National Agency for New Technologies, Energy and Sustainable Economic Development

This paper reports the genome sequence of domesticated tomato, a major crop plant, and a draft sequence for its closest wild relative; comparative genomics reveal very little divergence between the two genomes but some important differences with the potato genome, another important food crop in the genus Solanum. Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera1 and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium2, and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness.

Potato (Solanum tuberosum L.) is the world’s most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop. The genome of the potato (Solanum tuberosum L.), a staple crop vital to food security, has been sequenced. The Potato Genome Sequencing Consortium sequenced a homozygous doubled-monoploid potato clone as well as a heterozygous diploid clone. Genome analysis reveals traces of at least two genome duplication events and genes specific to Asterids, a large clade of flowering plants of which the potato is the first to be sequenced. Gene presence/absence variants and other potentially deleterious mutations are frequent and may be the cause of inbreeding depression. The genome sequence will facilitate genetic improvements in the potato with a view to improving yield and to increasing disease and stress resistance of this crop, which is a now a significant component of worldwide food production and is becoming increasingly important in the developing world.

Environmental life cycle assessment (LCA) has developed fast over the last three decades. Whereas LCA developed from merely energy analysis to a comprehensive environmental burden analysis in the 1970s, full-fledged life cycle impact assessment and life cycle costing models were introduced in the 1980s and 1990 s, and social-LCA and particularly consequential LCA gained ground in the first decade of the 21st century. Many of the more recent developments were initiated to broaden traditional environmental LCA to a more comprehensive Life Cycle Sustainability Analysis (LCSA). Recently, a framework for LCSA was suggested linking life cycle sustainability questions to knowledge needed for addressing them, identifying available knowledge and related models, knowledge gaps, and defining research programs to fill these gaps. LCA is evolving into LCSA, which is a transdisciplinary integration framework of models rather than a model in itself. LCSA works with a plethora of disciplinary models and guides selecting the proper ones, given a specific sustainability question. Structuring, selecting, and making the plethora of disciplinary models practically available in relation to different types of life cycle sustainability questions is the main challenge.

Author(s): de Bernardis, P.; Ade, P.A.R.; Bock, J.J.; Bond, J.R.; Borrill, J.; Boscaleri, A.; Coble, K.; Crill, B.P.; De Gasperis, G.; Farese, P.C.; Ferreira, P.G.; Ganga, K.; Giacometti, M.; Hivon, E.; Hristov, V.V.; Iacoangeli, A.; Jaffe, A.H.; Lange, A.E.; Martinis, L.; Masi, S.; Mason, P.; Mauskopf, P.D.; Melchiorri, A.; Miglio, L.; Montroy, T.; Netterfield, C.B.; Pascale, E.; Piacentini, F.; Pogosyan, D.; Prunet, S.; Rao, S.; Romeo, G.; Ruhl, J.E.; Scaramuzzi, F.; Sforna, D.; Vittorio, N.

Most associate liquid crystals with their everyday use in laptop computers, mobile phones, digital cameras, and other electronic devices. However, in contrast to their rodlike (calamitic) counterparts, first described in 1907 by Vorländer, disklike (discotic, columnar) liquid crystals, which were discovered in 1977 by Chandrasekhar et al., offer further applications as a result of their orientation in the columnar mesophase, making them ideal candidates for molecular wires in various optical and electronic devices such as photocopiers, laser printers, photovoltaic cells, light-emitting diodes, field-effect transistors, and holographic data storage. Beginning with an overview of the various mesophases and characterization methods, this Review will focus on the major classes of columnar mesogens rather than presenting a library of columnar liquid crystals. Emphasis will be given to efficient synthetic procedures, and relevant mesomorphic and physical properties. Finally, some applications and perspectives in materials science and molecular electronics will be discussed.

Progress in the area of MHD stability and disruptions, since the publication of the 1999 ITER Physics Basis document (1999 Nucl. Fusion 39 2137-2664), is reviewed. Recent theoretical and experimental research has made important advances in both understanding and control of MHD stability in tokamak plasmas. Sawteeth are anticipated in the ITER baseline ELMy H-mode scenario, but the tools exist to avoid or control them through localized current drive or fast ion generation. Active control of other MHD instabilities will most likely be also required in ITER. Extrapolation from existing experiments indicates that stabilization of neoclassical tearing modes by highly localized feedback-controlled current drive should be possible in ITER. Resistive wall modes are a key issue for advanced scenarios, but again, existing experiments indicate that these modes can be stabilized by a combination of plasma rotation and direct feedback control with non-axisymmetric coils. Reduction of error fields is a requirement for avoiding non-rotating magnetic island formation and for maintaining plasma rotation to help stabilize resistive wall modes. Recent experiments have shown the feasibility of reducing error fields to an acceptable level by means of non-axisymmetric coils, possibly controlled by feedback. The MHD stability limits associated with advanced scenarios are becoming well understood theoretically, and can be extended by tailoring of the pressure and current density profiles as well as by other techniques mentioned here. There have been significant advances also in the control of disruptions, most notably by injection of massive quantities of gas, leading to reduced halo current fractions and a larger fraction of the total thermal and magnetic energy dissipated by radiation. These advances in disruption control are supported by the development of means to predict impending disruption, most notably using neural networks. In addition to these advances in means to control or ameliorate the consequences of MHD instabilities, there has been significant progress in improving physics understanding and modelling. This progress has been in areas including the mechanisms governing NTM growth and seeding, in understanding the damping controlling RWM stability and in modelling RWM feedback schemes. For disruptions there has been continued progress on the instability mechanisms that underlie various classes of disruption, on the detailed modelling of halo currents and forces and in refining predictions of quench rates and disruption power loads. Overall the studies reviewed in this chapter demonstrate that MHD instabilities can be controlled, avoided or ameliorated to the extent that they should not compromise ITER operation, though they will necessarily impose a range of constraints.

Abstract A semi-empirical model to simulate thermodynamic properties of f.c.c. transition metals is proposed. The attractive energy is derived within a second-moment approximation of the tight-binding scheme. The repulsive pairwise interaction is assumed to be of a Born-Mayer type and the parameters of the potential have been adjusted on the bulk modulus, the elastic constants and the cohesive energy. Bulk vibrational properties and defect energies for vacancies, interstitials and surfaces are estimated. Moreover, molecular dynamics simulations with this potential model to evaluate the high-temperature behaviour are presented. In particular, we have calculated the root-mean-square displacement and the thermal expansion as a function of temperature for Cu and Ni. These results allow us to test the anharmonicity of the potential. The agreement with experiment is quite good for low and intermediate temperatures. At high temperatures (T0·65Tm where T m is the melting temperature) the mean-square displacement increases too rapidly. Some possible origins of this discrepancy are discussed.

We present in this paper new and updated calculations of the ionization equilibrium for all the elements from H to Ni. We collected for these elements all the data available in the literature for the ionization and radiative plus dielectronic recombination rates. In particular, the dielectronic rates have been fitted with a single formula and the related coefficients are tabulated. Our results are compared with previous works.

Zinc-finger proteins (ZNFs) are one of the most abundant groups of proteins and have a wide range of molecular functions. Given the wide variety of zinc-finger domains, ZNFs are able to interact with DNA, RNA, PAR (poly-ADP-ribose) and other proteins. Thus, ZNFs are involved in the regulation of several cellular processes. In fact, ZNFs are implicated in transcriptional regulation, ubiquitin-mediated protein degradation, signal transduction, actin targeting, DNA repair, cell migration, and numerous other processes. The aim of this review is to provide a comprehensive summary of the current state of knowledge of this class of proteins. Firstly, we describe the actual classification of ZNFs, their structure and functions. Secondly, we focus on the biological role of ZNFs in the development of organisms under normal physiological and pathological conditions.

Factors affecting sorption of organic pollutants by natural sorbents (soils, sediments, clays, humic materials, and dissolved organic matters) and sorption coefficients for selected pollutants are reviewed on the basis of the literature results and interpretations; with 681 references examined. The most significant aspects of the sorption process are discussed: sorption isotherms and sorption kinetics; effects of sorbent physico-chemical characteristics (pH, cation exchange capacity, ionic strength, surface area, etc.); effect of the temperature; sorption of volatile compounds; effect of the presence of a cosolvent; association with dissolved organic matter; effect of the sorbent concentration; “hysteresis” or nonsingularity in the sorption–desorption process, and its implications in the transport of these contaminants through soil columns. The experimental and prediction methods adopted for the determination and estimation of the sorption coefficients are also described. Literature sorption coefficients for selected hydrophobic, polar, and ionizable compounds are collected. The compounds taken into consideration belong to the following classes: monoaromatic hydrocarbons, polycyclic aromatic hydrocarbons, chlorinated alkyl and aryl compounds, phenol and chlorinated phenols, polychlorobiphenyls, dioxins, and pesticides. The respective sorption coefficients (log Kd) and organic carbon-referenced sorption coefficients (log Koc) are tabulated together with the most relevant characteristics of the respective sorbent, the measurement temperature, and the experimental methods. The log Koc values are averaged and compared with other experimental and estimated literature data. Differences of sorption coefficients on soils and sediments and effect of pH on sorption coefficients for ionizable compounds are evidentiated.

Metal hydrides are known as a potential efficient, low-risk option for high-density hydrogen storage since the late 1970s. In this paper, the present status and the future perspectives of the use of metal hydrides for hydrogen storage are discussed. Since the early 1990s, interstitial metal hydrides are known as base materials for Ni – metal hydride rechargeable batteries. For hydrogen storage, metal hydride systems have been developed in the 2010s [1] for use in emergency or backup power units, i. e. for stationary applications. With the development and completion of the first submarines of the U212 A series by HDW (now Thyssen Krupp Marine Systems) in 2003 and its export class U214 in 2004, the use of metal hydrides for hydrogen storage in mobile applications has been established, with new application fields coming into focus. In the last decades, a huge number of new intermetallic and partially covalent hydrogen absorbing compounds has been identified and partly more, partly less extensively characterized. In addition, based on the thermodynamic properties of metal hydrides, this class of materials gives the opportunity to develop a new hydrogen compression technology. They allow the direct conversion from thermal energy into the compression of hydrogen gas without the need of any moving parts. Such compressors have been developed and are nowadays commercially available for pressures up to 200 bar. Metal hydride based compressors for higher pressures are under development. Moreover, storage systems consisting of the combination of metal hydrides and high-pressure vessels have been proposed as a realistic solution for on-board hydrogen storage on fuel cell vehicles. In the frame of the “Hydrogen Storage Systems for Mobile and Stationary Applications” Group in the International Energy Agency (IEA) Hydrogen Task 32 “Hydrogen-based energy storage”, different compounds have been and will be scaled-up in the near future and tested in the range of 500 g to several hundred kg for use in hydrogen storage applications.

Western diets are characterised by a high intake of meat, dairy products and eggs, causing an intake of saturated fat and red meat in quantities that exceed dietary recommendations. The associated livestock production requires large areas of land and lead to high nitrogen and greenhouse gas emission levels. Although several studies have examined the potential impact of dietary changes on greenhouse gas emissions and land use, those on health, the agricultural system and other environmental aspects (such as nitrogen emissions) have only been studied to a limited extent. By using biophysical models and methods, we examined the large-scale consequences in the European Union of replacing 25–50% of animal-derived foods with plant-based foods on a dietary energy basis, assuming corresponding changes in production. We tested the effects of these alternative diets and found that halving the consumption of meat, dairy products and eggs in the European Union would achieve a 40% reduction in nitrogen emissions, 25–40% reduction in greenhouse gas emissions and 23% per capita less use of cropland for food production. In addition, the dietary changes would also lower health risks. The European Union would become a net exporter of cereals, while the use of soymeal would be reduced by 75%. The nitrogen use efficiency (NUE) of the food system would increase from the current 18% to between 41% and 47%, depending on choices made regarding land use. As agriculture is the major source of nitrogen pollution, this is expected to result in a significant improvement in both air and water quality in the EU. The resulting 40% reduction in the intake of saturated fat would lead to a reduction in cardiovascular mortality. These diet-led changes in food production patterns would have a large economic impact on livestock farmers and associated supply-chain actors, such as the feed industry and meat-processing sector.

Kongsfjorden-Krossfjorden and the adjacent West Spitsbergen Shelf meet at the common mouth of the two fjord arms. This paper presents our most up-to-date information about the physical environment of this fjord system and identifies important gaps in knowledge. Particular attention is given to the steep physical gradients along the main fjord axis, as well as to seasonal environmental changes. Physical processes on different scales control the large-scale circulation and small-scale (irreversible) mixing of water and its constituents. It is shown that, in addition to the tide, run-off (glacier ablation, snowmelt, summer rainfall and ice calving) and local winds are the main driving forces acting on the upper water masses in the fjord system. The tide is dominated by the semi-diurnal component and the freshwater supply shows a marked seasonal variation pattern and also varies interannually. The wind conditions are characterized by prevailing katabatic winds, which at times are strengthened by the geostrophic wind field over Svalbard. Rotational dynamics have a considerable influence on the circulation patterns within the fjord system and give rise to a strong interaction between the fjord arms. Such dynamics are also the main reason why variations in the shelf water density field, caused by remote forces (tide and coastal winds), propagate as a Kelvin wave into the fjord system. This exchange affects mainly the intermediate and deep water, which is also affected by vertical convection processes driven by cooling of the surface and brine release during ice formation in the inner reaches of the fjord arms. Further aspects covered by this paper include the geological and geomorphological characteristics of the Kongsfjorden area, climate and meteorology, the influence of glaciers, freshwater supply, sea ice conditions, sedimentation processes as well as underwater radiation conditions. The fjord system is assumed to be vulnerable to possible climate changes, and thus is very suitable as a site for the demonstration and investigation of phenomena related to climate change.

In this paper we continue the description of a second-generation regional climate model (RegCM2) initiated in the companion paper by Giorgi et al. We first discuss the inclusion in the model of the cumulus cloud scheme developed by Grell (referred to as OCC). The sensitivity of summertime and wintertime results to different closures and parameter settings in the GCC scheme are examined in model simulations conducted over Europe. While wintertime precipitation is found to vary only slightly between the experiments, a wide range of results is found in the summer runs. The GCC scheme produces more rain than a Kuo-type scheme, responds strongly to variations in the surface energy and moisture fluxes, and performs best when used in conjunction with the most advanced physics processes of RegCM2. Modifications to the standard model relaxation boundary condition procedure, which allow smoother assimilation of driving lateral boundary data, are also discussed. Further testing of RegCM2, which is more physically comprehensive, about three times more computationally efficient, and more portable than the previous version of the model, is continuing.

Abstract. Present day tropospheric ozone and its changes between 1850 and 2100 are considered, analysing 15 global models that participated in the Atmospheric Chemistry and Climate Model Intercomparison Project (ACCMIP). The ensemble mean compares well against present day observations. The seasonal cycle correlates well, except for some locations in the tropical upper troposphere. Most (75 %) of the models are encompassed with a range of global mean tropospheric ozone column estimates from satellite data, but there is a suggestion of a high bias in the Northern Hemisphere and a low bias in the Southern Hemisphere, which could indicate deficiencies with the ozone precursor emissions. Compared to the present day ensemble mean tropospheric ozone burden of 337 ± 23 Tg, the ensemble mean burden for 1850 time slice is ~30% lower. Future changes were modelled using emissions and climate projections from four Representative Concentration Pathways (RCPs). Compared to 2000, the relative changes in the ensemble mean tropospheric ozone burden in 2030 (2100) for the different RCPs are: −4% (−16%) for RCP2.6, 2% (−7%) for RCP4.5, 1% (−9%) for RCP6.0, and 7% (18%) for RCP8.5. Model agreement on the magnitude of the change is greatest for larger changes. Reductions in most precursor emissions are common across the RCPs and drive ozone decreases in all but RCP8.5, where doubled methane and a 40–150% greater stratospheric influx (estimated from a subset of models) increase ozone. While models with a high ozone burden for the present day also have high ozone burdens for the other time slices, no model consistently predicts large or small ozone changes; i.e. the magnitudes of the burdens and burden changes do not appear to be related simply, and the models are sensitive to emissions and climate changes in different ways. Spatial patterns of ozone changes are well correlated across most models, but are notably different for models without time evolving stratospheric ozone concentrations. A unified approach to ozone budget specifications and a rigorous investigation of the factors that drive tropospheric ozone is recommended to help future studies attribute ozone changes and inter-model differences more clearly.

We present in this paper new and updated calculations of the ionization equilibrium for all the elements from H to Ni. We collected for these elements all the data available in the literature for the ionization and radiative plus dielectronic recombination rates. In particular, the dielectronic rates have been fitted with a single formula and the related coefficients are tabulated. Our results are compared with previous works.

BACKGROUND: The sperm chromatin structure assay (SCSA) has been suggested as a predictor of fertility in vivo as well as in vitro. The available data however, have been based on limited numbers of treatments. We aimed to define the clinical role of SCSA in assisted reproduction. METHODS: A total of 998 cycles [387 intrauterine insemination (IUI), 388 IVF and 223 ICSI] from 637 couples were included. SCSA results were expressed as DNA fragmentation index (DFI) and high DNA stainable (HDS) cell fractions. Outcome parameters were biochemical pregnancy (BP), clinical pregnancy (CP) and delivery (D). RESULTS: For IUI, the odds ratios (ORs) for BP, CP and D were significantly lower for couples with DFI >30% as compared with those with DFI < or =30%. No statistical difference between the outcomes of ICSI versus IVF in the group with DFI < or =30% was seen. In the DFI >30% group, the results of ICSI were significantly better than those of IVF. CONCLUSIONS: DFI can be used as an independent predictor of fertility in couples undergoing IUI. As a result, we propose that all infertile men should be tested with SCSA as a supplement to the standard semen analysis. When DFI exceeds 30%, ICSI should be the method of choice.

Flow cytometry was used to analyse the DNA content of nuclei isolated from intact plant tissues and from callus and cell suspension cultures invitro. Cell nuclei were isolated either mechanically (chopping, syringing) or by a hypotonic lysis of isolated protoplasts. Although both methods gave similar results, a slight shift to lower ploidy levels was observed after protoplast isolation from intact tissues and calli. No differences were observed if the two methods were compared using cell suspension cultures. The results showed that flow cytometry is a rapid method of nuclear DNA content analysis in intact plant tissues and variousin vitro cultures.

Abstract. The Earth system model EC-Earth3 for contributions to CMIP6 is documented here, with its flexible coupling framework, major model configurations, a methodology for ensuring the simulations are comparable across different high-performance computing (HPC) systems, and with the physical performance of base configurations over the historical period. The variety of possible configurations and sub-models reflects the broad interests in the EC-Earth community. EC-Earth3 key performance metrics demonstrate physical behavior and biases well within the frame known from recent CMIP models. With improved physical and dynamic features, new Earth system model (ESM) components, community tools, and largely improved physical performance compared to the CMIP5 version, EC-Earth3 represents a clear step forward for the only European community ESM. We demonstrate here that EC-Earth3 is suited for a range of tasks in CMIP6 and beyond.

Summary The relationship between adsorption and pH, termed the adsorption envelope, varies with the p K a, of the conjugate acid of the anion, for several adsorbents in presence of an excess of specifically adsorbed anions. At pH values where the acid is fully dissociated, specific adsorption occurs only to the extent of the positive charge of the surface and little specific adsorption is found at pH values more alkaline than the zero point of charge (zpc). With incompletely dissociated acids, anion adsorption can also take place at pH values more alkaline than the zpc providing the pH is somewhere near a p K a value of the acid, where the energy required to abstract a proton from the acid is at a minimum. The proton is required for the removal of a surface OH which provides a site for the anion. Specific anion adsorption (i) from a fully dissociated acid can reduce the positive charge of the surface to zero and (ii) from a weak acid can make even a negative surface more negative. Thus specific adsorption shifts the zpc to more acid values. The relationship between anion adsorption and OH release is not necessarily simple. The ideas proposed for anion adsorption have implications for cation adsorption and incorporation in an oxide surface.