Exploring DCO+^+ as a tracer of thermal inversion in the disk around the Herbig Ae star HD163296

We aim to reproduce the DCO$^+$ emission in the disk around HD163296 using a simple 2D chemical model for the formation of DCO$^+$ through the cold deuteration channel and a parametric treatment of the warm deuteration channel. We use data from ALMA in band 6 to obtain a resolved spectral imaging data cube of the DCO$^+$ $J$=3--2 line in HD163296 with a synthesized beam of 0."53$\times$ 0."42. We adopt a physical structure of the disk from the literature that reproduces the spectral energy distribution. We then apply a simplified chemical network for the formation of DCO$^+$ that uses the physical structure of the disk as parameters along with a CO abundance profile, a constant HD abundance and a constant ionization rate. Finally, from the resulting DCO$^+$ abundances, we calculate the non-LTE emission using the 3D radiative transfer code LIME. The observed DCO$^+$ emission is reproduced by a model with cold deuteration producing abundances up to $1.6\times 10^{-11}$. Warm deuteration, at a constant abundance of $3.2\times 10^{-12}$, becomes fully effective below 32 K and tapers off at higher temperatures, reproducing the lack of DCO$^+$ inside 90 AU. Throughout the DCO$^+$ emitting zone a CO abundance of $2\times 10^{-7}$ is found, with $\sim$99\% of it frozen out below 19 K. At radii where both cold and warm deuteration are active, warm deuteration contributes up to 20\% of DCO$^+$, consistent with detailed chemical models. The decrease of DCO$^+$ at large radii is attributed to a temperature inversion at 250 AU, which raises temperatures above values where cold deuteration operates. Increased photodesorption may also limit the radial extent of DCO$^+$. The corresponding return of the DCO$^+$ layer to the midplane, together with a radially increasing ionization fraction, reproduces the local DCO$^+$ emission maximum at $\sim$260 AU.Comment: 9 pages, 5 figures, accepted 7th July 201

DCO+^+, DCN and N2_2D+^+ reveal three different deuteration regimes in the disk around the Herbig Ae star HD163296

The formation pathways of deuterated species trace different regions of protoplanetary disks and may shed light into their physical structure. We aim to constrain the radial extent of main deuterated species; we are particularly interested in spatially characterizing the high and low temperature pathways for enhancing deuteration of these species. We observed the disk surrounding the Herbig Ae star HD 163296 using ALMA in Band 6 and obtained resolved spectral imaging data of DCO$^+$ ($J$=3-2), DCN ($J$=3-2) and N$_2$D$^+$ ($J$=3-2). We model the radial emission profiles of DCO$^+$, DCN and N$_2$D$^+$, assuming their emission is optically thin, using a parametric model of their abundances and radial excitation temperature estimates. DCO$^+$ can be described by a three-region model, with constant-abundance rings centered at 70 AU, 150 AU and 260 AU. The DCN radial profile peaks at about ~60 AU and N$_2$D$^+$ is seen in a ring at ~160 AU. Simple models of both molecules using constant abundances reproduce the data. Assuming reasonable average excitation temperatures for the whole disk, their disk-averaged column densities (and deuterium fractionation ratios) are 1.6-2.6$\times 10^{12}$ cm$^{-2}$ (0.04-0.07), 2.9-5.2$\times 10^{12}$ cm$^{-2}$ ($\sim$0.02) and 1.6-2.5 $\times 10^{11}$ cm$^{-2}$ (0.34-0.45) for DCO$^+$, DCN and N$_2$D$^+$, respectively. Our simple best-fit models show a correlation between the radial location of the first two rings in DCO$^+$ and the DCN and N$_2$D$^+$ abundance distributions that can be interpreted as the high and low temperature deuteration pathways regimes. The origin of the third DCO$^+$ ring at 260 AU is unknown but may be due to a local decrease of ultraviolet opacity allowing the photodesorption of CO or due to thermal desorption of CO as a consequence of radial drift and settlement of dust grains

Increased H2_2CO production in the outer disk around HD 163296

Three formaldehyde lines were observed (H$_2$CO 3$_{03}$--2$_{02}$, H$_2$CO 3$_{22}$--2$_{21}$, and H$_2$CO 3$_{21}$--2$_{20}$) in the protoplanetary disk around the Herbig Ae star HD 163296 with ALMA at 0.5 arcsecond (60 AU) spatial resolution. H$_2$CO 3$_{03}$--2$_{02}$ was readily detected via imaging, while the weaker H$_2$CO 3$_{22}$--2$_{21}$ and H$_2$CO 3$_{21}$--2$_{20}$ lines required matched filter analysis to detect. H$_2$CO is present throughout most of the gaseous disk, extending out to 550 AU. An apparent 50 AU inner radius of the H$_2$CO emission is likely caused by an optically thick dust continuum. The H$_2$CO radial intensity profile shows a peak at 100 AU and a secondary bump at around 300 AU, suggesting increased production in the outer disk. Different parameterizations of the H$_2$CO abundance were compared to the observed visibilities with $\chi^2$ minimization, using either a characteristic temperature, a characteristic radius or a radial power law index to describe the H$_2$CO chemistry. Similar models were applied to ALMA Science Verification data of C$^{18}$O. In all modeling scenarios, fits to the H$_2$CO data show an increased abundance in the outer disk. The overall best-fit H$_2$CO model shows a factor of two enhancement beyond a radius of 270$\pm$20 AU, with an inner abundance of $2\!-\!5 \times 10^{-12}$. The H$_2$CO emitting region has a lower limit on the kinetic temperature of $T > 20$ K. The C$^{18}$O modeling suggests an order of magnitude depletion in the outer disk and an abundance of $4\!-\!12 \times 10^{-8}$ in the inner disk. The increase in H$_2$CO outer disk emission could be a result of hydrogenation of CO ices on dust grains that are then sublimated via thermal desorption or UV photodesorption, or more efficient gas-phase production beyond about 300 AU if CO is photodisocciated in this region

Thioredoxin and glutathione systems differ in parasitic and free-living platyhelminths

<p>Abstract</p> <p>Background</p> <p>The thioredoxin and/or glutathione pathways occur in all organisms. They provide electrons for deoxyribonucleotide synthesis, function as antioxidant defenses, in detoxification, Fe/S biogenesis and participate in a variety of cellular processes. In contrast to their mammalian hosts, platyhelminth (flatworm) parasites studied so far, lack conventional thioredoxin and glutathione systems. Instead, they possess a linked thioredoxin-glutathione system with the selenocysteine-containing enzyme thioredoxin glutathione reductase (TGR) as the single redox hub that controls the overall redox homeostasis. TGR has been recently validated as a drug target for schistosomiasis and new drug leads targeting TGR have recently been identified for these platyhelminth infections that affect more than 200 million people and for which a single drug is currently available. Little is known regarding the genomic structure of flatworm TGRs, the expression of TGR variants and whether the absence of conventional thioredoxin and glutathione systems is a signature of the entire platyhelminth phylum.</p> <p>Results</p> <p>We examine platyhelminth genomes and transcriptomes and find that all platyhelminth parasites (from classes Cestoda and Trematoda) conform to a biochemical scenario involving, exclusively, a selenium-dependent linked thioredoxin-glutathione system having TGR as a central redox hub. In contrast, the free-living platyhelminth <it>Schmidtea mediterranea </it>(Class Turbellaria) possesses conventional and linked thioredoxin and glutathione systems. We identify TGR variants in <it>Schistosoma </it>spp. derived from a single gene, and demonstrate their expression. We also provide experimental evidence that alternative initiation of transcription and alternative transcript processing contribute to the generation of TGR variants in platyhelminth parasites.</p> <p>Conclusions</p> <p>Our results indicate that thioredoxin and glutathione pathways differ in parasitic and free-living flatworms and that canonical enzymes were specifically lost in the parasitic lineage. Platyhelminth parasites possess a unique and simplified redox system for diverse essential processes, and thus TGR is an excellent drug target for platyhelminth infections. Inhibition of the central redox wire hub would lead to overall disruption of redox homeostasis and disable DNA synthesis.</p

Diluted antiferromagnet in a ferromagnetic enviroment

The question of robustness of a network under random ``attacks'' is treated in the framework of critical phenomena. The persistence of spontaneous magnetization of a ferromagnetic system to the random inclusion of antiferromagnetic interactions is investigated. After examing the static properties of the quenched version (in respect to the random antiferromagnetic interactions) of the model, the persistence of the magnetization is analysed also in the annealed approximation, and the difference in the results are discussed

Concerted Transport and Phosphorylation of Diacylglycerol at ER-PM Contacts Sites Regulates Phospholipid Dynamics During Stress

A universal response of plants to environmental stresses is the activation of plasma membrane (PM) phospholipase C (PLC) that hydrolyzes phosphatidylinositol phosphate (PIP) to produce soluble inositol phosphate (IP) and diacylglycerol (DAG). DAG produced in this way can be either phosphorylated by PM diacylglycerol kinases (DGKs) to produce the second messenger phosphatidic acid (PA) or transferred to the endoplasmic reticulum (ER) by the Synaptotagmin 1 (SYT1) protein at ER-PM Contact Sites (CS). In Arabidopsis, the clearance of DAG at the PM (avoiding deleterious accumulation) by the transfer activity of SYT is essential to maintain PM stability after stress. In this study we identify that DGK1 and DGK2 form a module with SYT1 at ER-PM CS through interaction of their C1 and C2 domains respectively. Global transcriptomic and metabolomic analyses confirms that SYT1 and DGK1/DGK2 are functionally related and lipidomic analysis supports the hypothesis that DGK1 and DGK2 function at the ER by phosphorylating DAG transferred by SYT1 from the PM. DGK1 and DGK2 show structural similarity to human DGKε, the DGK isoform that function at ER-PM CS in the phosphoinositide (PI) cycle. Our data indicate that components of the PI cycle are conserved between animals and plants and provide a novel mechanism leading to an increase in the efficiency of the PI cycle by channeling the transport and hydrolysis of DAG at the ER-PM CS

Relationship Between Aerosol Optical Depth and Particulate Matter Over Singapore: Effects of Aerosol Vertical Distributions

As part of the Seven Southeast Asian Studies (7SEAS) program, an Aerosol Robotic Network (AERONET) sun photometer and a Micro-Pulse Lidar Network (MPLNET) instrument have been deployed at Singapore to study the regional aerosol environment of the Maritime Continent (MC). In addition, the Navy Aerosol Analysis and Prediction System (NAAPS) is used to model aerosol transport over the region. From 24 September 2009 to 31 March 2011, the relationships between ground-, satellite- and model-based aerosol optical depth (AOD) and particulate matter with aerodynamic equivalent diameters less than 2.5 microns (PM2.5) for air quality applications are investigated. When MPLNET-derived aerosol scale heights are applied to normalize AOD for comparison with surface PM2.5 data, the empirical relationships are shown to improve with an increased 11%, 10% and 5% in explained variances, for AERONET, MODIS and NAAPS respectively. The ratios of root mean square errors to standard deviations for the relationships also show corresponding improvements of 8%, 6% and 2%. Aerosol scale heights are observed to be bimodal with a mode below and another above the strongly-capped/deep near-surface layer (SCD; 0-1.35 km). Aerosol extinctions within the SCD layer are well-correlated with surface PM2.5 concentrations, possibly due to strong vertical mixing in the region

VLT/X-shooter spectroscopy of the afterglow of the Swift GRB 130606A: Chemical abundances and reionisation at z∼6z\sim6

The reionisation of the Universe is thought to have ended around z~6, as inferred from spectroscopy of distant bright background sources, such as quasars (QSO) and gamma-ray burst (GRB) afterglows. Furthermore, spectroscopy of a GRB afterglow provides insight in its host galaxy, which is often too dim and distant to study otherwise. We present the high S/N VLT/X-shooter spectrum of GRB130606A at z=5.913. We aim to measure the degree of ionisation of the IGM between 5.02<z<5.84 and to study the chemical abundance pattern and dust content of its host galaxy. We measured the flux decrement due to absorption at Ly$\alpha$, $\beta$ and $\gamma$ wavelength regions. The hydrogen and metal absorption lines formed in the host galaxy were fitted with Voigt profiles to obtain column densities. Our measurements of the Ly$\alpha$-forest optical depth are consistent with previous measurements of QSOs, but have a much smaller uncertainty. The analysis of the red damping wing yields a neutral fraction $x_{HI}<0.05$ (3$\sigma$). We obtain column density measurements of several elements. The ionisation corrections due to the GRB is estimated to be negligible (<0.03 dex), but larger corrections may apply due to the pre-existing radiation field (up to 0.4 dex based on sub-DLA studies). Our measurements confirm that the Universe is already predominantly ionised over the redshift range probed in this work, but was slightly more neutral at z>5.6. GRBs are useful probes of the ionisation state of the IGM in the early Universe, but because of internal scatter we need a larger statistical sample to draw robust conclusions. The high [Si/Fe] in the host can be due to dust depletion, alpha-element enhancement, or a combination of both. The very high value of [Al/Fe]=2.40+/-0.78 might connected to the stellar population history. We estimate the host metallicity to be -1.7<[M/H]<-0.9 (2%-13% of solar). (trunc.)Comment: 15 pages, 12 figure

Cuspons, peakons and regular gap solitons between three dispersion curves

A general wave model with the cubic nonlinearity is introduced to describe a situation when the linear dispersion relation has three branches, which would intersect in the absence of linear couplings between the three waves. Actually, the system contains two waves with a strong linear coupling between them, to which a third wave is then coupled. This model has two gaps in its linear spectrum. Realizations of this model can be made in terms of temporal or spatial evolution of optical fields in, respectively, a planar waveguide or a bulk-layered medium resembling a photonic-crystal fiber. Another physical system described by the same model is a set of three internal wave modes in a density-stratified fluid. A nonlinear analysis is performed for solitons which have zero velocity in the reference frame in which the group velocity of the third wave vanishes. Disregarding the self-phase modulation (SPM) term in the equation for the third wave, we find two coexisting families of solitons: regular ones, which may be regarded as a smooth deformation of the usual gap solitons in a two-wave system, and cuspons with a singularity in the first derivative at their center. Even in the limit when the linear coupling of the third wave to the first two vanishes, the soliton family remains drastically different from that in the linearly uncoupled system; in this limit, regular solitons whose amplitude exceeds a certain critical value are replaced by peakons. While the regular solitons, cuspons, and peakons are found in an exact analytical form, their stability is tested numerically, which shows that they all may be stable. If the SPM terms are retained, we find that there again coexist two different families of generic stable soliton solutions, namely, regular ones and peakons.Comment: a latex file with the text and 10 pdf files with figures. Physical Review E, in pres