flow pattern and sense of flow. According to their location in the vertical profile, three magnetic fabric domains are identified: (1) at the borders, qualified as chilled margins (~0–50 cm), low anisotropies suggest that low velocity gradients and heterogeneous flow paths occurred during the initial emplacement stages; (2) in the centre of the sill, where low anisotropies are observed, low shear gradients and magma displacement close to pure translation is inferred and (3) in the intermediate zones, high anisotropy values are ascribed to zones having undergone high shear gradients. The mean magnetic lineations from the top surface and basal contact indicate an almost horizontal and NW–SE orientation (azimuth: 310°) which agrees with the preferred orientation of iron oxide grain clusters and with the elongation of vesicles considered as coaxial with the magma flow direction. Moreover, the magnetic foliation planes and the lineations show both a mirror imbrication relative to the average upper and lower border surfaces of the sill, pointing to a flow direction towards the SE. Based on these results and on the interpretation of two seismic reflection lines, we show that the Cabo Raso magnetic anomaly, located 25 km to NW of the FF-sill, is associated to Cretaceous magmatic intrusions from which the sill likely originated. This tectono-magmatic setting is discussed with respect to the West Iberia Late Cretaceous magmatism, integrating magnetic anomalies, isotope chronology and tectonics.

Description: Large-scale chemical lateral heterogeneities are inferred in the Earth's lowermost mantle by seismological studies. We explore the model space of thermochemical convection that can maintain reservoirs of dense material for a long period of time, by using similar analysis in 3-D spherical geometry. In this study, we focus on the parameters thought to be important in controlling the stability and structure of primordial dense reservoirs in the lower mantle, including the chemical density contrast between the primordial dense material and the regular mantle material (buoyancy ratio), thermal and chemical viscosity contrasts, volume fraction of primordial dense material and the Clapeyron slope of the phase transition at 660 km depth. We find that most of the findings from the 3-D Cartesian study still apply to 3-D spherical cases after slight modifications. Varying buoyancy ratio leads to different flow patterns, from rapid upwelling to stable layering; and large thermal viscosity contrasts are required to generate long wavelength chemical structures in the lower mantle. Chemical viscosity contrasts in a reasonable range have a second-order role in modifying the stability of the dense anomalies. The volume fraction of the initial primordial dense material does not effect the results with large thermal viscosity contrasts, but has significant effects on calculations with intermediate and small thermal viscosity contrasts. The volume fraction of dense material at which the flow pattern changes from unstable to stable depends on buoyancy ratio and thermal viscosity contrast. An endothermic phase transition at 660 km depth acts as a ‘filter’ allowing cold slabs to penetrate while blocking most of the dense material from penetrating to the upper mantle.

Description: Theory has been long established for computing the elastic response of a spherically symmetric terrestrial planetary body to both body tide and surface loading forces. However, for a planet with laterally heterogeneous mantle structure, the response is usually computed using a fully numerical approach. In this paper, we develop a semi-analytic method based on perturbation theory to solve for the elastic response of a planetary body with lateral heterogeneities in its mantle. We present a derivation of the governing equations for our second-order perturbation method and use them to study the high-order tidal effects caused by mode coupling between degree-2 body tide forcing and the laterally heterogeneous elastic structure of the mantle. We test our method by applying it to the Moon in which small long-wavelength lateral heterogeneities are assumed to exist in the elastic moduli of the lunar mantle. The tidal response of the Moon is determined mode by mode, for lateral heterogeneities with different depth ranges within the mantle and different horizontal scales. Our perturbation method solutions are compared with numerical results, showing remarkable agreement between the two methods. We conclude that our perturbation method provides accurate results and can be adapted to address a variety of forward and inverse response problems.

Description: The Indochina block is important to our understanding of the extrusion model as a consequence of the Indo-Eurasia collision. The lithospheric structure of this block, however, remains obscured due to a lack of sufficient instrumentation for high resolution seismic imaging. We present a shear velocity model derived from Rayleigh wave phase velocity tomography using data from recently deployed seismic networks in this region. Our inversion results for lithospheric structure show strong correlations with tectonic history in this block. A prominent slow-velocity anomaly (5 per cent) is observed in northern Indochina along the Ailao Shan-Red River (ASRR) shear zone including Chuxiong basin, Lanping-Simao fold belt and Thailand rift basin, which has seen extensive deformation events since Eocene. The Khorat Plateau basin is characterized by thick continental keel type lithosphere, consistent with palaeomagnetic and geological observations indicating this basin has experienced much less deformation than the surrounding regions. Additionally, our inversion imaged a sharp, lithospheric-scale velocity contrast across the southeastern segment of ASRR, indicative of a thin and thus relatively weak lithosphere southwest of Red River Fault. The thin lithosphere, low asthenospheric seismic velocities we observe and the average crustal thicknesses in the region suggest that the topography high is dynamically supported by upwelling asthenosphere rather than thickening of the crust/lithosphere. Based on the occurrence of Palaeogene volcanism and its timing, we prefer an explanation of thinning of the lithosphere and allowing a throughgoing fault rather than emplacement of a thin terrane to explain the thin lithosphere. Therefore, the anomalously thin lithosphere between Khorat Plateau and the ASRR in conjunction with other geological observations is generally consistent with the extrusion model for Indochina, which requires localization of lithospheric deformation around tectonic blocks.

Description: A series of linear analysis was performed on the onset of thermal convection of highly compressible fluids, in order to deepen the fundamental insights into the mantle convection of massive super-Earths in the presence of strong adiabatic compression. We consider the temporal evolution (growth or decay) of an infinitesimal perturbation superimposed to a highly compressible fluid which is in a hydrostatic (motionless) and conductive state in a basally heated horizontal layer. As a model of pressure-dependence in material properties, we employed an exponential decrease in thermal expansivity α and exponential increase in (reference) density with depth. The linearized equations for conservation of mass, momentum and internal (thermal) energy are numerically solved for the critical Rayleigh number as well as the vertical profiles of eigenfunctions for infinitesimal perturbations. The above calculations are repeatedly carried out by systematically varying (i) the dissipation number (Di), (ii) the temperature at the top surface and (iii) the magnitude of pressure-dependence in α and . Our analysis demonstrated that the onset of thermal convection is strongly affected by the adiabatic compression, in response to the changes in the static stability of thermal stratification in the fluid layer. For sufficiently large Di where a thick sublayer of stable stratification develops in the layer, for example, the critical Rayleigh number explosively increases with Di, together with drastic decreases in the length scales of perturbations both in vertical and horizontal directions. In particular, for very large Di, a thick ‘stratosphere’ occurs in the fluid layer where the vertical motion is significantly suppressed, resulting in a shrink of the incipient convection in a thin sublayer of unstable thermal stratification. In addition, when Di exceeds a threshold value above which a thermal stratification becomes stable in the entire layer, no perturbation is allowed to grow with time regardless of the Rayleigh number and/or the horizontal wavelength. We also found that the effect of adiabatic compression becomes prominent for higher temperature at the top surface of the fluid layer. These findings may imply the crucial importance of adiabatic compression in understanding the dynamics and evolution of the mantles of massive super-Earths, particularly for those orbiting their parent stars very closely.

Description: Understanding the role of a given transcription factor (TF) in regulating gene expression requires precise mapping of its binding sites in the genome. Chromatin immunoprecipitation-exo, an emerging technique using exonuclease to digest TF unbound DNA after ChIP, is designed to reveal transcription factor binding site (TFBS) boundaries with near-single nucleotide resolution. Although ChIP-exo promises deeper insights into transcription regulation, no dedicated bioinformatics tool exists to leverage its advantages. Most ChIP-seq and ChIP-chip analytic methods are not tailored for ChIP-exo, and thus cannot take full advantage of high-resolution ChIP-exo data. Here we describe a novel analysis framework, termed MACE (model-based analysis of ChIP-exo) dedicated to ChIP-exo data analysis. The MACE workflow consists of four steps: (i) sequencing data normalization and bias correction; (ii) signal consolidation and noise reduction; (iii) single-nucleotide resolution border peak detection using the Chebyshev Inequality and (iv) border matching using the Gale-Shapley stable matching algorithm. When applied to published human CTCF, yeast Reb1 and our own mouse ONECUT1/HNF6 ChIP-exo data, MACE is able to define TFBSs with high sensitivity, specificity and spatial resolution, as evidenced by multiple criteria including motif enrichment, sequence conservation, direct sequence pileup, nucleosome positioning and open chromatin states. In addition, we show that the fundamental advance of MACE is the identification of two boundaries of a TFBS with high resolution, whereas other methods only report a single location of the same event. The two boundaries help elucidate the in vivo binding structure of a given TF, e.g. whether the TF may bind as dimers or in a complex with other co-factors.

Description: Standard techniques for computed tomography imaging are not directly applicable to a carbonate rock because of the geometric complexity of its pore space. In this study, we first characterized the pore structure in Majella limestone with 30 per cent porosity. Microtomography data acquired on this rock was partitioned into three distinct domains: macropores, solid grains, and an intermediate domain made up of voxels of solid embedded with micropores below the resolution. A morphological analysis of the microtomography images shows that in Majella limestone both the solid and intermediate domains are interconnected in a manner similar to that reported previously in a less porous limestone. We however show that the macroporosity in Majella limestone is fundamentally different, in that it has a percolative backbone which may contribute significantly to its permeability. We then applied for the first time 3-D-volumetric digital image correlation (DIC) to characterize the mode of mechanical failure in this limestone. Samples were triaxially deformed over a wide range of confining pressures. Tomography imaging was performed on these samples before and after deformation. Inelastic compaction was observed at all tested pressures associated with both brittle and ductile behaviors. Our DIC analysis reveals the structure of compacting shear bands in Majella limestone deformed in the transitional regime. It also indicates an increase of geometric complexity with increasing confinement—from a planar shear band, to a curvilinear band, and ultimately to a diffuse multiplicity of bands, before shear localization is inhibited as the failure mode completes the transition to delocalized cataclastic flow.

Description: On Earth, oceanic plates subduct beneath a variety of overriding plate (OP) styles, from relatively thin and negatively buoyant oceanic OPs to thick and neutrally/positively buoyant continental OPs. The inclusion of an OP in numerical models of self-consistent subduction has been shown to reduce the rate that subducting slabs roll back relative to the equivalent single plate models. We use dynamic, 2-D subduction models to investigate how the mechanical properties, namely viscosity, thickness, and density, of the OP modify the slab rollback rate and the state of stress of the OP. In addition, we examine the role of the subducting plate (SP) viscosity. Because OP deformation accommodates the difference between the slab rollback rate and the far-field OP velocity, we find that the temporal variations in the rollback rate results in temporal variations in OP stress. The slabs in our models roll back rapidly until they reach the lower mantle viscosity increase, at which point the rollback velocity decreases. Concurrent with this reduction in rollback rate is a switch from an OP dominated by extensional stresses to a compressional OP. As in single plate models, the viscosity of the SP exerts a strong control on subducting slab kinematics; weaker slabs exhibit elevated sinking velocities and rollback rates. The SP viscosity also exerts a strong control on the OP stress regime. Weak slabs, either due to reduced bulk viscosity or stress-dependent weakening, have compressional OPs, while strong slabs have dominantly extensional OPs. While varying the viscosity of the OP alone does not substantially affect the OP stress state, we find that the OP thickness and buoyancy plays a substantial role in dictating the rate of slab rollback and OP stress state. Models with thick and/or negatively buoyant OPs have reduced rollback rates, and increased slab dip angles, relative to slabs with thin and/or positively buoyant OPs. Such elevated trench rollback for models with positively buoyant OPs induces extensional stresses in the OP, while OPs that are strongly negatively buoyant are under compression. While rollback is driven by the negative buoyancy of the subducting slab in such models of free subduction, we conclude that the physical properties of the OP potentially play a significant role in modulating both rollback rates and OP deformation style on Earth.