The effect of chosen extraterrestrial solar spectrum on clear-sky atmospheric absorption and heating rates in the near infrared

The extraterrestrial solar spectrum (ESS) is an important component in near infrared (near-IR) radiative transfer calculations. However, the impact of a particular choice of the ESS in these regions has been given very little attention. A line-by-line (LBL) transfer model has been used to calculate the absorbed solar irradiance and solar heating rates in the near-IR from 2000-10000 cm−1(1-5 μm) using different ESS. For overhead sun conditions in a mid-latitude summer atmosphere, the absorbed irradiances could differ by up to about 11 Wm−2 (8.2%) while the tropospheric and stratospheric heating rates could differ by up to about 0.13 K day−1 (8.1%) and 0.19 K day−1 (7.6%). The spectral shape of the ESS also has a small but non-negligible impact on these factors in the near-IR.

Molecular archaeology of Flaviviridae untranslated regions: duplicated RNA structures in the replication enhancer of flaviviruses and pestiviruses emerged via convergent evolution.

RNA secondary structures in the 3'untranslated regions (3'UTR) of the viruses of the family Flaviviridae, previously identified as essential (promoters) or beneficial (enhancers) for replication, have been analysed. Duplicated enhancer elements are revealed as a global feature in the evolution of the 3'UTR of distantly related viruses within the genera Flavivirus and Pestivirus. For the flaviviruses, duplicated structures occur in the 3'UTR of all four distantly related ecological virus subgroups (tick-borne, mosquito-borne, no known vector and insect-specific flaviviruses (ISFV). RNA structural differences distinguish tick-borne flaviviruses with discrete pathogenetic characteristics. For Aedes- and Culex-associated ISFV, secondary RNA structures with different conformations display numerous short ssRNA direct repeats, exposed as loops and bulges. Long quadruplicate regions comprise almost the entire 3'UTR of Culex-associated ISFV. Extended duplicated sequence and associated RNA structures were also discovered in the 3'UTR of pestiviruses. In both the Flavivirus and Pestivirus genera, duplicated RNA structures were localized to the enhancer regions of the 3'UTR suggesting an adaptive role predominantly in wild-type viruses. We propose sequence reiteration might act as a scaffold for dimerization of proteins involved in assembly of viral replicase complexes. Numerous nucleotide repeats exposed as loops/bulges might also interfere with host immune responses acting as a molecular sponge to sequester key host proteins or microRNAs.

Methane in the atmosphere of the transiting hot Neptune GJ436b?

We present an analysis of seven primary transit observations of the hot Neptune GJ436b at 3.6, 4.5, and 8 μm obtained with the Infrared Array Camera on the Spitzer Space Telescope. After correcting for systematic effects, we fitted the light curves using the Markov Chain Monte Carlo technique. Combining these new data with the EPOXI, Hubble Space Telescope, and ground-based V, I, H, and Ks published observations, the range 0.5-10 μm can be covered. Due to the low level of activity of GJ436, the effect of starspots on the combination of transits at different epochs is negligible at the accuracy of the data set. Representative climate models were calculated by using a three-dimensional, pseudospectral general circulation model with idealized thermal forcing. Simulated transit spectra of GJ436b were generated using line-by-line radiative transfer models including the opacities of the molecular species expected to be present in such a planetary atmosphere. A new, ab-initio-calculated, line list for hot ammonia has been used for the first time. The photometric data observed at multiple wavelengths can be interpreted with methane being the dominant absorption after molecular hydrogen, possibly with minor contributions from ammonia, water, and other molecules. No clear evidence of carbon monoxide and carbon dioxide is found from transit photometry. We discuss this result in the light of a recent paper where photochemical disequilibrium is hypothesized to interpret secondary transit photometric data. We show that the emission photometric data are not incompatible with the presence of abundant methane, but further spectroscopic data are desirable to confirm this scenario.

Bond-selective energy redistribution in the chemisorption of CH3D and CD3H on Pt{1 1 0}-(1 2): a first-principles molecular dynamics study

We have investigated the chemisorption of CH3D and CD3H on Pt{11 0}-(1 2) by performing first-principles molecular dynamics simulations of the recombinative desorption of CH3D (from adsorbed methyl and deuterium) and of CD3H (from adsorbed trideuteromethyl and hydrogen). Vibrational analysis of the symmetry adapted internal coordinates of the desorbing molecules shows that excitation of the single C– D (C–H) bond in the parent molecule is strongly correlated with energy excess in the reaction coordinate. The results of the molecular dynamics simulations are consistent with observed mode- and bond-specific reactivity measurements for chemisorption of methane and its isotopomers on platinum and nickel surfaces.

Molecular insights of p47phox phosphorylation dynamics in the regulation of NADPH oxidase activation and superoxide production

Phagocyte superoxide production by a multicomponent NADPH oxidase is important in host defense against microbial invasion. However inappropriate NADPH oxidase activation causes inflammation. Endothelial cells express NADPH oxidase and endothelial oxidative stress due to prolonged NADPH oxidase activation predisposes many diseases. Discovering the mechanism of NADPH oxidase activation is essential for developing novel treatment of these diseases. The p47phox is a key regulatory subunit of NADPH oxidase; however, due to the lack of full protein structural information, the mechanistic insight of p47phox phosphorylation in NADPH oxidase activation remains incomplete. Based on crystal structures of three functional domains, we generated a computational structural model of the full p47phox protein. Using a combination of in silico phosphorylation, molecular dynamics simulation and protein/protein docking, we discovered that the C-terminal tail of p47phox is critical for stabilizing its autoinhibited structure. Ser-379 phosphorylation disrupts H-bonds that link the C-terminal tail to the autoinhibitory region (AIR) and the tandem Src homology 3 (SH3) domains, allowing the AIR to undergo phosphorylation to expose the SH3 pocket for p22phox binding. These findings were confirmed by site-directed mutagenesis and gene transfection of p47phox_/_ coronary microvascular cells. Compared with wild-type p47phoxcDNAtransfected cells, the single mutation of S379A completely blocked p47phox membrane translocation, binding to p22phox and endothelial O2 . production in response to acute stimulation of PKC. p47phox C-terminal tail plays a key role in stabilizing intramolecular interactions at rest. Ser-379 phosphorylation is a molecular switch which initiates p47phox conformational changes and NADPH oxidase-dependent superoxide production by cells.

Intensities and self-broadening coefficients of the strongest water vapour lines in the 2.7 and 6.25μm absorption bands

Intensities and self-broadening coefficients are presented for about 460 of the strongest water vapour lines in the spectral regions 1400–1840 cm−1 and 3440–3970 cm−1 at room temperature, obtained from rather unique measurements using a 5-mm-path-length cell. The retrieved spectral line parameters are compared with those in the HITRAN database ver. 2008 and 2012 and with recent ab-initio calculations. Both the retrieved intensities and half-widths are on average in reasonable agreement with those in HITRAN-2012. Maximum systematic differences do not exceed 4% for intensities (1600 cm−1 band) and 7% for self-broadening coefficients (3600 cm−1 band). For many lines however significant disagreements were detected with the HITRAN-2012 data, exceeding the average uncertainty of the retrieval. In addition, water vapour line parameters for 5300 cm−1 (1.9 μm) band reported by us in 2005 were also compared with HITRAN-2012, and show average differences of 4–5% for both intensities and half-widths.