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The mammalian liver consists of hexagon-shaped lobules that are radially polarized by blood flow and morphogens. Key liver genes have been shown to be differentially expressed along the lobule axis, a phenomenon termed zonation, but a detailed genome-wide reconstruction of this spatial division of labour has not been achieved. Here we measure the entire transcriptome of thousands of mouse liver cells and infer their lobule coordinates on the basis of a panel of zonated landmark genes, characterized with single-molecule fluorescence in situ hybridization. Using this approach, we obtain the zonation profiles of all liver genes with high spatial resolution. We find that around 50% of liver genes are significantly zonated and uncover abundant non-monotonic profiles that peak at the mid-lobule layers. These include a spatial order of bile acid biosynthesis enzymes that matches their position in the enzymatic cascade. Our approach can facilitate the reconstruction of similar spatial genomic blueprints for other mammalian organs.

mRNA is thought to predominantly reside in the cytoplasm, where it is translated and eventually degraded. Although nuclear retention of mRNA has a regulatory potential, it is considered extremely rare in mammals. Here, to explore the extent of mRNA retention in metabolic tissues, we combine deep sequencing of nuclear and cytoplasmic RNA fractions with single-molecule transcript imaging in mouse beta cells, liver, and gut. We identify a wide range of protein-coding genes for which the levels of spliced polyadenylated mRNA are higher in the nucleus than in the cytoplasm. These include genes such as the transcription factor ChREBP, Nlrp6, Glucokinase, and Glucagon receptor. We demonstrate that nuclear retention of mRNA can efficiently buffer cytoplasmic transcript levels from noise that emanates from transcriptional bursts. Our study challenges the view that transcripts predominantly reside in the cytoplasm and reveals a role of the nucleus in dampening gene expression noise.

We examine the dynamics structure of the rich cluster A1689, combining VLT/VIMOS spectroscopy with Subaru/Suprime-Cam imaging. The radial velocity distribution of [?]500 cluster members is bounded by a pair of clearly defined velocity caustics, with a maximum amplitude of [?]|4000| km s-1 at [?] 300 h -1 kpc, beyond which the amplitude steadily declines, approaching zero velocity at a limiting radius of [?]2 h -1 Mpc. We derive the three-dimensional velocity anisotropy and galaxy number density profiles using a model-independent method to solve the Jeans equation, simultaneously incorporating the observed velocity dispersion profile, the galaxy counts from deep Subaru imaging, and our previously derived cluster mass profile from a joint lensing and X-ray analysis. The velocity anisotropy is found to be predominantly radial at large radius, becoming increasingly tangential towards the center, in accord with expectations. We also analyze the galaxy data independently of our previous analysis using two different methods: The first is based on a solution of the Jeans equation assuming an Navarro-Frenk-White (NFW) form for the mass distribution, whereas in the second method the caustic amplitude is used to determine the escape velocity. The cluster virial mass derived by both of these dynamical methods is in good agreement with results from our earlier lensing and X-ray analysis. We also confirm the high NFW concentration parameter, with results from both methods combined to yield c vir > 13 (1s). The inferred virial radius is consistent with the limiting radius where the caustics approach zero velocity and where the counts of cluster members drop off, suggesting that infall onto A1689 is currently not significant.

We present a multiwavelength analysis of a sample of four hot (TX > 8 keV) X-ray galaxy clusters (A1689, A2261, A2142, and A2390) using joint AMiBA Sunyaev-Zel'dovich effect (SZE) and Subaru weak-lensing observations, combined with published X-ray temperatures, to examine the distribution of mass and the intracluster medium (ICM) in massive cluster environments. Our observations show that A2261 is very similar to A1689 in terms of lensing properties. Many tangential arcs are visible around A2261, with an effective Einstein radius [?]40'' (at z [?] 1.5), which when combined with our weak-lensing measurements implies a mass profile well fitted by a Navarro-Frenk-White model with a high concentration c vir [?] 10, similar to A1689 and to other massive clusters. The cluster A2142 shows complex mass substructure, and displays a shallower profile (c vir [?] 5), consistent with detailed X-ray observations which imply recent interaction. The AMiBA map of A2142 exhibits an SZE feature associated with mass substructure lying ahead of the sharp northwest edge of the X-ray core suggesting a pressure increase in the ICM. For A2390 we obtain highly elliptical mass and ICM distributions at all radii, consistent with other X-ray and strong-lensing work. Our cluster gas fraction measurements, free from the hydrostatic equilibrium assumption, are overall in good agreement with published X-ray and SZE observations, with the sample-averaged gas fraction of [?]f gas(

We present a new XMM-Newton observation of the ultraluminous infrared galaxy (ULIRG) NGC 6240. We analyze the reflecting grating spectrometer (RGS) data, as well as data from the other instruments, and find a starburst-dominated 0.5-3 keV spectrum with global properties resembling those observed in M82 but with a much higher luminosity. We show that the starburst region can be divided into an outer zone, beyond a radius of about 2.1 kpc, with a gas temperature of about 107 K, and a central region with temperatures in the range (2-6) x 107 K. The gas in the outer region emits most of the observed O VIII Lya line, and the gas in the inner region the emission lines of higher ionization ions, including a strong Fe XXV line. We also identify a small inner part, very close to the active nuclei, with typical Seyfert 2 properties, including a large amount of photoionized gas producing a strong Fe Ka 6.4 keV line. The combined abundance, temperature, and emission measure analysis indicates supersolar Ne/O, Mg/O, Si/O, S/O, and possibly also Fe/O. The analysis suggests densities in the range of (0.07-0.28)[?]-1/2 cm-3 and a total thermal gas mass of ~4 x 108[?]1/2 M, where [?] is the volume filling factor. We used a simple model to argue that a massive starburst with an age of [?]2 x 107 yr can explain most of the observed properties of the source. NGC 6240 is perhaps the clearest case of an X-ray-bright luminous AGN that is in a merger and whose soft X-ray spectrum is dominated by a powerful starburst.

We use extensive measurements of the cluster A1689 to assess the expected similarity in the dynamics of galaxies and dark matter (DM) in their motion as collisionless "particles" in the cluster gravitational potential. To do so, we derive the radial profile of the specific kinetic energy of the cluster galaxies from the Jeans equation and observational data. Assuming that the specific kinetic energies of galaxies and DM are roughly equal, we obtain the mean value of the DM velocity anisotropy parameter and the DM density profile. Since this deduced profile has a scale radius that is higher than inferred from lensing observations, we tested the validity of the assumption by repeating the analysis using results of simulations for the profile of the DM velocity anisotropy. Results of both analyses indicate a significant difference between the kinematics of galaxies and DM within r [?] 0.3r vir. This finding is also reflected in the shape of the galaxy number density profile, which flattens markedly with respect to the steadily rising DM profile at small radii. Thus, r [?] 0.3r vir seems to be a transition region interior to which collisional effects significantly modify the dynamical properties of the galaxy population with respect to those of DM in A1689.