A graph theoretical analysis of the energy landscape of model polymers

In systems characterized by a rough potential energy landscape, local energetic minima and saddles define a network of metastable states whose topology strongly influences the dynamics. Changes in temperature, causing the merging and splitting of metastable states, have non trivial effects on such networks and must be taken into account. We do this by means of a recently proposed renormalization procedure. This method is applied to analyze the topology of the network of metastable states for different polypeptidic sequences in a minimalistic polymer model. A smaller spectral dimension emerges as a hallmark of stability of the global energy minimum and highlights a non-obvious link between dynamic and thermodynamic properties.Comment: 15 pages, 15 figure

Environmentally induced changes in antioxidant phenolic compounds levels in wild plants

[EN] Different adverse environmental conditions cause oxidative stress in plants by generation of reactive oxygen species (ROS). Accordingly, a general response to abiotic stress is the activation of enzymatic and non-enzymatic antioxidant systems. Many phenolic compounds, especially flavonoids, are known antioxidants and efficient ROS scavengers in vitro, but their exact role in plant stress responses in nature is still under debate. The aim of our work is to investigate this role by correlating the degree of environmental stress with phenolic and flavonoid levels in stress-tolerant plants. Total phenolic and antioxidant flavonoid contents were determined in 19 wild species. Meteorological data and plant and soil samples were collected in three successive seasons from four Mediterranean ecosystems: salt marsh, dune, semiarid and gypsum habitats. Changes in phenolic and flavonoid levels were correlated with the environmental conditions of the plants and were found to depend on both the taxonomy and ecology of the investigated species. Despite species-specific differences, principal component analyses of the results established a positive correlation between plant phenolics and several environmental parameters, such as altitude, and those related to water stress: temperature, evapotranspiration, and soil water deficit. The correlation with salt stress was, however, very weak. The joint analysis of all the species showed the lowest phenolic and flavonoid levels in the halophytes from the salt marsh. This finding supports previous data indicating that the halophytes analysed here do not undergo oxidative stress in their natural habitat and therefore do not need to activate antioxidant systems as a defence against salinity.This work has been funded by the Spanish Ministry of Science and Innovation (Project CGL2008-00438/BOS), with contribution from the European Regional Development Fund. Thanks to Dr. Rafael Herrera for critical reading of the manuscript.Bautista, I.; Boscaiu, M.; Lidón, A.; Llinares Palacios, JV.; Lull, C.; Donat-Torres, MP.; Mayoral García-Berlanga, O.... (2016). Environmentally induced changes in antioxidant phenolic compounds levels in wild plants. Acta Physiologiae Plantarum. 38(1):1-15. https://doi.org/10.1007/s11738-015-2025-2S115381Agati G, Biricolti S, Guidi L, Ferrini F, Fini A, Tattini M (2011) The biosynthesis of flavonoids is enhanced similarly by UV radiation and root zone salinity in L. vulgare leaves. 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Lifestyle, efficiency and limits: modelling transport energy and emissions using a socio-technical approach

It is well-known that societal energy consumption and pollutant emissions from transport are influenced not only by technical efficiency, mode choice and the carbon/pollutant content of energy but also by lifestyle choices and socio-cultural factors. However, only a few attempts have been made to integrate all of these insights into systems models of future transport energy demand or even scenario analysis. This paper addresses this gap in research and practice by presenting the development and use of quantitative scenarios using an integrated transport-energy-environment systems model to explore four contrasting futures for Scotland that compare transport-related ‘lifestyle’ changes and socio-cultural factors against a transition pathway focussing on transport electrification and the phasing out of conventionally fuelled vehicles using a socio-technical approach. We found that radical demand and supply strategies can have important synergies and trade-offs between reducing life cycle greenhouse gas and air quality emissions. Lifestyle change alone can have a comparable and earlier effect on transport carbon and air quality emissions than a transition to EVs with no lifestyle change. Yet, the detailed modelling of four contrasting futures suggests that both strategies have limits to meeting legislated carbon budgets, which may only be achieved with a combined strategy of radical change in travel patterns, mode and vehicle choice, vehicle occupancy and on-road driving behaviour with high electrification and phasing out of conventional petrol and diesel road vehicles. The newfound urgency of ‘cleaning up our act’ since the Paris Agreement and Dieselgate scandal suggests that we cannot just wait for the ‘technology fix’

Accurate detection of complex structural variations using single-molecule sequencing

Structural variations are the greatest source of genetic variation, but they remain poorly understood because of technological limitations. Single-molecule long-read sequencing has the potential to dramatically advance the field, although high error rates are a challenge with existing methods. Addressing this need, we introduce open-source methods for long-read alignment (NGMLR; https://github.com/philres/ngmlr ) and structural variant identification (Sniffles; https://github.com/fritzsedlazeck/Sniffles ) that provide unprecedented sensitivity and precision for variant detection, even in repeat-rich regions and for complex nested events that can have substantial effects on human health. In several long-read datasets, including healthy and cancerous human genomes, we discovered thousands of novel variants and categorized systematic errors in short-read approaches. NGMLR and Sniffles can automatically filter false events and operate on low-coverage data, thereby reducing the high costs that have hindered the application of long reads in clinical and research settings

Astrocyte networks and intercellular calcium propagation

International audienceAstrocytes organize in complex networks through connections by gap junction channels that are regulated by extra-and intracellular signals. Calcium signals generated in individual cells, can propagate across these networks in the form of intercellular calcium waves, mediated by diffusion of second messengers molecules such as inositol 1,4,5-trisphosphate. The mechanisms underpinning the large variety of spatiotemporal patterns of propagation of astrocytic calcium waves however remain a matter of investigation. In the last decade, awareness has grown on the morphological diversity of astrocytes as well as their connections in networks, which seem dependent on the brain area, developmental stage, and the ultra-structure of the associated neuropile. It is speculated that this diversity underpins an equal functional variety but the current experimental techniques are limited in supporting this hypothesis because they do not allow to resolve the exact connectivity of astrocyte networks in the brain. With this aim we present a general framework to model intercellular calcium wave propagation in astrocyte networks and use it to specifically investigate how different network topologies could influence shape, frequency and propagation of these waves

The green, the red, and the sunlight

Sunlight irradiance is extremely heterogeneous in the urban environment. In urban canyons, trees do not receive direct sunlight over extended periods and may experience chronic low-light stress, particularly if light-demanding species are planted. In contrast, in urban plazas, where reflected radiation sums up to direct sunlight, plants may suffer from a chronic excess of solar irradiance. In the latter case, incoming total irradiance may largely exceed the amount required for photosynthesis, and leaves are consequently exposed to photo-oxidative stress and generation of Reactive Oxygen Species (ROS). Excess light stress may become severe when coupled with other environmental stressors, such as drought, that severely constrain photosynthesis and, consequently, the usage of sunlight energy for carbon fixation. ROS disrupt cell membranes, lead to leaf necrosis, and hinder recovery of plant performance when stress is relieved. This reduces benefit provisioning and increases management costs of urban trees. Harsh, highly irradiated urban plazas are already quite an inhospitable place for trees, and will become even more unfavorable in the near future, because of rapid climate change. In a previous study conducted on a herbaceous species it was observed that the red cultivar was more tolerant to a sudden drought spell, and the associated photo-oxidative damage than the green cultivar. This was attributed to the photoprotective role provided by anthocyanins located in the epidermal layer of the red cultivar. Here we hypothesized that cyanic cultivars of woody species might be particularly suitable for planting in urban plazas, because of epidermal anthocyanins may attenuate the detrimental effects of excess light stress. To test this hypothesis, we conducted experiments in which plants were exposed to either sudden (Exp. 1) or chronic (Exp. 2) excess light stress using constitutive cyanic (\u2018Crimson King\u2019), transiently cyanic (\u2018Deborah\u2019), and acyanic (\u2018Summershade\u2019) cultivars of Acer platanoides. In Exp. 1, sudden excess light stress was imposed by 1-month drought cycle. In Exp. 2, chronic excess light stress was imposed by increasing pavement albedo from 5% to 30%. Results illustrate evidence of the photoprotective role of epidermal anthocyanins, but also highlight some physiological consequences of \u201cbeing red\u201d which may affect the landscape performance of red cultivars

Changes in non-structural carbohydrates in olive (Olea europaea) leaves during root zone salinity stress

Self-rooted olive (Olea europaea L.) plants were grown in hydroponics at various NaCI concentrations (from 0 to 200 mM) for 28 to 32 days followed by 28 to 30 days of relief from salinity over two growing seasons. Olive leaves accumulated both glucose and mannitol during the period of salinity stress. The concentrations of fructose, myo-inositol, galactose, galactinol, sucrose, raffinose, and stachyose were not significantly affected by salinity. Starch content was decreased by salinity. The mannitol/glucose and mannitol/soluble carbohydrates ratios increased as the extent NaCI concentration was increased, but returned to the control levels during the relief period. The increase in mannitol or glucose molar concentrations, expressed on a leaf tissue water basis, was partially due to a reduction in leaf tissue water content under salinity stress. However, an increase in mannitol concentration was also observed when expressed on a dry weight basis. The accumulation of mannitol in leaf tissue preceded any reduction in leaf area rate or net assimilation rate. The increase in leaf mannitol or glucose concentration was positively correlated with the increasing level of salinity at the root zone, but not with the accumulation of Na+ in the shoot. The role of mannitol, a potential osmoregulator in leaf mesophyll during salinity stress, is discussed in relation to the complex carbohydrate composition of olive leaves