RNAi and single-cell RNA-seq characterize the mechanism of endosymbiosis between coral and dinoflagellates.

MotivationComputational inference of genome organization based on Hi-C sequencing has greatly aided the understanding of chromatin and nuclear organization in three dimensions (3D). However, existing computational methods fail to address the cell population heterogeneity. Here we describe a probabilistic-modeling-based method called CscoreTool-M that infers multiple 3D genome sub-compartments from Hi-C data.ResultsThe compartment scores inferred using CscoreTool-M represents the probability of a genomic region locating in a specific sub-compartment. Compared to published methods, CscoreTool-M is more accurate in inferring sub-compartments corresponding to both active and repressed chromatin. The compartment scores calculated by CscoreTool-M also help to quantify the levels of heterogeneity in sub-compartment localization within cell populations. By comparing proliferating cells and terminally differentiated non-proliferating cells, we show that the proliferating cells have higher genome organization heterogeneity, which is likely caused by cells at different cell-cycle stages. By analyzing 10 sub-compartments, we found a sub-compartment containing chromatin potentially related to the early-G1 chromatin regions proximal to the nuclear lamina in HCT116 cells, suggesting the method can deconvolve cell cycle stage-specific genome organization among asynchronously dividing cells. Finally, we show that CscoreTool-M can identify sub-compartments that contain genes enriched in housekeeping or cell-type-specific functions.

The mineral record contains chemical signatures that reflect the evolving redox conditions of Earth's crust, and reveal trends in the bioavailability of life's critical elements. In particular, shifting redox states of transition metal elements that are used as co-factors by enzymes across all domains of life can be tracked in preserved mineral chemistry. The transition metal iron (Fe) is one of the most abundant elements in Earth's core, mantle, and crust, and is commonly a major constituent of rock-forming minerals. Additionally, Fe is the most widely used metal in biology, and Earth's redox history has profoundly impacted the chemical speciation and availability of Fe in aqueous systems. The diverse mineral chemistry of Fe can therefore reveal new insights into the redox evolution of Earth's crust and subsequent biological impacts. Here, we apply a new mineral chemistry network analysis platform, dragon, to investigate the mineral chemistry of iron (Fe) over geologic-time. We present bipartite network graphs of iron minerals linked to their constituent elements or ions for several geological time intervals. These graphs illustrate the increasing importance of oxygen (O) abundance in the atmosphere from the Paleoarchean to the Mesoproterozoic in regard to the the emergence of new Fe minerals, as well as the influence of free O on trends in element electronegativity in mineral formation and electron transfer processes. The proportion of oxygen containing Fe minerals had the sharpest increase during the time periods of the Kenorland and Columbia supercontinent assembly events. Indeed, the rise of O is associated with O becoming more centralized in the network as well as with an increase through time in the number of Fe minerals containing combinations of high and low electronegativity elements. The importance of oxygen in the expansion of Fe mineral chemical diversity, and its influence on the bioavailability of Fe in the environment, is illustrated clearly in the Fe mineral chemistry network.

The heat extracted from the core by the overlying mantle across the core-mantle boundary controls the thermal evolution of the core. This in turn leads to the solidification of the inner core in association with the exsolution of light alloying elements into the liquid outer core. Although the temperature (T) at the inner core boundary (ICB) would be adjusted to account for the effects of the light elements, the melting T of Fe places an upper bound at the ICB and it is a vital point in the thermal profile of the core. Here, we determine the melting T of Fe in the multi-anvil press by characterizing the interface of Fe-W interaction. Our data place a tighter constraint on the melting curve of Fe between 8 and 21 GPa, that is directly applicable to small planetary bodies and serves as an anchor for melting curve of Fe at higher pressure.

New Raman and NMR spectroscopy data on hydrous Ca aluminosilicate melts and glasses, with eutectic quartz-anorthite-wollastonite composition, are presented here. The glasses were obtained by rapid quench of melts equilibrated at high P and high T in a piston-cylinder apparatus. In situ Raman observations of the structure of the melts were also performed during hydrothermal diamond cell experiments. Using the intensities of the similar to 860 cm(-1) and similar to 1630 cm(-1) Raman signals, respectively assigned to vibrations of T-OH and H2Omol species, we determined the speciation of water in the glasses. T-OH and H2Omol values compare well with those determined from infrared (IR) spectra, except above similar to 5 wt% total water where IR determinations actually underestimate the proportion of hydroxyl groups. The analysis of the polarized Raman spectra and of the Si-29 MAS NMR spectra of the hydrous glasses suggests limited changes in glass polymerization with variations in dissolved water content. However, at high temperatures, in situ Raman spectroscopy observations indicate that the hydrous melt structure differs very strongly from that of a glass containing a comparable concentration of dissolved water. Because of this, this study reinforces the fact that using glass data to try understanding high temperature processes in hydrous melts, like viscous flow or water diffusion toward bubbles during volcanic degassing, may not be very appropriate.

Hydrogen stable isotope values of hydrated volcanic glass as a proxy for the isotopic composition of past meteoric waters provide an opportunity for reconstructing past climates. Here we present new hydrogen stable isotope values from 63 individual tuffs from the Afar region in the lower Awash Valley of eastern Ethiopia. The hydrogen isotopic results from volcanic glass spanning the last 6.4 Ma show a wide distribution with values ranging be-tween-89 and -32 parts per thousand (VSMOW). The variability is consistent with the observed paleo-depositional setting (i.e., lower values for fluvial settings while higher values are recorded in lacustrine settings). The reconstructed hydrogen isotopic values of parent waters are considerably lower than those of modern meteoric waters, sug-gesting a bias toward lower values during the hydration of volcanic glass. Reconstructed hydrogen stable isotope values of water derived from volcanic glass differ from other proxies of regional climate in northeast Africa, pointing to the controls of local meteoric waters on the hydrogen isotopic composition of volcanic glass. There is agreement between the reconstructed isotopic composition of parent waters and the lowest hydrogen isotopic values of modern precipitation in the Awash catchment that correspond to periods of large rainfall. This correspondence probably indicates that volcanic glass is preferentially hydrated during the wettest seasons. To test this idea, we compared the isotopic results from volcanic glass with the reconstructed isotopic composition of surface waters from soil carbonates deposited during the Pliocene and Pleistocene in the lower Awash Valley. The comparison reveals a considerable difference between proxies, with volcanic glass recording lower isotopic values than soil carbonates. Evaporative isotopic enrichment of water in shallow (<1 m) soil profiles probably accounts for the elevated values in soil carbonates. In contrast, the presence of smectite-rich vertisols above volcanic deposits appears to retard infiltration of meteoric waters deep into the subsurface. During rainfall events, vertisols swell and prevent all but the largest rainfall events from penetrating deep (>1 m) into the profiles and promoting the hydration of volcanic glass that display systematically lower isotopic values of meteoric waters than the mean annual rainfall.

The maize female gametophyte is comprised of four cell types: two synergids, an egg cell, a central cell, and a variable number of antipodal cells. In maize, these cells are produced after three rounds of free-nuclear divisions followed by cellularization, differentiation, and proliferation of the antipodal cells. Cellularization of the eight-nucleate syncytium produces seven cells with two polar nuclei in the central cell. Nuclear localization is tightly controlled in the embryo sac. This leads to precise allocation of the nuclei into the cells upon cellularization. Nuclear positioning within the syncytium is highly correlated with their identity after cellularization. Two mutants are described with extra polar nuclei, abnormal antipodal cell morphology, and reduced antipodal cell number, as well as frequent loss of antipodal cell marker expression. Mutations in one of these genes, indeterminate gametophyte2 encoding a MICROTUBULE ASSOCIATED PROTEIN65-3 homolog, shows a requirement for MAP65-3 in cellularization of the syncytial embryo sac as well as for normal seed development. The timing of the effects of ig2 suggests that the identity of the nuclei in the syncytial female gametophyte can be changed very late before cellularization.