Density-Enhanced Gas and Dust Shells in a New Chemical Model for IRC+10216

A new chemical model is presented for the carbon-rich circumstellar envelope (CSE) of the asymptotic giant branch star IRC+10216. The model includes shells of matter with densities that are enhanced relative to the surrounding circumstellar medium. The chemical model uses an updated reaction network including reactions from the RATE06 database and a more detailed anion chemistry. In particular, new mechanisms are considered for the formation of CN-, C3N-, and C2H-, and for the reactions of hydrocarbon anions with atomic nitrogen and with the most abundant cations in the CSE. New reactions involving H- are included which result in the production of significant amounts of C2H- and CN- in the inner envelope. The calculated radial molecular abundance profiles for the hydrocarbons C2H, C4H, and C6H and the cyanopolyynes HC3N and HC5N show narrow peaks which are in better agreement with observations than previous models. Thus, the narrow rings observed in molecular microwave emission surrounding IRC+10216 are interpreted as arising in regions of the envelope where the gas and dust densities are greater than the surrounding circumstellar medium. Our models show that CN- and C2H- may be detectable in IRC+10216 despite the very low theorized radiative electron attachment rates of their parent neutral species. We also show that magnesium isocyanide (MgNC) can be formed in the outer envelope through radiative association involving Mg+ and the cyanopolyyne species.

Metals in the Exosphere of the Highly Irradiated Planet WASP-12b

We present near-UV transmission spectroscopy of the highly irradiated transiting exoplanet WASP-12b, obtained with the Cosmic Origins Spectrograph on the Hubble Space Telescope. The spectra cover three distinct wavelength ranges: NUVA (2539-2580 Å), NUVB (2655-2696 Å), and NUVC (2770-2811 Å). Three independent methods all reveal enhanced transit depths attributable to absorption by resonance lines of metals in the exosphere of WASP-12b. Light curves of total counts in the NUVA and NUVC wavelength ranges show a detection at a 2.5s level. We detect extra absorption in the Mg II ??2800 resonance line cores at the 2.8s level. The NUVA, NUVB, and NUVC light curves imply effective radii of 2.69 ± 0.24 R J , 2.18 ± 0.18 R J , and 2.66 ± 0.22 R J respectively, suggesting the planet is surrounded by an absorbing cloud which overfills the Roche lobe. We detect enhanced transit depths at the wavelengths of resonance lines of neutral sodium, tin, and manganese, and at singly ionized ytterbium, scandium, manganese, aluminum, vanadium, and magnesium. We also find the statistically expected number of anomalous transit depths at wavelengths not associated with any known resonance line. Our data are limited by photon noise, but taken as a whole the results are strong evidence for an extended absorbing exosphere surrounding the planet. The NUVA data exhibit an early ingress, contrary to model expectations; we speculate this could be due to the presence of a disk of previously stripped material.

Spatial characterization of salt accumulation in early stage limestone weathering using probe permeametry

This research characterizes the weathering of natural building stone using an unsteady-state portable probe permeameter. Variations between the permeability properties of fresh rock and the same rocks after the early stages of a salt weathering simulation are used to examine the effects of salt accumulation on spatial variations in surface rock permeability properties in two limestones from Spain. The Fraga and Tudela limestones are from the Ebro basin and are of Miocene age. Both stone types figure largely in the architectural heritage of Spain and, in common with many other building limestones, they are prone to physical damage from salt crystallization in pore spaces. To examine feedbacks associated with salt accumulation during the early stages of this weathering process, samples of the two stone types were subjected to simulated salt weathering under laboratory conditions using magnesium sulphate and sodium chloride at concentrations of 5% and 15%. Permeability mapping and statistical analysis (aspatial statistics and spatial prediction) before and after salt accumulation are used to assess changes in the spatial variability of permeability and to correlate these changes with salt movement, porosity change, potential rock deterioration and textural characteristics. Statistical analyses of small-scale permeability measurements are used to evaluate the drivers for decay and hence aid the prediction of the weathering behaviour of the two limestones.

Interaction of prothrombin with a phospholipid surface: evidence for a membrane-induced conformational change

Prothrombin interacts with phosphatidylserine containing platelet membranes via its N-terminal, gamma-carboxyglutamate (gla) residue-rich domain. Once bound it is cleaved to form the active protease, thrombin (factor IIa). Human prothrombin was cleaved with cathepsin G in the absence of calcium and magnesium ions. Under these conditions, the gla domain was removed. Phospholipid protected the protein from this proteolytic event, and this suggests that a conformational change may be induced by interaction with phospholipids. Binding of prothrombin to a surface containing 20% phosphatidylserine/80% phosphatidylcholine was detected by surface plasmon resonance, whereas no interaction with gla-domainless prothrombin was observed. Binding of intact prothrombin in the presence of calcium ions showed complex association kinetics, suggesting multiple modes of initial interaction with the surface. The kinetics of the dissociation phase could be fitted to a two-phase, exponential decay. This implies that there are at least two forms of the protein on the surface one of which dissociates tenfold more slowly than the other. Taken together, these data suggest that, on binding to a membrane surface, prothrombin undergoes a conformational change to a form which binds more tightly to the membrane.

The chemical composition of two supergiants in the dwarf irregular galaxy WLM

The chemical composition of two stars in WLM has been determined from high-quality Ultraviolet-Visual Echelle Spectrograph (UVES) data obtained at the VLT-UT2. The model atmospheres analysis shows that they have the same metallicity, [Fe/H] = - 0.38 +/- 0.20 (+/- 0.29). Reliable magnesium abundances are determined from several lines of two ionization states in both stars resulting in [Mg/Fe] = - 0.24 +/- 0.16 (+/- 0.28). This result suggests that the [alpha(Mg)/Fe] ratio in WLM may be suppressed relative to solar abundances ( also supported by differential abundances relative to similar stars in NGC 6822 and the Small Magellanic Cloud [SMC]). The absolute Mg abundance, [Mg/H] = -0.62, is high relative to what is expected from the nebulae though, where two independent spectroscopic analyses of the H II regions in WLM yield [O/H] = - 0.89. Intriguingly, the oxygen abundance determined from the O I lambda6158 feature in one WLM star is [O/H] = - 0.21 +/- 0.10 (+/- 0.05), corresponding to 5 times higher than the nebular oxygen abundance. This is the first time that a significant difference between stellar and nebular oxygen abundances has been found, and currently, there is no simple explanation for this difference. The two stars are massive supergiants with distances that clearly place them in WLM. They are young ( less than or equal to 10 Myr) and should have a similar composition to the ISM. Additionally, differential abundances suggest that the O/Fe ratio in the WLM star is consistent with similar stars in NGC 6822 and the SMC, galaxies where the average stellar oxygen abundances are in excellent agreement with the nebular results. If the stellar abundances reflect the true composition of WLM, then this galaxy lies well above the metallicity-luminosity relationship for dwarf irregular galaxies. It also suggests that WLM is more chemically evolved than currently interpreted from its color-magnitude diagram. The similarities between the stars in WLM and NGC 6822 suggest that these two galaxies may have had similar star formation histories.

The WaaL O-antigen lipopolysaccharide ligase has features in common with metal ion-independent inverting glycosyltransferases(*)

WaaL is a membrane enzyme that catalyzes a key step in lipopolysaccharide (LPS) synthesis: the glycosidic bonding of a sugar at the proximal end of the undecaprenyl-diphosphate (Und-PP) O-antigen with a terminal sugar of the lipid A-core oligosaccharide (OS). Utilizing an in vitro assay, we demonstrate here that ligation with purified Escherichia coli WaaL occurs without adenosine-5'-triphosphate (ATP) and magnesium ions. Furthermore, E. coli and Pseudomonas aeruginosa WaaL proteins cannot catalyze ATP hydrolysis in vitro. We also show that a lysine substitution of the arginine (Arg)-215 residue renders an active protein, whereas WaaL mutants with alanine replacements in the periplasmic-exposed residues Arg-215, Arg-288 and histidine (His)-338 and also the membrane-embedded aspartic acid-389 are nonfunctional. An in silico approach, combining predicted topological information with the analysis of sequence conservation, confirms the importance of a positive charge at the small periplasmic loop of WaaL, since an Arg corresponding to Arg-215 was found at a similar position in all the WaaL homologs. Also, a universally conserved H[NSQ]X(9)GXX[GTY] motif spanning the C-terminal end of the predicted large periplasmic loop and the membrane boundary of the transmembrane helix was identified. The His residue in this motif corresponds to His-338. A survey of LPS structures in which the linkage between O-antigen and lipid A-core OS was elucidated reveals that it is always in the beta-configuration, whereas the sugars bound to Und-PP are in the alpha-configuration. Together, our biochemical and in silico data argue that WaaL proteins use a common reaction mechanism and share features of metal ion-independent inverting glycosyltransferases.

FhCaBP4: A Fasciola hepatica calcium binding protein with EF-hand and dynein light chain domains

In trematodes, there is a family of proteins which combine EF-hand-containing domains with dynein light chain (DLC)-like domains. A member of this family from the liver fluke, Fasciola hepatica-FhCaBP4-has been identified and characterised biochemically. FhCaBP4 has an N-terminal domain containing two imperfect EF-hand sequences and a C-terminal dynein light chain-like domain. Molecular modelling predicted that the two domains are joined by a flexible linker. Native gel electrophoresis demonstrated that FhCaBP4 binds to calcium, manganese, barium and strontium ions, but not to magnesium or zinc ions. The hydrophobic, fluorescent probe 8-anilinonaphthalene-1-sulphonate bound more tightly to FhCaBP4 in the presence of calcium ions. This suggests that the protein undergoes a conformational change on ion binding which increases the number of non-polar residues on the surface. FhCaBP4 was protected from limited proteolysis by the calmodulin antagonist W7, but not by trifluoperazine or praziquantel. Protein-protein cross-linking experiments showed that FhCaBP4 underwent calcium ion-dependent dimerisation. Since DLCs are commonly dimeric, it is likely that FhCaBP4 dimerises through this domain. The molecular model reveals that the calcium ion-binding site is located close to a key sequence in the DLC-like domain, suggesting a plausible mechanism for calcium-dependent dimerisation.

FhCaBP3: A Fasciola hepatica calcium binding protein with EF-hand and dynein light chain domains

A DNA sequence encoding a protein with predicted EF-hand and dynein light chain binding domains was identified in a Fasciola hepatica EST library. Sequence analysis of the encoded protein revealed that the most similar known protein was the Fasciola gigantica protein FgCaBP3 and so this newly identified protein was named FhCaBP3. Molecular modelling of FhCaBP3 predicted a highly flexible N-terminal region, followed by a domain containing two EF-hand motifs the second of which is likely to be a functioning divalent ion binding site. The C-terminal domain of the protein contains a dynein light chain like region. Interestingly, molecular modelling predicts that calcium ion binding to the N-terminal domain destabilises the ß-sheet structure of the C-terminal domain. FhCaBP3 can be expressed in, and purified from, Escherichia coli. The recombinant protein dimerises and the absence of calcium ions appeared to promote dimerisation. Native gel shift assays demonstrated that the protein bound to calcium and manganese ions, but not to magnesium, barium, zinc, strontium, nickel, copper or cadmium ions. FhCaBP3 interacted with the calmodulin antagonists trifluoperazine, N-(6-aminohexyl)-5-chloro-1-naphthalenesulfonamide and chlorpromazine as well as the myosin regulatory light chain-binding drug praziquantel. Despite sequence and structural similarities to other members of the same protein family from F. hepatica, FhCaBP3 has different biochemical properties to the other well characterised family members, FH22 and FhCaBP4. This suggests that each member of this trematode calcium-binding family has discrete functional roles within the organism.

Analysis of Betaine and Choline Contents of Aleurone, Bran, and Flour Fractions of Wheat (Triticum aestivum L.) Using 1H Nuclear Magnetic Resonance (NMR) Spectroscopy

In conventional milling, the aleurone layer is combined with the bran fraction. Studies indicate that the bran fraction of wheat contains the majority of the phytonutrients betaine and choline, with relatively minor concentrations in the refined flour. This present study suggests that the wheat aleurone layer (Triticum aestivum L. cv. Tiger) contains the greatest concentration of both betaine and choline (1553.44 and 209.80 mg/100 g of sample, respectively). The bran fraction contained 866.94 and 101.95 mg/100 g of sample of betaine and choline, respectively, while the flour fraction contained 23.30 mg/100 g of sample (betaine) and 28.0 mg/100 g of sample (choline). The betaine content for
the bran was lower, and the choline content was higher compared to previous studies, although it is known that there is large variation in betaine and choline contents between wheat cultivars. The ratio of betaine/choline in the aleurone fraction was approximately 7:1; in the bran, the ratio was approximately 8:1; and in the flour fraction, the ratio was approximately 1:1. The study further
emphasizes the superior phytonutrient composition of the aleurone layer.
INTRODUCTION
Wheat is a valuable source of betaine, choline (1, 2), B
vitamins, vitamin E, and a number of minerals, including iron,
zinc, magnesium, and phosphorus (3). Epidemiological studies
indicate that whole-grain consumption is protective against
several chronic diseases (4-12). It has not been fully elucidated
how whole-grain cereals or specific fractions (13) exert their
protective effect, but it is thought to be due to their content of
several nutrients associated with the reduced risk of disease.
Conventionally, whole grain is separated during milling into
bran, germ, and flour (14). The nutrient composition of these
fractions differ markedly; refined wheat flour contains approximately
50% less vitamins and minerals than whole-grain
flour (

Profiling the ionome of rice and its use in discriminating geographical origins at the regional scale, China

Element profile was investigated for their use to trace the geographical origin of rice (Oryza sativa L.) samples. The concentrations of 13 elements (calcium (Ca), potassium (K), magnesium (Mg), phosphorus (P), boron (B), manganese (Mn), iron (Fe), nickel (Ni), copper (Cu), arsenic (As), selenium (Se), molybdenum (Mo), and cadmium (Cd)) were determined in the rice samples by inductively coupled plasma optical emission and mass spectrometry. Most of the essential elements for human health in rice were within normal ranges except for Mo and Se. Mo concentrations were twice as high as those in rice from Vietnam and Spain. Meanwhile, Se concentrations were three times lower in the whole province compared to the Chinese average level of 0.088 mg/kg. About 12% of the rice samples failed the Chinese national food safety standard of 0.2 mg/kg for Cd. Combined with the multi-elemental profile in rice, the principal component analysis (PCA), discriminant function analysis (DFA) and Fibonacci index analysis (FIA) were applied to discriminate geographical origins of the samples. Results indicated that the FIA method could achieve a more effective geographical origin classification compared with PCA and DFA, due to its efficiency in making the grouping even when the elemental variability was so high that PCA and DFA showed little discriminatory power. Furthermore, some elements were identified as the most powerful indicators of geographical origin: Ca, Ni, Fe and Cd. This suggests that the newly established methodology of FIA based on the ionome profile can be applied to determine the geographical origin of rice.

The progenitor mass of the Type IIP supernova SN 2004et from late-time spectral modeling

SN 2004et is one of the nearest and best-observed Type IIP supernovae, with a progenitor detection as well as good photometric and spectroscopic observational coverage well into the nebular phase. Based on nucleosynthesis from stellar evolution/explosion models we apply spectral modeling to analyze its 140-700 day evolution from ultraviolet to mid-infrared. We find a M_ZAMS= 15 Msun progenitor star (with an oxygen mass of 0.8 Msun) to satisfactorily reproduce [O I] 6300, 6364 {\AA} and other emission lines of carbon, sodium, magnesium, and silicon, while 12 Msun and 19 Msun models under- and overproduce most of these lines, respectively. This result is in fair agreement with the mass derived from the progenitor detection, but in disagreement with hydrodynamical modeling of the early-time light curve. From modeling of the mid-infrared iron-group emission lines, we determine the density of the "Ni-bubble" to rho(t) = 7E-14*(t/100d)^-3 g cm^-3, corresponding to a filling factor of f = 0.15 in the metal core region (V = 1800 km/s). We also confirm that silicate dust, CO, and SiO emission are all present in the spectra.

Microbial community of the deep-sea brine Lake Kryos seawater-brine interface is active below the chaotropicity limit of life as revealed by recovery of mRNA

Within the complex of deep, hypersaline anoxic lakes (DHALs) of the Mediterranean Ridge, we identified a new, unexplored DHAL and named it ‘Lake Kryos’ after a nearby depression. This lake is filled with magnesium chloride (MgCl2)-rich, athalassohaline brine (salinity > 470 practical salinity units), presumably formed by the dissolution of Messinian bischofite. Compared with the DHAL Discovery, it contains elevated concentrations of kosmotropic sodium and sulfate ions, which are capable of reducing the net chaotropicily of MgCl2-rich solutions. The brine of Lake Kryos may therefore be biologically permissive at MgCl2 concentrations previously considered incompatible with life. We characterized the microbiology of the seawater–Kryos brine interface and managed to recover mRNA from the 2.27–3.03 MMgCl2 layer (equivalent to 0.747–0.631 water activity), thereby expanding the established chaotropicity window-for-life. The primary bacterial taxa present there were Kebrit Deep Bacteria 1 candidate division and DHAL-specific group of organisms, distantly related toDesulfohalobium. Two euryarchaeal candidate divisions, Mediterranean Sea Brine Lakes group 1 and halophilic cluster 1, accounted for > 85% of the rRNA-containing archaeal clones derived from the 2.27–3.03 M MgCl2 layer, but were minority community-members in the overlying interface-layers. These findings shed light on the plausibility of life in highly chaotropic environments, geochemical windows for microbial extremophiles, and have implications for habitability elsewhere in the Solar System.