ALBERT

Description: We investigated the effects of historic soil chemistry changes associated with acid rain, i.e., reduced soil pH and a shift from nitrogen (N)- to phosphorus (P)-limitation, on the coordination of leaf water demand and xylem hydraulic supply traits in two co-occurring temperate tree species differing in growth rate. Using a full-factorial design (N  x  P  x  pH), we measured leaf nutrient content, water relations, leaf-level and canopy-level gas exchange, total biomass and allocation, as well as stem xylem anatomy and hydraulic function for greenhouse-grown saplings of fast-growing Acer rubrum (L.) and slow-growing Quercus alba (L.). We used principle component analysis to characterize trait coordination. We found that N-limitation, but not P-limitation, had a significant impact on plant water relations and hydraulic coordination of both species. Fast-growing A. rubrum made hydraulic adjustments in response to N-limitation, but trait coordination was variable within treatments and did not fully compensate for changing allocation across N-availability. For slow-growing Q. alba , N-limitation engendered more strict coordination of leaf and xylem traits, resulting in similar leaf water content and hydraulic function across all treatments. Finally, low pH reduced the propensity of both species to adjust leaf water relations and xylem anatomical traits in response to nutrient manipulations. Our data suggest that a shift from N- to P-limitation has had a negative impact on the water relations and hydraulic function of A. rubrum to a greater extent than for Q. alba . We suggest that current expansion of A. rubrum populations could be tempered by acidic N-deposition, which may restrict it to more mesic microsites. The disruption of hydraulic acclimation and coordination at low pH is emphasized as an interesting area of future study.

Description: We have experimentally investigated a K-bearing altered mid-ocean ridge basalt (MORB) composition to which 10% CaCO 3 was added (GA1 + 10%cc), at temperatures of 1050–1400°C and pressures of 3·5–5·5 GPa. Experiments were conducted in piston-cylinder apparatus in Pt–Gr (Pt with inner graphite) and Au–Pd capsules. Sub-solidus assemblages for both sets of experiments contain clinopyroxene, garnet, carbonate, rutile, coesite and K-feldspar. Apatite was observed only in the Pt–Gr experiments. Melting behaviour in experiments using different capsule materials contrasted markedly. Experiments in Pt–Gr capsules showed the silicate solidus to be at temperatures less than 1100°C at 3·5 GPa and less than 1050°C at 4·5–5·0 GPa. These are similar (3·5 GPa) or lower (4·5–5·0 GPa) temperatures compared with the carbonate solidus (1075–1125°C at 3·5–5·0 GPa). Melts in the Pt–Gr runs evolve with increasing degree of melting from K-rich silicate melts at the lowest degree of melting to carbonate–silicate immiscible liquids and silicate–carbonate melts at intermediate degrees of melting, and finally to silicate melts at the highest degrees of melting. Experiments in Au–Pd capsules were performed only at 5·0 GPa. The carbonate solidus is between 1200 and 1225°C (at least 100°C higher than in the experiments in Pt–Gr capsules at the same pressure–temperature conditions). The first melts to be produced are carbonatitic and exhibit increasing SiO 2 content with increasing temperature. This contrast in melting behaviour is explained by the relatively rapid diffusion of H through the Pt–Gr capsules, resulting in formation of H 2 O, and thus dramatically depressing both the silicate and the carbonate solidi in the Pt–Gr experiments compared with those in the Au–Pd experiments. This presumably reflects the lower permeability of Au–Pd to H, resulting in a much lower H 2 O/CO 2 ratio in the Au–Pd encapsulated experiments. The presence of water in the melt was demonstrated by Fourier transform infrared (FTIR) spectroscopic analysis of one Pt–Gr experiment, indicating ~0·5 wt % H 2 O in the bulk composition. Further confirmation that H 2 O plays such a role in the Pt–Gr experiments was provided by an additional experiment performed in a Au–Pd capsule with ~10 wt % H 2 O specifically added. In this experiment immiscible carbonate and silicate melts were observed. Carbonate–silicate liquid immiscibility is considered to occur as a result of the H 2 O present in the system. These results can be applied to natural systems in several ways. First, the presence of a small amount of either silicate melt or H 2 O-fluid in the system will act as a ‘flux’, depressing the carbonate solidus to much lower temperatures than in anhydrous systems. Second, the full trend in melt evolution from silicate-rich to carbonate-rich melts, which is also observed in inclusions in diamonds, can be explained by melting of K- and CO 2 -bearing, water-undersaturated MORB compositions. In cratonic environments low-degree silicate and immiscible silicate and carbonate melts will metasomatize the overlying mantle in different ways, producing, in the first instance, Si enrichment and crystallization of additional orthopyroxene, phlogopite, pyrope-rich garnet and consuming olivine, and, in the second case, carbonate metasomatism, with additional magnesite–dolomite, clinopyroxene and apatite. Both metasomatic styles have been described in natural peridotite xenoliths from the cratonic lithosphere.

Description: The role of water in the uppermost mantle has been explored to 6 GPa (~200 km) by a novel experimental approach in which the silicate melting solidus, the stability of hydrous phases and the H 2 O contents in nominally anhydrous minerals (NAMs) were determined. The composition studied is a fertile lherzolite modelled as a source for mid-ocean ridge basalts (MORB). The use of crushed olivine as traps for melt or fluid inclusions allows a distinction to be made between quenched hydrous silicate melt and quench material from water-rich vapour phase. The vapor-saturated solidus (water-rich vapor) of fertile lherzolite increases in temperature ( T ) from a minimum of 970°C at 1·5 GPa (~50 km) to 1375°C at 6 GPa. The Ca-rich amphibole pargasite is stable to the vapour-saturated solidus to 3 GPa (~100 km). Based on normative components, at 2·5 GPa the near-solidus melt (1–2%) in mantle with very low H 2 O content is transitional between sodic–dolomitic carbonatite and olivine melilitite. With higher melt fraction (~5%) at higher T or higher H 2 O content it is olivine-rich basanite. Both immediately below and above the solidus, the H 2 O content in residual lherzolite is ~200 ppm retained in NAMs at 2·5 and 4 GPa. The experimentally determined vapour-saturated solidus corrects recent numerical models of melting of lherzolite + H 2 O based on inferred high solubilities of H 2 O in NAMs and accounts for a discrepant experimental determination of the vapour-saturated solidus in which very high water/rock ratios were used. At 2·5 ± 0·1 GPa, the water content of experimental charges was varied from 0·05 to 14·5 wt %. Below the solidus and with increasing water content from 0·05 to 2·9 wt %, pargasite decreases in K 2 O and Na 2 O content and is absent in experiments with 7·25 and 14·5 wt % H 2 O. Also with increasing water content from 0·05 to 14·5 wt % H 2 O, the Na 2 O content of clinopyroxene decreases from 1·6 wt % to below the limit of detection (0·2 wt %). The destabilization of pargasite and change of clinopyroxene composition at 2·5 GPa and 1000°C are attributed to the leaching role (Na 2 O and K 2 O particularly) of the water-rich vapour at high water/rock ratios. The hydrous mineral pargasite is the major site of H 2 O storage in fertile uppermost mantle lherzolite but pargasite is unstable at pressures ( P ) 〉3 GPa (~100 km depth), causing a sharp drop in the water storage capacity of the upper mantle from 〉2000 to ~200 ppm. For small H 2 O contents (〈2000 ppm approximately), the temperature of the vapour-undersaturated solidus of fertile upper mantle lherzolite decreases sharply with increasing P at ~90 km depth. The negative d T /d P for the vapour-undersaturated solidus has important rheological and geodynamic consequences. In oceanic intraplate settings, the geotherm passes from subsolidus pargasite-bearing lherzolite to garnet lherzolite with incipient melting, creating the rheological boundary at ~90 km depth, between lithosphere and asthenosphere. The asthenosphere becomes geochemically zoned with the ‘enriched’ intraplate basalt source (〉500 ppm H 2 O) overlying the ‘depleted’ MORB source (~200 ppm H 2 O) in the deeper asthenosphere. Water also plays a significant role at convergent margins, where hydrous silicate melting in the mantle wedge is initiated at the vapour-saturated solidus. Melting of lherzolite at or near the vapour-saturated solidus does not fully dehydrate residual lherzolite or harzburgite. Residual lithosphere returned to the upper mantle may carry ~100–200 ppm H 2 O. At 6 GPa the low K/Na model mantle composition (MORB-source mantle) with 〉200 ppm H 2 O has normal rather than supercritical melting behaviour with the solidus at 1375°C, which is ~350°C below the C + H-free solidus.

Description: : We introduce a new forward-time simulator, Admix’em, that allows for rapid and realistic simulations of admixed populations with selection. Complex selection can be achieved through user-defined fitness and mating-preference probability functions. Users can specify realistic genomic landscapes and model neutral SNPs in addition to sites under selection. Admix’em is designed to simulate selection in admixed populations but can also be used as a general population simulator. Usage and examples are in the supplement. Availability and Implementation: C ++ and OpenMP, supports 64-bit Linux/Unix-like platforms. https://github.com/melop/admixem . Contact: rcui@age.mpg.de Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Negative assortative, or disassortative, mating describes the scenario when individuals tend to mate with dissimilar phenotypes more often than by random chance alone. This form of nonrandom mating has the power to select for the maintenance of polymorphism in conspicuous traits, for example, when females prefer mates that have a different trait value than their own. The livebearing variable platyfish, Xiphophorus variatus , exhibits high polymorphism for a melanic pigmentation trait called tailspots, which results in variation in a conspicuous visual cue. Livebearers often exhibit female mating preferences based on morphological traits and disassortative mating has been suggested in a related species. Whether mating choice contributes to the maintenance of tailspot variation has never been tested. Here, we examined mating preferences of wild-caught females for pairs of male stimuli differing in their tailspot pattern. Females showed no evidence for either assortative or disassortative association preferences, spending equal time with males of different patterns. These results corroborate data on natural mating patterns in X. variatus , suggesting that mate choice for tailspots is either nonexistent or at least insufficient to account for the maintenance of tailspot variation.

Description: Site-directed RNA editing (SDRE) is a strategy to precisely alter genetic information within mRNAs. By linking the catalytic domain of the RNA editing enzyme ADAR to an antisense guide RNA, specific adenosines can be converted to inosines, biological mimics for guanosine. Previously, we showed that a genetically encoded iteration of SDRE could target adenosines expressed in human cells, but not efficiently. Here we developed a reporter assay to quantify editing, and used it to improve our strategy. By enhancing the linkage between ADAR's catalytic domain and the guide RNA, and by introducing a mutation in the catalytic domain, the efficiency of converting a U A G premature termination codon (PTC) to tryptophan (U G G) was improved from ~11 % to ~70 %. Other PTCs were edited, but less efficiently. Numerous off-target edits were identified in the targeted mRNA, but not in randomly selected endogenous messages. Off-target edits could be eliminated by reducing the amount of guide RNA with a reduction in on-target editing. The catalytic rate of SDRE was compared with those for human ADARs on various substrates and found to be within an order of magnitude of most. These data underscore the promise of site-directed RNA editing as a therapeutic or experimental tool.

Description: The incorporation of water in olivine and pyroxenes interlayered within fertile lherzolite compositions was explored experimentally near the wet solidus of lherzolite at 2·5 and 4 GPa. The concentrations and activities of water were varied to establish the partitioning of water between nominally anhydrous minerals (NAMs) and the hydrous minerals pargasite and phlogopite. The water content in NAMs was determined by Fourier-transform infrared (FTIR) spectroscopy. The main absorption bands in NAMs from these experiments are very similar to those generally found in natural upper mantle peridotites. Olivine, orthopyroxene and clinopyroxene contain 32–190, 290–320 and 910–980 ppm of water under the studied conditions. The partition coefficients between coexisting clinopyroxene and orthopyroxene ( D cpx/opx ) are 2·7 ± 1·1 and 3·5 ± 1·5 at 2·5 and 4 GPa respectively, whereas values for coexisting orthopyroxene and olivine ( D opx/ol ) are 6·7 ± 2 and 4·7 ± 1·1, at 2·5 and 4 GPa respectively. The storage capacity in NAMs in a model mantle composition close to the vapour-saturated solidus (water-rich vapour) is ~190 ppm at both 2·5 and 4 GPa. Pargasite is the most important phase accommodating significant amounts of water in the uppermost mantle. Its breakdown with increasing pressure at 3 GPa at the vapour-saturated solidus (which is at ~1025°C at 2·5 GPa) results in a sharp drop in the water storage capacity of peridotite from ~1000 ppm to ~190 ppm H 2 O. At pressures 〉3 GPa, melting in fertile lherzolite begins at the vapour-saturated solidus if the bulk H 2 O concentration exceeds ~190 ppm.

Description: Antimicrobial peptides (AMPs) are anti-infectives that may represent a novel and untapped class of biotherapeutics. Increasing interest in AMPs means that new peptides (natural and synthetic) are discovered faster than ever before. We describe herein a new version of the Database of Antimicrobial Activity and Structure of Peptides (DBAASPv.2, which is freely accessible at http://dbaasp.org ). This iteration of the database reports chemical structures and empirically-determined activities (MICs, IC50, etc.) against more than 4200 specific target microbes for more than 2000 ribosomal, 80 non-ribosomal and 5700 synthetic peptides. Of these, the vast majority are monomeric, but nearly 200 of these peptides are found as homo- or heterodimers. More than 6100 of the peptides are linear, but about 515 are cyclic and more than 1300 have other intra-chain covalent bonds. More than half of the entries in the database were added after the resource was initially described, which reflects the recent sharp uptick of interest in AMPs. New features of DBAASPv.2 include: (i) user-friendly utilities and reporting functions, (ii) a ‘Ranking Search’ function to query the database by target species and return a ranked list of peptides with activity against that target and (iii) structural descriptions of the peptides derived from empirical data or calculated by molecular dynamics (MD) simulations. The three-dimensional structural data are critical components for understanding structure–activity relationships and for design of new antimicrobial drugs. We created more than 300 high-throughput MD simulations specifically for inclusion in DBAASP. The resulting structures are described in the database by novel trajectory analysis plots and movies. Another 200+ DBAASP entries have links to the Protein DataBank. All of the structures are easily visualized directly in the web browser.

Description: Planets open gaps in discs. Gap opening is typically modelled by considering the planetary Lindblad torque which repels disc gas away from the planet’s orbit. But gaps also clear because the planet consumes local material. We present a simple, easy-to-use, analytic framework for calculating how gaps deplete and how the disc’s structure as a whole changes by the combined action of Lindblad repulsion and planetary consumption. The final mass to which a gap-embedded gas giant grows is derived in tandem. The analytics are tested against 1D numerical experiments and calibrated using published multidimensional simulations. In viscous alpha discs, the planet, while clearing a gap, initially accretes practically all of the gas that tries to diffuse past, rapidly achieving super-Jupiter if not brown dwarf status. By contrast, in inviscid discs – that may still accrete on to their central stars by, say, magnetized winds – planets open deep, repulsion-dominated gaps. Then only a small fraction of the disc accretion flow is diverted on to the planet, which grows to a fraction of a Jupiter mass. Transitional disc cavities might be cleared by families of such low-mass objects opening inviscid, repulsion-dominated, overlapping gaps which allow most of the outer disc gas to flow unimpeded on to host stars.