Heppa III Intercomparison Experiment on Electron Precipitation Impacts: 2. Model‐Measurement Intercomparison of Nitric Oxide (NO) During a Geomagnetic Storm in April 2010

Precipitating auroral and radiation belt electrons are considered to play an important part in the natural forcing of the middle atmosphere with a possible impact on the climate system. Recent studies suggest that this forcing is underestimated in current chemistry-climate models. The HEPPA III intercomparison experiment is a collective effort to address this point. In this study, we apply electron ionization rates from three data-sets in four chemistry-climate models during a geomagnetically active period in April 2010. Results are evaluated by comparison with observations of nitric oxide (NO) in the mesosphere and lower thermosphere. Differences between the ionization rate data-sets have been assessed in a companion study. In the lower thermosphere, NO densities differ by up to one order of magnitude between models using the same ionization rate data-sets due to differences in the treatment of NO formation, model climatology, and model top height. However, a good agreement in the spatial and temporal variability of NO with observations lends confidence that the electron ionization is represented well above 80 km. In the mesosphere, the averages of model results from all chemistry-climate models differ consistently with the differences in the ionization-rate data-sets, but are within the spread of the observations, so no clear assessment on their comparative validity can be provided. However, observed enhanced amounts of NO in the mid-mesosphere below 70 km suggest a relevant contribution of the high-energy tail of the electron distribution to the hemispheric NO budget during and after the geomagnetic storm on April 6

HEPPA III Intercomparison Experiment on Electron Precipitation Impacts: 1. Estimated Ionization Rates During a Geomagnetic Active Period in April 2010

Precipitating auroral and radiation belt electrons are considered an important part of the natural forcing of the climate system. Recent studies suggest that this forcing is underestimated in current chemistry-climate models. The High Energy Particle Precipitation in the Atmosphere III intercomparison experiment is a collective effort to address this point. Here, eight different estimates of medium energy electron (MEE) (urn:x-wiley:21699380:media:jgra56926:jgra56926-math-0001) ionization rates are assessed during a geomagnetic active period in April 2010. The objective is to understand the potential uncertainty related to the MEE energy input. The ionization rates are all based on the Medium Energy Proton and Electron Detector (MEPED) on board the NOAA/POES and EUMETSAT/MetOp spacecraft series. However, different data handling, ionization rate calculations, and background atmospheres result in a wide range of mesospheric electron ionization rates. Although the eight data sets agree well in terms of the temporal variability, they differ by about an order of magnitude in ionization rate strength both during geomagnetic quiet and disturbed periods. The largest spread is found in the aftermath of enhanced geomagnetic activity. Furthermore, governed by different energy limits, the atmospheric penetration depth varies, and some differences related to latitudinal coverage are also evident. The mesospheric NO densities simulated with the Whole Atmospheric Community Climate Model driven by highest and lowest ionization rates differ by more than a factor of eight. In a follow-up study, the atmospheric responses are simulated in four chemistry-climate models (CCM) and compared to satellite observations, considering both the CCM structure and the ionization forcing

Differential Base Stacking Interactions Induced by Trimethylene Interstrand DNA Cross-Links in the 5′-CpG-3′ and 5′-GpC-3′ Sequence Contexts

Synthetically derived trimethylene interstrand DNA cross-links have been used as surrogates for the native cross-links that arise from the 1,N 2-deoxyguanosine adducts derived from R,β-unsaturated aldehydes. The native enal-mediated cross-linking occurs in the 5′-CpG-3 ′ sequence context but not in the 5′-GpC-3 ′ sequence context. The ability of the native enal-derived 1,N 2-dG adducts to induce interstrand DNA cross-links in the 5′-CpG-3 ′ sequence as opposed to the 5′-GpC-3 ′ sequence is attributed to the destabilization of the DNA duplex in the latter sequence context. Here, we report higher accuracy solution structures of the synthetically derived trimethylene cross-links, which are refined from NMR data with the AMBER force field. When the synthetic trimethylene cross-links are placed into either the 5′-CpG-3′ or the 5′-GpC-3 ′ sequence contexts, the DNA duplex maintains B-DNA geometry with structural perturbations confined to the cross-linked base pairs. Watson-Crick hydrogen bonding is conserved throughout the duplexes. Although different from canonical B-DNA stacking, the cross-linked and the neighbor base pairs stack in the 5′-CpG-3 ′ sequence. In contrast, the stacking at the cross-linked base pairs in the 5′-GpC-3 ′ sequence is greatly perturbed. The π-stacking interactions between the crosslinked and the neighbor base pairs are reduced. This is consistent with remarkable chemical shift perturbations of the C 5 H5 and H6 nucleobase protons that shifted downfield by 0.4-0.5 ppm. In contrast

Structural determinants of the SINE B2 element embedded in the long non-coding RNA activator of translation AS Uchl1

Pervasive transcription of mammalian genomes leads to a previously underestimated level of complexity in gene regulatory networks. Recently, we have identified a new functional class of natural and synthetic antisense long non-coding RNAs (lncRNA) that increases translation of partially overlapping sense mRNAs. These molecules were named SINEUPs, as they require an embedded inverted SINE B2 element for their UP-regulation of translation. Mouse AS Uchl1 is the representative member of natural SINEUPs. It was originally discovered for its role in increasing translation of Uchl1 mRNA, a gene associated with neurodegenerative diseases. Here we present the secondary structure of the SINE B2 Transposable Element (TE) embedded in AS Uchl1. We find that specific structural regions, containing a short hairpin, are required for the ability of AS Uchl1 RNA to increase translation of its target mRNA. We also provide a high-resolution structure of the relevant hairpin, based on NMR observables. Our results highlight the importance of structural determinants in embedded TEs for their activity as functional domains in lncRNAs

Stacking Interactions in Denaturation of DNA Fragments

A mesoscopic model for heterogeneous DNA denaturation is developed in the framework of the path integral formalism. The base pair stretchings are treated as one-dimensional, time dependent paths contributing to the partition function. The size of the paths ensemble, which measures the degree of cooperativity of the system, is computed versus temperature consistently with the model potential physical requirements. It is shown that the ensemble size strongly varies with the molecule backbone stiffness providing a quantitative relation between stacking and features of the melting transition. The latter is an overall smooth crossover which begins from the \emph{adenine-thymine} rich portions of the fragment. The harmonic stacking coupling shifts, along the $T$-axis, the occurrence of the multistep denaturation but it does not change the character of the crossover. The methods to compute the fractions of open base pairs versus temperature are discussed: by averaging the base pair displacements over the path ensemble we find that such fractions signal the multisteps of the transition in good agreement with the indications provided by the specific heat plots.Comment: European Physical Journal E (2011) in pres