Hydrophobicity with atomic resolution: Steady-state and ultrafast X-ray absorption and molecular dynamics studies

Static and time-resolved X-ray absorption spectroscopy (XAS) is used to probe the solvent shell structure around iodide and iodine. In particular, we characterize the changes observed upon electron abstraction of aqueous iodide, which reflects the transition from hydrophilic to hydrophobic solvation after impulsive electron abstraction from iodide. The static spectrum of aqueous iodide, which is analyzed using quantum mechanical/molecular mechanics (QM/MM) molecular dynamics (MD) simulations, indicates that the hydrogens of the closest water molecules point toward the iodide, as expected for hydrophilic solvation. In addition, these simulations demonstrate a small anisotropy in the solvent shell. Following electron abstraction, most of the water molecules move away from iodine, while one comes closer to form a complex with it that survives for 3-4 ps. This lifetime is governed by the reorganization of the main solvation shell, basically the time it takes for the water molecules to reform a hydrogen bond network in the hydrophobic solvation shel

Gene expression analysis of the innate immune system during early rearing and weaning of meagre (Argyrosomus regius)

The present study is the first report of some representative innate immune genes in meagre (Argyrosomus regius) larvae. This study has specifically focused on the growth period from hatching to the juvenile stage, a critical time in marine fish development when reliance on innate immune mechanisms are required for survival. We report molecular cloning of partial open reading frames and expression patterns for some innate immune genes (c3, cox2, met, lyzc, mxp, myd88, nod2, nod3). In addition, phylogenetic analyses of some of the sequences obtained was performed where confusion among closely allied isoforms may have existed. These results show the met isoform from meagre is met II, an isoform more similar to a homolog described in Larimichthys crocea; lysozyme (lyzc) corresponds to the c-type and NOD isoforms (nod2, nod3) separate into different clades confirming their distinctness within a common evolutionary history. Gene expression profiles of innate genes were investigated, for nine developmental stages, from 8 days post-hatching (dph) to 120 dph. Present results demonstrated that c3, cox2, met II, lyzc, mxp, myd88, nod2, and nod3 were expressed in all stages of larval development and displayed distinct expression profiles in separate tissues (kidney, spleen gut and gill). Moreover, expression patterns suggested theses innate immune genes may be influenced by feeding practices, i.e. switching from live prey (rotifer and Artemia) and weaning onto an inert commercial diet. In addition to evaluating changes in gene expression during early development, this study evaluated the modulation of gene expression by means of in vivo trials in juveniles that were stimulated with PAMPs (LPS, poly I:C, β-glucan). These results revealed significant changes in mRNA levels of target genes in the kidney, spleen, gut and gills. However, expression profiles differed in magnitude depending on the stimulant and/or tissue. These results are discussed in terms of their relevance and potential application in aquaculture practices.info:eu-repo/semantics/acceptedVersio

Characterisation of arginase paralogues in salmonids and their modulation by immune stimulation/ infection

Acknowledgements OB was supported by a PhD studentship from the Marine Collaboration Research Forum (MarCRF), which is a collaboration between the University of Aberdeen and Marine Scotland Science, Marine Laboratory (MSS), and through Scottish Government project AQ0080. EW was supported by a PhD studentship from the Ministry of Science and Technology of Thailand and Mahasarakham University. TW received funding from the Marine Alliance for Science and Technology for Scotland (MASTS), a pooling initiative funded by the Scottish Funding Council (grant reference HR09011), and JWH was supported by the Swiss National Science Foundation (grant reference CRSII3_147649-1).Peer reviewedPostprin

Hydrophobicity with atomic resolution: Steady-state and ultrafast X-ray absorption and molecular dynamics studies

Static and time-resolved X-ray absorption spectroscopy (XAS) is used to probe the solvent shell structure around iodide and iodine. In particular, we characterize the changes ob served upon electron abstraction of aqueous iodide, which reflects the transition from hydrophilic to hydrophobic solvation after impulsive electron abstraction from iodide. The static spectrum of aqueous iodide, which is analyzed using quantum mechanical/molecular mechanics (QM/MM) molecular dynamics (MD) simulations, indicates that the hydrogens of the closest water molecules point toward the iodide, as expected for hydrophilic solvation. In addition, these simulations demonstrate a small anisotropy in the solvent shell. Following electron abstraction, most of the water molecules move away from iodine, while one comes closer to form a complex with it that survives 3-4 ps. This lifetime is governed by the reorganization of the main solvation shell, basically the time it takes for the water molecules to reform a hydrogen bond network in the hydrophobic solvation shell

Spectra and Light Curves of Failed Supernovae

Astronomers have proposed a number of mechanisms to produce supernova explosions. Although many of these mechanisms are now not considered primary engines behind supernovae, they do produce transients that will be observed by upcoming ground-based surveys and NASA satellites. Here we present the first radiation-hydrodynamics calculations of the spectra and light curves from three of these "failed" supernovae: supernovae with considerable fallback, accretion induced collapse of white dwarfs, and energetic helium flashes (also known as type .Ia supernovae).Comment: 33 pages, 14 figure

Directly observing squeezed phonon states with femtosecond x-ray diffraction

Squeezed states are quantum states of a harmonic oscillator in which the variance of two conjugate variables each oscillate out of phase. Ultrafast optical excitation of crystals can create squeezed phonon states, where the variance of the atomic displacements oscillates due to a sudden change in the interatomic bonding strength. With femtosecond x-ray diffraction we measure squeezing oscillations in bismuth and conclude that they are consistent with a model in which electronic excitation softens all phonon modes by a constant scaling factor

Early Observations And Analysis Of The Type Ia SN 2014J In M82

We present optical and near infrared (NIR) observations of the nearby Type Ia SN 2014J. Seventeen optical and 23 NIR spectra were obtained from 10 days before (-10d) to 10 days after (+10d) the time of maximum B-band brightness. The relative strengths of absorption features and their patterns of development can be compared at one day intervals throughout most of this period. Carbon is not detected in the optical spectra, but we identify C I lambda 1.0693 in the NIR spectra. Mg II lines with high oscillator strengths have higher initial velocities than other Mg II lines. We show that the velocity differences can be explained by differences in optical depths due to oscillator strengths. The spectra of SN 2014J show that it is a normal SN Ia, but many parameters are near the boundaries between normal and high-velocity subclasses. The velocities for OI, Mg II, Si II, S Ca a, and Fell suggest that SN 2014J has a layered structure with little or no mixing. That result is consistent with the delayed detonation explosion models. We also report photometric observations, obtained from -10d to +29d, in the UBVRIJH and K-s bands. The template fitting package SNooPy is used to interpret the light curves and to derive photometric parameters. Using R-v = 1.46, which is consistent with previous studies, SNooPy finds that A(v) = 1.80 for E(B - V)(host) = 1.23 +/- 0.06 mag. The maximum B-band brightness of -19.19 +/- 0.10 mag was reached on February 1.74 UT +/- 0.13 days and the supernova has a decline parameter, Delta m(15), of 1.12 +/- 0.02 mag.Department of Space, Government of IndiaHungarian OTKA NN-107637NSF AST-1109801, AST-1151462, AST-1211196NSF Astronomy and Astrophysics Postdoctoral Fellowship AST-1302771NASA through a grant from the Space Telescope Science Institute GO-12540NASA NAS5-26555Swedish Research CouncilSwedish National Space BoardDanish Agency for Science and Technology and Innovation realized through a Sapere Aude Level 2 grantAstronom

Ontogeny and modulation after PAMPs stimulation of β-defensin, hepcidin, and piscidin antimicrobial peptides in meagre (Argyrosomus regius)

Antimicrobial peptides (AMPs), components of innate immunity, play an important role in protecting fish. In this study we report the molecular cloning of full open reading frames and characterization of expression of three AMP genes (β-defensin (defb), hepcidin (hep2), piscidin (pisc) in meagre (Argyrosomus regius). A phylogenetic analysis of the expressed sequences obtained shows the defensin isoform forms a clade with the other members of the beta class of this family, hepcidin corresponds to hepcidin 2, and piscidin corresponds to class I of its respective family. Gene expression profiles of AMPs was investigated, by means of quantification of mRNA in nine development stages, from 8 days post-hatching (dph) to accomplishment of juvenile form (120 dph). During development it was demonstrated defb, hep2, pisc were expressed in all stages of larval development and in juvenile tissues (kidney, spleen gut and gill). Moreover, expression patterns suggest the expression levels of theses AMPs are influenced by live prey (rotifer, Artemia) and first intake of commercial diet. Induction experiments in vivo (24 h) and in vitro (4, 12, 24 h) with PAMPs (LPS, poly (I:C), β-glucan) revealed significant changes in gene expression of the three AMP genes, in kidney, spleen, gut and gill. However, expression profiles differed in magnitude and time course response. defb expression shows a similar trend in vivo and in vitro in kidney at 24 h after LPS and β-glucan stimulation. The hep2 expression levels were up-regulated upon β-glucan challenge in vivo, more in gut and gills than kidney, while in vitro hep2 expression was up-regulated in kidney cells by LPS, poly (I:C), β-glucan (4 h). pisc expression was up-regulated in kidney cells, splenocytes by β-glucan, but in gill cells by poly (I:C) and β-glucan in vivo. However, pisc expression was upregulated in kidney cells by β-glucan and gill cells by LPS at 4 post-stimulation in vitro. These data suggest that AMPs play an important role in defense against pathogens, with each AMP having differing efficacies against specific types of microorganisms, although follow-up studies focusing on the biological activities in fish are needed.info:eu-repo/semantics/acceptedVersio

Role of humic acid in the stability of Ag nanoparticles in suboxic conditions

Stability and temporal changes in size distributions have been observed for citrate- (cit) and polyvinylpyrrolidone- (PVP) capped silver nanoparticles (AgNPs), in the presence or absence of sulfide and natural organic matter (NOM, as humic acid), while under suboxic conditions. There were substantial differences in the influence of the two capping agents, with PVP–AgNPs showing few or no significant changes in apparent stability or particle size distribution under the conditions examined, while the apparent size distributions of citrate-capped AgNPs changed rapidly. Sulfide and humic acid each individually caused immediate increases in cit–AgNP size distributions, which were then relatively stable over 60–145 days. This may be due to sulfide bridging and cation bridging, respectively. However, in competition, it was the influence of the humic acid that dominated that of the sulfide. These observations have implications for environmental fate and toxicity of AgNP. The increased stability in the presence of even low concentrations of NOM may limit the rapidity of Ag dispersal but may also concentrate the dose received by organisms, which subsequently ingest the stabilized particles

SN2012ab: A Peculiar Type IIn Supernova with Aspherical Circumstellar Material

We present photometry, spectra, and spectropolarimetry of supernova (SN) 2012ab, mostly obtained over the course of $\sim 300$ days after discovery. SN 2012ab was a Type IIn (SN IIn) event discovered near the nucleus of spiral galaxy 2MASXJ12224762+0536247. While its light curve resembles that of SN 1998S, its spectral evolution does not. We see indications of CSM interaction in the strong intermediate-width emission features, the high luminosity (peak at absolute magnitude $M=-19.5$), and the lack of broad absorption features in the spectrum. The H$\alpha$ emission undergoes a peculiar transition. At early times it shows a broad blue emission wing out to $-14{,}000$ km $\mathrm{s^{-1}}$ and a truncated red wing. Then at late times ($>$ 100$\,$days) it shows a truncated blue wing and a very broad red emission wing out to roughly $+20{,}000$ km $\mathrm{s^{-1}}$. This late-time broad red wing probably arises in the reverse shock. Spectra also show an asymmetric intermediate-width H$\alpha$ component with stronger emission on the red side at late times. The evolution of the asymmetric profiles requires a density structure in the distant CSM that is highly aspherical. Our spectropolarimetric data also suggest asphericity with a strong continuum polarization of $\sim 1-3$% and depolarization in the H$\alpha$ line, indicating asphericity in the CSM at a level comparable to that in other SNe IIn. We estimate a mass-loss rate of $\dot{M} = 0.050\, {\rm M}_{\odot}\,\mathrm{yr^{-1}}$ for $v_{\rm pre} = 100$$\,$km$\,$$\mathrm{s^{-1}}$ extending back at least 75$\,$yr prior to the SN. The strong departure from axisymmetry in the CSM of SN 2012ab may suggest that the progenitor was an eccentric binary system undergoing eruptive mass loss.Comment: 18 pages, 12 figure