Showing papers by "Spanish National Research Council published in 2009"

The electronic properties of graphene

Abstract: This article reviews the basic theoretical aspects of graphene, a one-atom-thick allotrope of carbon, with unusual two-dimensional Dirac-like electronic excitations. The Dirac electrons can be controlled by application of external electric and magnetic fields, or by altering sample geometry and/or topology. The Dirac electrons behave in unusual ways in tunneling, confinement, and the integer quantum Hall effect. The electronic properties of graphene stacks are discussed and vary with stacking order and number of layers. Edge (surface) states in graphene depend on the edge termination (zigzag or armchair) and affect the physical properties of nanoribbons. Different types of disorder modify the Dirac equation leading to unusual spectroscopic and transport properties. The effects of electron-electron and electron-phonon interactions in single layer and multilayer graphene are also presented.

The Seventh Data Release of the Sloan Digital Sky Survey

Abstract: This paper describes the Seventh Data Release of the Sloan Digital Sky Survey (SDSS), marking the completion of the original goals of the SDSS and the end of the phase known as SDSS-II. It includes 11,663 deg^2 of imaging data, with most of the ~2000 deg^2 increment over the previous data release lying in regions of low Galactic latitude. The catalog contains five-band photometry for 357 million distinct objects. The survey also includes repeat photometry on a 120° long, 2°.5 wide stripe along the celestial equator in the Southern Galactic Cap, with some regions covered by as many as 90 individual imaging runs. We include a co-addition of the best of these data, going roughly 2 mag fainter than the main survey over 250 deg^2. The survey has completed spectroscopy over 9380 deg^2; the spectroscopy is now complete over a large contiguous area of the Northern Galactic Cap, closing the gap that was present in previous data releases. There are over 1.6 million spectra in total, including 930,000 galaxies, 120,000 quasars, and 460,000 stars. The data release includes improved stellar photometry at low Galactic latitude. The astrometry has all been recalibrated with the second version of the USNO CCD Astrograph Catalog, reducing the rms statistical errors at the bright end to 45 milliarcseconds per coordinate. We further quantify a systematic error in bright galaxy photometry due to poor sky determination; this problem is less severe than previously reported for the majority of galaxies. Finally, we describe a series of improvements to the spectroscopic reductions, including better flat fielding and improved wavelength calibration at the blue end, better processing of objects with extremely strong narrow emission lines, and an improved determination of stellar metallicities.

Shifting the genomic gold standard for the prokaryotic species definition

Abstract: DNA-DNA hybridization (DDH) has been used for nearly 50 years as the gold standard for prokaryotic species circumscriptions at the genomic level. It has been the only taxonomic method that offered a numerical and relatively stable species boundary, and its use has had a paramount influence on how the current classification has been constructed. However, now, in the era of genomics, DDH appears to be an outdated method for classification that needs to be substituted. The average nucleotide identity (ANI) between two genomes seems the most promising method since it mirrors DDH closely. Here we examine the work package JSpecies as a user-friendly, biologist-oriented interface to calculate ANI and the correlation of the tetranucleotide signatures between pairwise genomic comparisons. The results agreed with the use of ANI to substitute DDH, with a narrowed boundary that could be set at ≈95–96%. In addition, the JSpecies package implemented the tetranucleotide signature correlation index, an alignment-free parameter that generally correlates with ANI and that can be of help in deciding when a given pair of organisms should be classified in the same species. Moreover, for taxonomic purposes, the analyses can be produced by simply randomly sequencing at least 20% of the genome of the query strains rather than obtaining their full sequence.

Polyphenols: Chemistry, Dietary Sources, Metabolism, and Nutritional Significance

Abstract: Polyphenols constitute one of the most numerous and ubiquitous groups of plant metabolites and are an integral part of both human and animal diets. Ranging from simple phenolic molecules to highly polymerized compounds with molecular weights of greater than 30,000 Da, the occurrence of this complex group of substances in plant foods is extremely variable. Polyphenols traditionally have been considered antinutrients by animal nutritionists, because of the adverse effect of tannins, one type of polyphenol, on protein digestibility. However, recent interest in food phenolics has increased greatly, owing to their antioxidant capacity (free radical scavenging and metal chelating activities) and their possible beneficial implications in human health, such as in the treatment and prevention of cancer, cardiovascular disease, and other pathologies. Much of the literature refers to a single group of plant phenolics, the flavonoids. This review offers an overview of the nutritional effects of the main groups of polyphenolic compounds, including their metabolism, effects on nutrient bioavailability, and antioxidant activity, as well as a brief description of the chemistry of polyphenols and their occurrence in plant foods.

Early-warning signals for critical transitions

Abstract: Complex dynamical systems, ranging from ecosystems to financial markets and the climate, can have tipping points at which a sudden shift to a contrasting dynamical regime may occur. Although predicting such critical points before they are reached is extremely difficult, work in different scientific fields is now suggesting the existence of generic early-warning signals that may indicate for a wide class of systems if a critical threshold is approaching.

Acquisition of phosphorus and nitrogen in the rhizosphere and plant growth promotion by microorganisms

Abstract: The rhizosphere is a complex environment where roots interact with physical, chemical and biological properties of soil. Structural and functional characteristics of roots contribute to rhizosphere processes and both have significant influence on the capacity of roots to acquire nutrients. Roots also interact extensively with soil microorganisms which further impact on plant nutrition either directly, by influencing nutrient availability and uptake, or indirectly through plant (root) growth promotion. In this paper, features of the rhizosphere that are important for nutrient acquisition from soil are reviewed, with specific emphasis on the characteristics of roots that influence the availability and uptake of phosphorus and nitrogen. The interaction of roots with soil microorganisms, in particular with mycorrhizal fungi and non-symbiotic plant growth promoting rhizobacteria, is also considered in relation to nutrient availability and through the mechanisms that are associated with plant growth promotion.

The Genetic Architecture of Maize Flowering Time

Abstract: Flowering time is a complex trait that controls adaptation of plants to their local environment in the outcrossing species Zea mays (maize). We dissected variation for flowering time with a set of 5000 recombinant inbred lines (maize Nested Association Mapping population, NAM). Nearly a million plants were assayed in eight environments but showed no evidence for any single large-effect quantitative trait loci (QTLs). Instead, we identified evidence for numerous small-effect QTLs shared among families; however, allelic effects differ across founder lines. We identified no individual QTLs at which allelic effects are determined by geographic origin or large effects for epistasis or environmental interactions. Thus, a simple additive model accurately predicts flowering time for maize, in contrast to the genetic architecture observed in the selfing plant species rice and Arabidopsis.

Recent advances in rechargeable battery materials: a chemist’s perspective

Abstract: The constant increase in global energy demand, together with the awareness of the finite supply of fossil fuels, has brought about an imperious need to take advantage of renewable energy sources. At the same time, concern over CO2 emissions and future rises in the cost of gasoline has boosted technological efforts to make hybrid and electric vehicles available to the general public. Energy storage is a vital issue to be addressed within this scenario, and batteries are certainly a key player. In this tutorial review, the most recent and significant scientific advances in the field of rechargeable batteries, whose performance is dependent on their underlying chemistry, are covered. In view of its utmost current significance and future prospects, special emphasis is given to progress in lithium-based technologies.

Epithelial-mesenchymal transitions: the importance of changing cell state in development and disease

Abstract: The events that convert adherent epithelial cells into individual migratory cells that can invade the extracellular matrix are known collectively as epithelial-mesenchymal transition (EMT). Throughout evolution, the capacity of cells to switch between these two cellular states has been fundamental in the generation of complex body patterns. Here, we review the EMT events that build the embryo and further discuss two prototypical processes governed by EMT in amniotes: gastrulation and neural crest formation. Cells undergo EMT to migrate and colonize distant territories. Not surprisingly, this is also the mechanism used by cancer cells to disperse throughout the body.

Chemical and Structural Properties of Carbonaceous Products Obtained by Hydrothermal Carbonization of Saccharides

Abstract: Carbon-rich-quick scheme: A carbon-rich solid product made up of uniform micrometer-sized spheres of tunable diameter has been synthesized by the hydrothermal carbonization of saccharides. These microspheres possess a core-shell chemical structure based on the different nature of the oxygen functionalities between the core and the outer layer (see figure).A carbon-rich solid product, here denoted as hydrochar, has been synthesized by the hydrothermal carbonization of three different saccharides (glucose, sucrose, and starch) at temperatures ranging from 170 to 240 degrees C. This material is made up of uniform spherical micrometer-sized particles that have a diameter in the 0.4-6 mum range, which can be modulated by modifying the synthesis conditions (i.e., the concentration of the aqueous saccharide solution, the temperature of the hydrothermal treatment, the reaction time, and type of saccharide). The formation of the carbon-rich solid through the hydrothermal carbonization of saccharides is the consequence of dehydration, condensation, or polymerization and aromatization reactions. The microspheres thus obtained possess, from a chemical point of view, a core-shell structure consisting of a highly aromatic nucleus (hydrophobic) and a hydrophilic shell containing a high concentration of reactive oxygen functional groups (i.e., hydroxyl/phenolic, carbonyl, or carboxylic).

Alien species in a warmer world: risks and opportunities

Abstract: Climate change and biological invasions are key processes affecting global biodiversity, yet their effects have usually been considered separately. Here, we emphasise that global warming has enabled alien species to expand into regions in which they previously could not survive and reproduce. Based on a review of climate-mediated biological invasions of plants, invertebrates, fishes and birds, we discuss the ways in which climate change influences biological invasions. We emphasise the role of alien species in a more dynamic context of shifting species' ranges and changing communities. Under these circumstances, management practices regarding the occurrence of 'new' species could range from complete eradication to tolerance and even consideration of the 'new' species as an enrichment of local biodiversity and key elements to maintain ecosystem services.

Variation in discrimination factors (Δ15N and Δ13C): the effect of diet isotopic values and applications for diet reconstruction

Abstract: Summary 1The use of stable isotopic techniques to study animal diets and trophic levels requires a priori estimates of discrimination factors (Δ13C and Δ15N, also called fractionation factors), which are the differences in isotopic composition between an animal and its diet. Previous studies have shown that these parameters depend on several sources of variation (e.g. taxon, environment, tissue) but diet as a source of variation still needs assessment. 2We conducted an extensive review of the literature (66 publications) concerning estimates of animal-diet Δ13C (n = 290) and Δ15N (n = 268). We analysed this data set to test the effect of diet isotopic ratio on the discrimination factor, taking into account taxa, tissues, environments and lipid extraction treatments. Our results showed differences among taxonomic classes for Δ13C, but not for Δ15N, and significant differences among tissues for both Δ13C and Δ15N. We found a significant negative relationship between both, Δ13C and Δ15N, with their corresponding diet isotopic ratios. This relationship was found also within taxonomic classes for mammals (Δ13C and Δ15N), birds (Δ13C), fishes (Δ13C and Δ15N) and invertebrates (Δ13C and Δ15N). From these relationships, we propose a method to calculate discrimination factors based on data on diet isotope ratios (termed the ‘Diet-Dependent Discrimination Factor’, DDDF). 3To investigate current practice in the use of discrimination factors, we reviewed studies that used multi-resource isotopic models. More than 60% of models used a discrimination factor coming from a different species or tissues, and in more than 70% of models, only one Δ13C or Δ15N was used for all resources, even if resources had very different isotopic ratios. Also, we estimated DDDFs for the studies that used isotopic models. More than 40% used Δ15N values and more than 33% used Δ13C values differing > 2‰ from estimated DDDFs. 4Synthesis and applications. Over the last decade, applied ecologists have discovered the potential of stable isotopes for animal diet reconstruction, but the successful adoption of the method relies on a good estimation of discrimination factors. We draw attention to the high variability in discrimination factors, advise caution in the use of single discrimination factors in isotopic models, and point to a method for obtaining adequate values for this parameter when discrimination factors cannot be measured experimentally. Future studies should focus on understanding why discrimination factors vary as a function of the isotopic value of the diet.

Refining the stress-gradient hypothesis for competition and facilitation in plant communities

Abstract: Summary 1. The stress-gradient hypothesis (SGH) predicts that the frequency of facilitative and competitive interactions will vary inversely across abiotic stress gradients, with facilitation being more common in conditions of high abiotic stress relative to more benign abiotic conditions. With notable exceptions, most tests of the SGH have studied the interaction between a single pair or a few pairs of species, and thus have evaluated shifts in the magnitude and direction of pair-wise interactions along stress gradients, rather than shifts in the general frequency of interactions. 2. The SGH has been supported by numerous studies in many ecosystems, has provided a crucial foundation for studying the interplay between facilitation and competition in plant communities, and has a high heuristic value. However, recent empirical research indicates that factors like the variation among species and the nature of the stress gradient studied add complexity not considered in the SGH, creating an opportunity to extend the SGH’s general conceptual framework. 3. We suggest that one approach for extending the SGH framework is to differentiate between the original idea of how ‘common’ interactions might be along stress gradients and the ubiquitous empirical approach of studying shifts in the strength of pair-wise interactions. Furthermore, by explicitly considering the life history of the interacting species (relative tolerance to stress vs. competitive ability) and the characteristics of the stress factor (resource vs. non-resource) we may be able to greatly refine specific predictions relevant to the SGH. 4. We propose that the general pattern predicted by the SGH would hold more frequently for some combinations of life histories and stress factor, particularly when the benefactor and beneficiary species are mostly competitive and stress-tolerant, respectively. However, we also predict that other combinations are likely to yield different results. For example, the effect of neighbours can be negative at both ends of the stress gradient when both interacting species have similar ‘competitive’ or ‘stress-tolerant’ life histories and the abiotic stress gradient is driven by a resource (e.g. water). 5. Synthesis. The extension of the SGH presented here provides specific and testable hypotheses to foster research and helps to reconcile potential discrepancies among previous studies. It represents an important step in incorporating the complexity and species-specificity of potential outcomes into models and theories addressing how plant‐plant interactions change along stress gradients.

Interaction between Phenolics and Gut Microbiota: Role in Human Health

Abstract: Dietary phenolic compounds are often transformed before absorption. This transformation modulates their biological activity. Different studies have been carried out to understand gut microbiota transformations of particular polyphenol types and identify the responsible microorganisms. Although there are potentially thousands of different phenolic compounds in the diet, they are typically transformed to a much smaller number of metabolites. The aim of this review was to discuss the current information about the microbial degradation metabolites obtained from different phenolics and their formation pathways, identifying their differences and similarities. The modulation of gut microbial population by phenolics was also reviewed in order to understand the two-way phenolic-microbiota interaction. Clostridium and Eubacterium genera, which are phylogenetically associated, are other common elements involved in the metabolism of many phenolics. The health benefits from phenolic consumption should be attributed to their bioactive metabolites and also to the modulation of the intestinal bacterial population.

On hesitant fuzzy sets and decision

Abstract: Intuitionistic Fuzzy Sets (IFS) are a generalization of fuzzy sets where the membership is an interval. That is, membership, instead of being a single value, is an interval. A large number of operations have been defined for this type of fuzzy sets, and several applications have been developed in the last years. In this paper we describe hesitant fuzzy sets. They are another generalization of fuzzy sets. Although similar in intention to IFS, some basic differences on their interpretation and on their operators exist. In this paper we review their definition, the main results and we present an extension principle, which permits to generalize existing operations on fuzzy sets to this new type of fuzzy sets. We also discuss their use in decision making.

The architecture of mutualistic networks minimizes competition and increases biodiversity

Abstract: The main theories of biodiversity either neglect species interactions or assume that species interact randomly with each other. However, recent empirical work has revealed that ecological networks are highly structured, and the lack of a theory that takes into account the structure of interactions precludes further assessment of the implications of such network patterns for biodiversity. Here we use a combination of analytical and empirical approaches to quantify the influence of network architecture on the number of coexisting species. As a case study we consider mutualistic networks between plants and their animal pollinators or seed dispersers. These networks have been found to be highly nested, with the more specialist species interacting only with proper subsets of the species that interact with the more generalist. We show that nestedness reduces effective interspecific competition and enhances the number of coexisting species. Furthermore, we show that a nested network will naturally emerge if new species are more likely to enter the community where they have minimal competitive load. Nested networks seem to occur in many biological and social contexts, suggesting that our results are relevant in a wide range of fields.

Measurement of the Cosmic Ray e+ + e- spectrum from 20 GeV to 1 TeV with the Fermi Large Area Telescope.

Abstract: Designed as a high-sensitivity gamma-ray observatory, the Fermi Large Area Telescope is also an electron detector with a large acceptance exceeding 2 m2 sr at 300 GeV. Building on the gamma-ray analysis, we have developed an efficient electron detection strategy which provides sufficient background rejection for measurement of the steeply falling electron spectrum up to 1 TeV. Our high precision data show that the electron spectrum falls with energy as E-3.0 and does not exhibit prominent spectral features. Interpretations in terms of a conventional diffusive model as well as a potential local extra component are briefly discussed.

Ecological networks--beyond food webs.

Abstract: Summary 1. A fundamental goal of ecological network research is to understand how the complexity observed in nature can persist and how this affects ecosystem functioning. This is essential for us to be able to predict, and eventually mitigate, the consequences of increasing environmental perturbations such as habitat loss, climate change, and invasions of exotic species. 2. Ecological networks can be subdivided into three broad types: ‘traditional’ food webs, mutualistic networks and host‐parasitoid networks. There is a recent trend towards cross-comparisons among network types and also to take a more mechanistic, as opposed to phenomenological, perspective. For example, analysis of network configurations, such as compartments, allows us to explore the role of co-evolution in structuring mutualistic networks and host‐parasitoid networks, and of body size in food webs. 3. Research into ecological networks has recently undergone a renaissance, leading to the production of a new catalogue of evermore complete, taxonomically resolved, and quantitative data. Novel topological patterns have been unearthed and it is increasingly evident that it is the distribution of interaction strengths and the configuration of complexity, rather than just its magnitude, that governs network stability and structure. 4. Another significant advance is the growing recognition of the importance of individual traits and behaviour: interactions, after all, occur between individuals. The new generation of high-quality networks is now enabling us to move away from describing networks based on species-averaged data and to start exploring patterns based on individuals. Such refinements will enable us to address more general ecological questions relating to foraging theory and the recent metabolic theory of ecology. 5. We conclude by suggesting a number of ‘dead ends’ and ‘fruitful avenues’ for future research into ecological networks.

Rogue waves and rational solutions of the nonlinear Schrödinger equation

Abstract: We present a method for finding the hierarchy of rational solutions of the self-focusing nonlinear Schrodinger equation and present explicit forms for these solutions from first to fourth order. We also explain their relation to the highest amplitude part of a field that starts with a plane wave perturbed by random small amplitude radiation waves. Our work can elucidate the appearance of rogue waves in the deep ocean and can be applied to the observation of rogue light pulse waves in optical fibers.

Mitochondrial glutathione, a key survival antioxidant.

Abstract: Mitochondria are the primary intracellular site of oxygen consumption and the major source of reactive oxygen species (ROS), most of them originating from the mitochondrial respiratory chain Among the arsenal of antioxidants and detoxifying enzymes existing in mitochondria, mitochondrial glutathione (mGSH) emerges as the main line of defense for the maintenance of the appropriate mitochondrial redox environment to avoid or repair oxidative modifications leading to mitochondrial dysfunction and cell death mGSH importance is based not only on its abundance, but also on its versatility to counteract hydrogen peroxide, lipid hydroperoxides, or xenobiotics, mainly as a cofactor of enzymes such as glutathione peroxidase or glutathione-S-transferase (GST) Many death-inducing stimuli interact with mitochondria, causing oxidative stress; in addition, numerous pathologies are characterized by a consistent decrease in mGSH levels, which may sensitize to additional insults From the evaluation of mGSH inf

(+)-7- iso -Jasmonoyl- L -isoleucine is the endogenous bioactive jasmonate

Abstract: Hormone-triggered activation of the jasmonate signaling pathway in Arabidopsis thaliana requires SCFCOI1-mediated proteasome degradation of JAZ repressors. (−)-JA-L-Ile is the proposed bioactive hormone, and SCFCOI1 is its likely receptor. We found that the biological activity of (−)-JA-L-Ile is unexpectedly low compared to coronatine and the synthetic isomer (+)-JA-L-Ile, which suggests that the stereochemical orientation of the cyclopentanone-ring side chains greatly affects receptor binding. Detailed GC-MS and HPLC analyses showed that the (−)-JA-L-Ile preparations currently used in ligand binding studies contain small amounts of the C7 epimer (+)-7-iso-JA-L-Ile. Purification of each of these molecules demonstrated that pure (−)-JA-L-Ile is inactive and that the active hormone is (+)-7-iso-JA-L-Ile, which is also structurally more similar to coronatine. In addition, we show that pH changes promote conversion of (+)-7-iso-JA-L-Ile to the inactive (−)-JA-L-Ile form, thus providing a simple mechanism that can regulate hormone activity through epimerization.