Penetrability of the inner mucus layer: who is out there?

Large numbers of microorganisms colonise the skin and mucous membranes of animals, with their highest density in the lower gastrointestinal tract. The impact of these microbes on the host can be demonstrated by comparing animals (usually mice) housed under germ-free conditions, or colonised with different compositions of microbes. Inbreeding and embryo manipulation programs have generated a wide variety of mouse strains with a fixed germ-line (isogenic) and hygiene comparisons robustly show remarkably strong interactions between the microbiota and the host, which can be summarised in three axioms. (I) Live microbes are largely confined to their spaces at body surfaces, provided the animal is not suffering from an infection. (II) There is promiscuous molecular exchange throughout the host and its microbiota in both directions [1]. (III) Every host organ system is profoundly shaped by the presence of body surface microbes. It follows that one must draw a line between live microbial and host “spaces” (I) to understand the crosstalk (II and III) at this interesting interface of the host-microbial superorganism. Of course, since microbes can adapt to very different niches, there has to be more than one line. In this issue of EMBO Reports, Johansson and colleagues have studied mucus, which is the main physical frontier for most microbes in the intestinal tract: they report how different non-pathogenic microbiota compositions affect its permeability and the functional protection of the epithelial surface [2].

The sacred musical compositions of the late Israel Lazarus Mombach : containing the services for Sabbaths and festivals, New Year and Day of Atonement, consecration hymns, psalms and choral wedding service

ed. by M. Keizer

Chemical compositions of solid particles present in the Greenland NEEM ice core over the last 110,000 years

This study reports the chemical composition of particles present along Greenland’s North Greenland Eemian Ice Drilling (NEEM) ice core, back to 110,000 years before present. Insoluble and soluble particles larger than 0.45 μm were extracted from the ice core by ice sublimation, and their chemical composition was analyzed using scanning electron microscope and energy dispersive X-ray spectroscopy and micro-Raman spectroscopy. We show that the dominant insoluble components are silicates, whereas NaCl, Na₂SO₄, CaSO ₄, and CaCO₃ represent major soluble salts. For the first time, particles of CaMg(CO₃)₂ and Ca(NO₃)₂ 4H₂O are identified in a Greenland ice core. The chemical speciation of salts varies with past climatic conditions. Whereas the fraction of Na salts (NaCl + Na₂SO₄) exceeds that of Ca salts (CaSO₄+ CaCO₃) during the Holocene (0.6–11.7 kyr B.P.), the two fractions are similar during the Bølling-Allerød period (12.9–14.6 kyr B.P.). During cold climate such as over the Younger Dryas (12.0–12.6 kyr B.P.) and the Last Glacial Maximum (15.0–26.9 kyr B.P.), the fraction of Ca salts exceeds that of Na salts, showing that the most abundant ion generally controls the salt budget in each period. High-resolution analyses reveal changing particle compositions: those in Holocene ice show seasonal changes, and those in LGM ice show a difference between cloudy bands and clear layers, which again can be largely explained by the availability of ionic components in the atmospheric aerosol body of air masses reaching Greenland.

Reconstruction of in-situ porosity and porewater compositions of low-permeability crystalline rocks: Magnitude of artefacts induced by drilling and sample recovery

Geological site characterisation programmes typically rely on drill cores for direct information on subsurface rocks. However, porosity, transport properties and porewater composition measured on drill cores can deviate from in-situ values due to two main artefacts caused by drilling and sample recovery: (1) mechanical disruption that increases porosity and (2) contamination of the porewater by drilling fluid. We investigated the effect and magnitude of these perturbations on large drill core samples (12–20 cm long, 5 cmdiameter) of high-grade, granitic gneisses obtained from 350 to 600 m depth in a borehole on Olkiluoto Island (SW Finland). The drilling fluid was traced with sodium–iodide. By combining out-diffusion experiments, gravimetry, UV-microscopy and iodide mass balance calculations, we successfully quantified the magnitudes of the artefacts: 2–6% increase in porosity relative to the bulk connected porosity and 0.9 to 8.9 vol.% contamination by drilling fluid. The spatial distribution of the drilling-induced perturbations was revealed by numerical simulations of 2D diffusion matched to the experimental data. This showed that the rims of the samples have a mechanically disrupted zone 0.04 to 0.22 cm wide, characterised by faster transport properties compared to the undisturbed centre (1.8 to 7.7 times higher pore diffusion coefficient). Chemical contamination was shown to affect an even wider zone in all samples, ranging from 0.15 to 0.60 cm, inwhich iodide enrichmentwas up to 180 mg/kgwater, compared to 0.5 mg/kgwater in the uncontaminated centre. For all samples in the present case study, it turned out that the magnitude of the artefacts caused by drilling and sample recovery is so small that no correction is required for their effects. Therefore, the standard laboratory measurements of porosity, transport properties and porewater composition can be taken as valid in-situ estimates. However, it is clear that the magnitudes strongly depend on site- and drilling-specific factors and therefore our results cannot be transferred simply to other locations. We recommend the approach presented in this study as a route to obtain reliable values in future drilling campaigns aimed at characterising in-situ bedrock properties.

Similarity Mapplet: Interactive Visualization of the Directory of Useful Decoys and ChEMBL in High Dimensional Chemical Spaces

An Internet portal accessible at www.gdb.unibe.ch has been set up to automatically generate color-coded similarity maps of the ChEMBL database in relation to up to two sets of active compounds taken from the enhanced Directory of Useful Decoys (eDUD), a random set of molecules, or up to two sets of user-defined reference molecules. These maps visualize the relationships between the selected compounds and ChEMBL in six different high dimensional chemical spaces, namely MQN (42-D molecular quantum numbers), SMIfp (34-D SMILES fingerprint), APfp (20-D shape fingerprint), Xfp (55-D pharmacophore fingerprint), Sfp (1024-bit substructure fingerprint), and ECfp4 (1024-bit extended connectivity fingerprint). The maps are supplied in form of Java based desktop applications called “similarity mapplets” allowing interactive content browsing and linked to a “Multifingerprint Browser for ChEMBL” (also accessible directly at www.gdb.unibe.ch) to perform nearest neighbor searches. One can obtain six similarity mapplets of ChEMBL relative to random reference compounds, 606 similarity mapplets relative to single eDUD active sets, 30 300 similarity mapplets relative to pairs of eDUD active sets, and any number of similarity mapplets relative to user-defined reference sets to help visualize the structural diversity of compound series in drug optimization projects and their relationship to other known bioactive compounds.