Global characterization and target identification of piRNAs and endo-siRNAs in mouse gametes and zygotes

44 p.-1 tab.-10 fig.A set of small RNAs known as rasRNAs (repeat-associated small RNAs) have been related to the down-regulation of Transposable Elements (TEs) to safeguard genome integrity. Two key members of the rasRNAs group are piRNAs and endo-siRNAs. We have performed a comparative analysis of piRNAs and endo-siRNAs present in mouse oocytes, spermatozoa and zygotes, identified by deep sequencing and bioinformatic analysis. The detection of piRNAs and endo-siRNAs in the spermatozoa and revealed also in zygotes, hints to their potential delivery to oocytes during fertilization. However, a comparative assessment of the three cell types indicates that both piRNAs and endo-siRNAs are mainly maternally inherited. Finally, we have assessed the role of the different rasRNA molecules in connection with amplification processes by way of the "ping-pong cycle". Our results suggest that the ping-pong cycle can act on other rasRNAs, such as tRNA- and rRNA-derived fragments, thus not only being restricted to TEs during gametogenesis. © 2014 Elsevier B.V.This work was funded by grants from The European Chemical Industry Council Long-range Research Initiative (CEFIC-LRi), from the MEDDTL (11-MRESPNRPE-9-CVS-072), France, from the CSIC (PIE 201020E016), Spain.Peer reviewe

Semi-inclusive charged-current neutrino-nucleus cross sections in the relativistic plane-wave impulse approximation

Neutrino-nucleus quasielastic scattering is studied in the plane-wave impulse approximation for three nuclear models: the relativistic Fermi gas (RFG), the independent-particle shell model (IPSM), and the natural orbitals (NO) model with Lorentzian dependence of the excitation energy. A complete study of the kinematics of the semi-inclusive process and the associated cross sections are presented and discussed for 40Ar and 12C. Inclusive cross sections are also obtained by integrating the semi-inclusive expressions over the outgoing hadron. Results are consistent with previous studies restricted to the inclusive channel. In particular, a comparison with the analytical results for the RFG model is performed. Explicit expressions for the hadronic tensor and the 10 semiinclusive nuclear responses are given. Theoretical predictions are compared with semi-inclusive experimental data from T2K experiment.Ministerio de Ciencia, Innovación y Universidades de España y FEDER (Fondo Europeo de Desarrollo Regional). FIS2017-88410-PJunta de Andalucía. FQM160 y SOMM17/6105/UG

Moving breathers in bent DNA with realistic parameters

Recent papers have considered moving breathers (MBs) in DNA models including long range interaction due to the dipole moments of the hydrogen bonds. We have recalculated the value of the charge transfer when hydrogen bonds stretch using quant um chemical methods which takes into account the whole nucleoside pairs. We explore the conseque nces of this value on the properties of MBs, including the range of frequencies for which they exi st and their effective masses. They are able to travel through bending points with fairly large c urvatures provided that their kinetic energy is larger than a minimum energy which depends on the cu rvature. These energies and the corresponding velocities are also calculated in function o f the curvatureMECD–FEDER project BMF2003- 03015/FIS

Moving breathers in a DNA model with competing short and long range dispersive interactions

Moving breathers is a means of transmitting information in DNA. We study the existence and properties of moving breathers in a DNA model with short range interaction, due to the stacking of the base pairs, and long range interaction, due to the finite dipole moment of the bond within each base pair. In our study, we have found that mobile breathers exist for a wide range of the parameter values, and the mobility of these breathers is hindered by the long range interaction. This fact is manifested by: (a) an increase of the effective mass of the breather with the dipole–dipole coupling parameter; (b) a poor quality of the movement when the dipole–dipole interaction increases; and (c) the existence of a threshold value of the dipole–dipole coupling above which the breather is not movable. An analytical formula for the boundaries of the regions where breathers are movable is calculated. Concretely, for each value of the breather frequency, it can be obtained the maximum value of the dipole–dipole coupling parameter and the maximum and minimum values of the stacking coupling parameter where breathers are movable. Numerical simulations show that, although the necessary conditions for the mobility are fulfilled, breathers are not always movable. Finally, the value of the dipole–dipole coupling constant is obtained through quantum chemical calculations. They show that the value of the coupling constant is small enough to allow a good mobility of breathers.European Commission under the RTN project LOCNET, HPRN-CT-1999-0016

SuSAv2 Model for Inelastic Neutrino-nucleus Scattering

The susperscaling model SuSAv2, already available for charged-current neutrino-nucleus cross sections in the quasielastic region, is extended to the full inelastic regime. In the model the resonance production and deep inelastic reactions are described through the extension to the neutrino sector of the SuSAv2 inelastic model developed for (e, e′) reactions, which combines phenomenological structure functions with a nuclear scaling function. This work also compares two different descriptions of the Δ resonance region, one based on a global scaling function for the full inelastic spectrum and the other on a semiphenomenological Δ scaling function extracted from (e, e′) data for this specific region and updated with respect to previous work. The results of the model are tested against (e, e′) data on C12, O16, Ca40, and Ar40 and applied to the study of the charged current inclusive neutrino cross-section on C12 and Ar40 measured by the T2K, MicroBooNE, ArgoNEUT, and MINERvA experiments, thus covering several kinematical regions.Ministerio de Ciencia e Innovación PID2020–114687 GB-I00Ministerio de Ciencia, Innovación y Universidades FIS2017-88410-Junta de Andalucía FQM160, SOMM17/6105/UGR, USE-21618-KUniversity of Tokyo FY2020, FY2021European Union 83948

Human Computer Interactions in Next-Generation of Aircraft Smart Navigation Management Systems: Task Analysis and Architecture under an Agent-Oriented Methodological Approach

The limited efficiency of current air traffic systems will require a next-generation of Smart Air Traffic System (SATS) that relies on current technological advances. This challenge means a transition toward a new navigation and air-traffic procedures paradigm, where pilots and air traffic controllers perform and coordinate their activities according to new roles and technological supports. The design of new Human-Computer Interactions (HCI) for performing these activities is a key element of SATS. However efforts for developing such tools need to be inspired on a parallel characterization of hypothetical air traffic scenarios compatible with current ones. This paper is focused on airborne HCI into SATS where cockpit inputs came from aircraft navigation systems, surrounding traffic situation, controllers' indications, etc. So the HCI is intended to enhance situation awareness and decision-making through pilot cockpit. This work approach considers SATS as a system distributed on a large-scale with uncertainty in a dynamic environment. Therefore, a multi-agent systems based approach is well suited for modeling such an environment. We demonstrate that current methodologies for designing multi-agent systems are a useful tool to characterize HCI. We specifically illustrate how the selected methodological approach provides enough guidelines to obtain a cockpit HCI design that complies with future SATS specifications.This work was supported in part by Projects MINECO TEC2011-28626-C02-01/02, by program CENIT-ATLANTIDA (cofinanced by Indra and Boeing R&TE), and by ULPGC Precompetitive Research Project (ULPGC Own Program).Publicad

The molar extinction coefficient of bacteriochlorophyll e and the pigment stoichiometry in Chlorobium phaeobacteroides

We have determined the molar extinction coefficient of bacteriochlorophyll (BChl) e, the main light-harvesting pigment from brown-coloured photosynthetic sulfur bacteria. The extinction coefficient was determined using pure[Pr,E]BChl eF isolated by reversed-phase HPLC from crude pigment extracts of Chlorobium (Chl.) phaeobacteroides strain CL1401. The extinction coefficients at the Soret and Qy bands were determined in four organic solvents. The extinction coefficient of BChl e differs from those of other related Chlorobium chlorophylls (BChl c and BChl d) but is similar to that of chlorophyll b. The determined extinction coefficient was used to calculate the stoichiometric BChl e to BChl a and BChl e to carotenoids ratios in whole cells and isolated chlorosomes from Chl. phaeobacteroides strain CL1401 using the spectrum-reconstruction method (SRCM) described by Naqvi et al. (1997) (Spectrochim Acta A Mol Biomol Spectrosc 53: 2229–2234). In isolated chlorosomes, BChl a content was ca. 1% of the total BChl content and the stoichiometric ratio of BChl e to carotenoids was 6. In whole cells,however, BChl a content was 3–4%, owing to the presence of BChl a-containing elements, i.e. FMO protein and reaction centre. An average of 5 BChl e molecules per carotenoid was determined in whole cells.EU(Contract No FMRX–CT96–0081). Ministerio de Educación y Ciencia (Ref. BIO96–1229–002–01)Peer reviewe

Automatic Recognition of Leaves by Shape Detection Pre-Processing with Ica

In this work we present a simulation of a recognition process with perimeter characterization of a simple plant leaves as a unique discriminating parameter. Data coding allowing for independence of leaves size and orientation may penalize performance recognition for some varieties. Border description sequences are then used to characterize the leaves. Independent Component Analysis (ICA) is then applied in order to study which is the best number of components to be considered for the classification task, implemented by means of an Artificial Neural Network (ANN). Obtained results with ICA as a pre-processing tool are satisfactory, and compared with some references our system improves the recognition success up to 80.8% depending on the number of considered independent components

Nanosecond laser photolysis studies of chlorosomes and artificial aggregates containing bacteriochlorophyll e: Evidence for the proximity of carotenoids and bacteriochlorophyll a in chlorosomes from Chlorobium phaeobacteroides strain CL1401

Time-resolved, laser-induced changes in absorbance, ΔA(λ; t), have been recorded with a view to probing pigment–pigment interactions in chlorosomes (control as well as carotenoid-depleted) and artificial aggregates of bacteriochlorophyll e (BChle). Control chlorosomes were isolated from Chlorobium phaeobacteroides strain CL1401, whose chromophores comprise BChle, bacteriochlorophyll a (BChla) and several carotenoid (Car) pigments; Car-depleted chlorosomes, from cells grown in cultures containing 2-hydroxybiphenyl. Artificial aggregates were prepared by dispersing BChle in aqueous phase in the presence of monogalactosyl diglyceride. In chlorosomes ΔA(λ; t) shows, besides a signal attributable to triplet Car (with a half-life of about 4 μs), signals in the Qy regions of both BChl. The BChla signal decays at the same rate as the Car signal, which is explained by postulating that some Car are in intimate contact with some baseplate BChla pigments, and that when a ground-state Car changes into a triplet Car, the absorption spectrum of its BChla neighbors undergoes a concomitant change (termed transient environment-induced perturbation). The signal in the Qy-region of BChle behaves differently: its amplitude falls, under reducing conditions, by more than a factor of two during the first 0.5 μs (a period during which the Car signal suffers negligible diminution), and is much smaller under nonreducing conditions. The BChle signal is also attributed to transient environment-induced perturbation, but in this case the perturber is a BChle photoproduct (probably a triplet or a radical ion). The absence of long-lived BChle triplets in all three systems, and of long-lived BChla triplets in chlorosomes, indicates that BChle in densely packed assemblies is less vulnerable to photodamage than monomeric BChle and that, in chlorosome, BChla rather than BChle needs, and receives, photoprotection from an adjacent Car.Research Council of Norway. EU (contract FMRX-CT96-0081)Peer reviewe