SECISearch3 and Seblastian: new tools for prediction of SECIS elements and selenoproteins

Selenoproteins are proteins containing an uncommon amino acid selenocysteine (Sec). Sec is inserted by a specific translational machinery that recognizes a stem-loop structure, the SECIS element, at the 3′ UTR of selenoprotein genes and recodes a UGA codon within the coding sequence. As UGA is normally a translational stop signal, selenoproteins are generally misannotated and designated tools have to be developed for this class of proteins. Here, we present two new computational methods for selenoprotein identification and analysis, which we provide publicly through the web servers at http://gladyshevlab.org/SelenoproteinPredictionServer or http://seblastian.crg.es. SECISearch3 replaces its predecessor SECISearch as a tool for prediction of eukaryotic SECIS elements. Seblastian is a new method for selenoprotein gene detection that uses SECISearch3 and then predicts selenoprotein sequences encoded upstream of SECIS elements. Seblastian is able to both identify known selenoproteins and predict new selenoproteins. By applying these tools to diverse eukaryotic genomes, we provide a ranked list of newly predicted selenoproteins together with their annotated cysteine-containing homologues. An analysis of a representative candidate belonging to the AhpC family shows how the use of Sec in this protein evolved in bacterial and eukaryotic lineages

Simulated last glacial maximum D14Catm and the deep glacial ocean carbon reservoir

∆14Catm has been estimated as 420 ± 80‰ (IntCal09) during the Last Glacial Maximum (LGM) compared to preindustrial times (0‰), but mechanisms explaining this difference are not yet resolved. ∆14Catm is a function of both cosmogenic production in the high atmosphere and of carbon cycling and partitioning in the Earth system. 10Be-based reconstructions show a contribution of the cosmogenic production term of only 200 ± 200‰ in the LGM. The remaining 220‰ have thus to be explained by changes in the carbon cycle. Recently, Bouttes et al. (2010, 2011) proposed to explain most of the difference in pCO2atm and δ13C between glacial and interglacial times as a result of brine-induced ocean stratification in the Southern Ocean. This mechanism involves the formation of very saline water masses that contribute to high carbon storage in the deep ocean. During glacial times, the sinking of brines is enhanced and more carbon is stored in the deep ocean, lowering pCO2atm. Moreover, the sinking of brines induces increased stratification in the Southern Ocean, which keeps the deep ocean well isolated from the surface. Such an isolated ocean reservoir would be characterized by a low ∆14C signature. Evidence of such 14C-depleted deep waters during the LGM has recently been found in the Southern Ocean (Skinner et al. 2010). The degassing of this carbon with low ∆14C would then reduce ∆14Catm throughout the deglaciation. We have further developed the CLIMBER-2 model to include a cosmogenic production of 14C as well as an interactive atmospheric 14C reservoir. We investigate the role of both the sinking of brine and cosmogenic production, alongside iron fertilization mechanisms, to explain changes in ∆14Catm during the last deglaciation. In our simulations, not only is the sinking of brine mechanism consistent with past ∆14C data, but it also explains most of the differences in pCO2atm and ∆14Catm between the LGM and preindustrial times. Finally, this study represents the first time to our knowledge that a model experiment explains glacial-interglacial differences in pCO2atm, δ13C, and ∆14C together with a coherent LGM climate

Separation control and efficiency improvement in a 2D diffuser by means of contoured cavities

The performance of a passive control method aimed at reducing and, possibly, eliminating boundary layer separation is evaluated by means of numerical simulation. The passive control, which consists of introducing appropriately-shaped cavities in solid walls, is applied to a plane diffuser. The Reynolds number is such that the turbulence can be neglected (Re = 500, based on the diffuser half-width at the inlet section and the inlet velocity on the axis). A configuration characterized by an area ratio of 2 and a divergence angle of 7 degrees is chosen, so that, without the introduction of the control, the flow is characterized by a large zone of steady asymmetrical boundary layer separation. In order to reduce the separated zone and to increase the efficiency of the diffuser, a couple of symmetric contoured cavities is introduced in the diverging walls. An optimization procedure is developed to obtain the cavity geometry that maximizes the pressure recovery in the diffuser and minimizes the boundary layer separation extent. The introduction of the optimal cavities leads to an increase in pressure recovery of the order of 13% and to a strong reduction of the separation extent. This result is due to a favourable modification of the velocity and vorticity fields in the near-wall region. The most important geometrical parameters are also identified and the robustness of the control to small changes in their values is investigated. It is found that the contoured cavities are effective as long as the flow is able to reattach immediately downstream of the cavities

Temperature dependent photoemission on 1T-TiSe2: Interpretation within the exciton condensate phase model

The charge density wave phase transition of 1T-TiSe2 is studied by angle-resolved photoemission over a wide temperature range. An important chemical potential shift which strongly evolves with temperature is evidenced. In the framework of the exciton condensate phase, the detailed temperature dependence of the associated order parameter is extracted. Having a mean-field-like behaviour at low temperature, it exhibits a non-zero value above the transition, interpreted as the signature of strong excitonic fluctuations, reminiscent of the pseudo-gap phase of high temperature superconductors. Integrated intensity around the Fermi level is found to display a trend similar to the measured resistivity and is discussed within the model.Comment: 8 pages, 6 figure

Cover crop introduction in a Mediterranean maize cropping system. Effects on soil variables and yield

Cover crops (CCs) are able to affect subsequent crop behaviour by acting on many soil variables and affecting the dynamics of different ecological processes. This study aimed to investigate the effects of introducing CC in continuous-maize cropping systems within Mediterranean areas. The experimental site was located in Central Italy, on a sandy loam and the research activity was carried out over two years (2019–2020). The two cropping systems in comparison differed from each other in terms of the CC cultivation: TR (treated, with CC) and CO (control, without CC). In both years, we observed a significant reduction (p < 0.05) of soil nitrate and water content for the TR system. In the shallowest layer (0–30 cm), nitrate content was reduced by up 80% and 65% (July 2019 and 2020), whereas soil moisture showed decreases ranging from 13% (July 2019) to 34% (May 2019). In 2019, the TR-maize (Zea mays L.) yield was statistically lower than CO (443 g dm m2), whereas in 2020 the yields of the two systems resulted statistically equivalent. This different behaviour can be explained with the serious delay in the CC sowing occurred in 2019 (12 December). Conversely, an increase in the apparent remaining N in the soil (+140 and +133 kg N ha1 for 2019 and 2020, respectively) and in the C (carbon) inputs (+4.78 and +7.39 t dm ha1 of biomass) were pointed out for the TR system. The large use of inputs in Mediterranean maize cropping systems limited some of the benefits from CCs, but their suitability has to be evaluated by considering all the involved effects, some of which need a long time to become appreciable

Recent advances in eco-friendly and cost-effective materials towards sustainable dye-sensitized solar cells

Dye-sensitized solar cells (DSSCs), as emerging photovoltaic technology, have been thoroughly and extensively investigated in the last three decades. Since their first appearance in 1991, DSSCs have gained increasing attention and have been classified as feasible alternatives to conventional photovoltaic devices due to their numerous advantages, such as cheap and simple preparation methods, the possibility of being integrated in buildings and astonishing performances under indoor and diffuse illumination conditions. Photoconversion efficiencies of up to 14% and 8% have been obtained for lab-scale devices and modules, respectively. Albeit the efforts made, these values seem arduous to be outdone, at least under simulated solar radiation. Nevertheless, recent lab-scale systems have demonstrated photoconversion efficiencies of up to 33% under indoor illumination (i.e. 1000 lux) leading to an actual Renaissance (or Revival) of these devices. It is worth mentioning that scientists in this field are developing innovative materials aiming at long-term and efficient devices, being the concept of sustainability often set apart. However, in light of effective commercialization of this technology, stability, efficiency and sustainability should be considered as the essential keywords. Nowadays, DSSCs are finding a “new way back” towards sustainability and rather a huge number of reports have focused on the preparation of green and cost-effective materials to replace the standard ones. In this scenario, the present review aims to give an overview of the most adopted strategies to enhance the sustainability of materials in classical DSSC components (e.g. sensitizer, redox couple, electrolyte and counter-electrode), including smart synthesis and deposition procedures, which currently represent utmost important topics in the scientific community