Showing papers by "Spanish National Research Council published in 2003"

Systematic functional analysis of the Caenorhabditis elegans genome using RNAi

Abstract: A principal challenge currently facing biologists is how to connect the complete DNA sequence of an organism to its development and behaviour. Large-scale targeted-deletions have been successful in defining gene functions in the single-celled yeast Saccharomyces cerevisiae, but comparable analyses have yet to be performed in an animal. Here we describe the use of RNA interference to inhibit the function of ∼86% of the 19,427 predicted genes of C. elegans. We identified mutant phenotypes for 1,722 genes, about two-thirds of which were not previously associated with a phenotype. We find that genes of similar functions are clustered in distinct, multi-megabase regions of individual chromosomes; genes in these regions tend to share transcriptional profiles. Our resulting data set and reusable RNAi library of 16,757 bacterial clones will facilitate systematic analyses of the connections among gene sequence, chromosomal location and gene function in C. elegans.

The nested assembly of plant-animal mutualistic networks

Abstract: Most studies of plant–animal mutualisms involve a small number of species. There is almost no information on the structural organization of species-rich mutualistic networks despite its potential importance for the maintenance of diversity. Here we analyze 52 mutualistic networks and show that they are highly nested; that is, the more specialist species interact only with proper subsets of those species interacting with the more generalists. This assembly pattern generates highly asymmetrical interactions and organizes the community cohesively around a central core of interactions. Thus, mutualistic networks are neither randomly assembled nor organized in compartments arising from tight, parallel specialization. Furthermore, nestedness increases with the complexity (number of interactions) of the network: for a given number of species, communities with more interactions are significantly more nested. Our results indicate a nonrandom pattern of community organization that may be relevant for our understanding of the organization and persistence of biodiversity.

The preparation of magnetic nanoparticles for applications in biomedicine

Abstract: This review is focused on describing state-of-the-art synthetic routes for the preparation of magnetic nanoparticles useful for biomedical applications. In addition to this topic, we have also described in some detail some of the possible applications of magnetic nanoparticles in the field of biomedicine with special emphasis on showing the benefits of using nanoparticles. Finally, we have addressed some relevant findings on the importance of having well-defined synthetic routes to produce materials not only with similar physical features but also with similar crystallochemical characteristics.

A very energetic supernova associated with the |[gamma]|-ray burst of 29 March 2003

Abstract: Over the past five years evidence has mounted that long-duration (greater than 2s) gamma-ray bursts (GRBs), the most brilliant of all astronomical explosions, signal the collapse of massive stars in our Universe. This evidence, originally based on the probable association of one unusual GRB with a supernova, now includes the association of GRBs with regions of massive star-formation in distant galaxies, tantalizing evidence of supernova-like light-curve 'bumps' in the optical afterglows of several bursts, and lines of freshly synthesized elements in the spectra of a few X-ray afterglows. These observations support, but do not yet conclusively validate, models based upon the deaths of massive stars, presumably associated with core collapse. Here we report evidence for a very energetic supernova (a hypernova), temporally and spatially coincident with a GRB at redshift z=0.1685. The timing of the supernova indicates that it exploded within a few days of the GRB, strongly suggesting that core-collapse events can give rise to GRBs. Amongst the GRB central engine models proposed to-date, the properties of this supernova thus favour the collapsar model.

The INTEGRAL mission

Abstract: The ESA observatory INTEGRAL (International Gamma-Ray Astrophysics Laboratory) is dedicated to the fine spectroscopy (2.5 keV FWHM @ 1 MeV) and fine imaging (angular resolution: 12 arcmin FWHM) of celestial gamma-ray sources in the energy range 15 keV to 10 MeV with concurrent source monitoring in the X-ray ( keV) and optical (V -band, 550 nm) energy ranges. INTEGRAL carries two main gamma-ray instruments, the spectrometer SPI (Vedrenne et al. [CITE]) – optimized for the high-resolution gamma-ray line spectroscopy (20 keV–8 MeV), and the imager IBIS (Ubertini et al. [CITE]) – optimized for high-angular resolution imaging (15 keV–10 MeV). Two monitors, JEM-X (Lund et al. [CITE]) in the () keV X-ray band, and OMC (Mas-Hesse et al. [CITE]) in optical Johnson V -band complement the payload. The ground segment includes the Mission Operations Centre at ESOC, ESA and NASA ground stations, the Science Operations Centre at ESTEC and the Science Data Centre near Geneva. INTEGRAL was launched on 17 October 2002. The observing programme is well underway and sky exposure (until June 2003) reaches ~1800 ks in the Galactic plane. The prospects are excellent for the scientific community to observe the high energy sky using state-of-the-art gamma-ray imaging and spectroscopy. This paper presents a high-level overview of INTEGRAL.

ETHYLENE RESPONSE FACTOR1 Integrates Signals from Ethylene and Jasmonate Pathways in Plant Defense

Abstract: Cross-talk between ethylene and jasmonate signaling pathways determines the activation of a set of defense responses against pathogens and herbivores. However, the molecular mechanisms that underlie this cross-talk are poorly understood. Here, we show that ethylene and jasmonate pathways converge in the transcriptional activation of ETHYLENE RESPONSE FACTOR1 (ERF1), which encodes a transcription factor that regulates the expression of pathogen response genes that prevent disease progression. The expression of ERF1 can be activated rapidly by ethylene or jasmonate and can be activated synergistically by both hormones. In addition, both signaling pathways are required simultaneously to activate ERF1, because mutations that block any of them prevent ERF1 induction by any of these hormones either alone or in combination. Furthermore, 35S:ERF1 expression can rescue the defense response defects of coi1 (coronative insensitive1) and ein2 (ethylene insensitive2); therefore, it is a likely downstream component of both ethylene and jasmonate signaling pathways. Transcriptome analysis in Col;35S:ERF1 transgenic plants and ethylene/jasmonate-treated wild-type plants further supports the notion that ERF1 regulates in vivo the expression of a large number of genes responsive to both ethylene and jasmonate. These results suggest that ERF1 acts downstream of the intersection between ethylene and jasmonate pathways and suggest that this transcription factor is a key element in the integration of both signals for the regulation of defense response genes.

The transcription factor Slug represses E-cadherin expression and induces epithelial to mesenchymal transitions: a comparison with Snail and E47 repressors.

Abstract: Transcriptional repression mechanisms have emerged as one of the crucial processes for the downregulation of E-cadherin expression during development and tumour progression. Recently, several E-cadherin transcriptional repressors have been characterized (Snail, E12/E47, ZEB-1 and SIP-1) and shown to act through an interaction with proximal E-boxes of the E-cadherin promoter. We have analyzed the participation of another member of the Snail family, Slug, and observed that it also behaves as a repressor of E-cadherin expression. Stable expression of Slug in MDCK cells leads to the full repression of E-cadherin at transcriptional level and triggers a complete epithelial to mesenchymal transition. Slug-induced repression of E-cadherin is mediated by its binding to proximal E-boxes, particularly to the E-pal element of the mouse promoter. Detailed analysis of the binding affinity of different repressors to the E-pal element indicates that Slug binds with lower affinity than Snail and E47 proteins. These results, together with the known expression patterns of these factors in embryonic development and carcinoma cell lines, support the idea that the in vivo action of the different factors in E-cadherin repression can be modulated by their relative concentrations as well as by specific cellular or tumour contexts.

The contribution of arbuscular mycorrhizal fungi in sustainable maintenance of plant health and soil fertility

Abstract: Beneficial plant–microbe interactions in the rhizosphere are primary determinants of plant health and soil fertility. Arbuscular mycorrhizas are the most important microbial symbioses for the majority of plants and, under conditions of P-limitation, influence plant community development, nutrient uptake, water relations and above-ground productivity. They also act as bioprotectants against pathogens and toxic stresses. This review discusses the mechanism by which these benefits are conferred through abiotic and biotic interactions in the rhizosphere. Attention is paid to the conservation of biodiversity in arbuscular mycorrhizal fungi (AMF). Examples are provided in which the ecology of AMF has been taken into account and has had an impact in landscape regeneration, horticulture, alleviation of desertification and in the bioremediation of contaminated soils. It is vital that soil scientists and agriculturalists pay due attention to the management of AMF in any schemes to increase, restore or maintain soil fertility.

Parameter Estimation in Biochemical Pathways: A Comparison of Global Optimization Methods

Abstract: Here we address the problem of parameter estimation (inverse problem) of nonlinear dynamic biochemical pathways. This problem is stated as a nonlinear programming (NLP) problem subject to nonlinear differential-algebraic constraints. These problems are known to be frequently ill-conditioned and multimodal. Thus, traditional (gradient-based) local optimization methods fail to arrive at satisfactory solutions. To surmount this limitation, the use of several state-of-the-art deterministic and stochastic global optimization methods is explored. A case study considering the estimation of 36 parameters of a nonlinear biochemical dynamic model is taken as a benchmark. Only a certain type of stochastic algorithm, evolution strategies (ES), is able to solve this problem successfully. Although these stochastic methods cannot guarantee global optimality with certainty, their robustness, plus the fact that in inverse problems they have a known lower bound for the cost function, make them the best available candidates.

Cryptographic requirements for chaotic secure communications

Abstract: In recent years, a great amount of secure communications systems based on chaotic synchronization have been published. Most of the proposed schemes fail to explain a number of features of fundamental importance to all cryptosystems, such as key definition, characterization, and generation. As a consequence, the proposed ciphers are difficult to realize in practice with a reasonable degree of security. Likewise, they are seldom accompanied by a security analysis. Thus, it is hard for the reader to have a hint about their security. In this work we provide a set of guidelines that every new cryptosystems would benefit from adhering to. The proposed guidelines address these two main gaps, i.e., correct key management and security analysis, to help new cryptosystems be presented in a more rigorous cryptographic way. Also some recommendations are offered regarding some practical aspects of communications, such as channel noise, limited bandwith, and attenuation.

A Survey of z > 5.7 Quasars in the Sloan Digital Sky Survey. II. Discovery of Three Additional Quasars at z > 6

Abstract: We present the discovery of three new quasars at z > 6 in ~ 1300 deg2 of Sloan Digital Sky Survey imaging data, J114816.64+525150.3 (z = 6.43), J104845.05+463718.3 (z = 6.23), and J163033.90+401209.6 (z = 6.05). The first two objects have weak Lyα emission lines; their redshifts are determined from the positions of the Lyman break. They are only accurate to ~0.05 and could be affected by the presence of broad absorption line systems. The last object has a Lyα strength more typical of lower redshift quasars. Based on a sample of six quasars at z > 5.7 that cover 2870 deg2 presented in this paper and in Paper I, we estimate the comoving density of luminous quasars at z ~ 6 and M1450 5.7 quasars and high-resolution, ground-based images (seeing ~04) of three additional z > 5.7 quasars show that none of them is gravitationally lensed. The luminosity distribution of the high-redshift quasar sample suggests the bright-end slope of the quasar luminosity function at z ~ 6 is shallower than Ψ ∝ L-3.5 (2 σ), consistent with the absence of strongly lensed objects.

Cyclin-dependent kinase 2 is essential for meiosis but not for mitotic cell division in mice

Abstract: We targeted the locus encoding the cyclin-dependent kinase 2 (CDK2) by homologous recombination in mouse embryonic stem (ES) cells. Embryonic fibroblasts lacking CDK2 proliferate normally and become immortal after continuous passage in culture. Elimination of a conditional Cdk2 allele in immortal cells does not have a significant effect on proliferation. Cdk2-/- mice are viable and survive for up to two years, indicating that CDK2 is also dispensable for proliferation and survival of most cell types. But CDK2 is essential for completion of prophase I during meiotic cell division in male and female germ cells, an unforeseen role for this cell cycle kinase.

Galaxy Star Formation as a Function of Environment in the Early Data Release of the Sloan Digital Sky Survey

Abstract: We present in this paper a detailed analysis of the effect of environment on the star formation activity of galaxies within the Early Data Release (EDR) of the Sloan Digital Sky Survey (SDSS). We have used the Halpha emission line to derive the star formation rate (SFR) for each galaxy within a volume-limited sample of 8598 galaxies with 0.05 less than or equal to z less than or equal to 0.095 and M (r*) less than or equal to 20.45. We find that the SFR of galaxies is strongly correlated with the local ( projected) galaxy density, and thus we present here a density-SFR relation that is analogous to the density-morphology relation. The effect of density on the SFR of galaxies is seen in three ways. First, the overall distribution of SFRs is shifted to lower values in dense environments compared with the field population. Second, the effect is most noticeable for the strongly star-forming galaxies (Halpha EW > 5 Angstrom) in the 75th percentile of the SFR distribution. Third, there is a break ( or characteristic density) in the density-SFR relation at a local galaxy density of similar to1 h(75)(-2) Mpc(-2). To understand this break further, we have studied the SFR of galaxies as a function of clustercentric radius from 17 clusters and groups objectively selected from the SDSS EDR data. The distribution of SFRs of cluster galaxies begins to change, compared with the field population, at a clustercentric radius of 3-4 virial radii (at the >1sigma statistical significance), which is consistent with the characteristic break in density that we observe in the density-SFR relation. This effect with clustercentric radius is again most noticeable for the most strongly star-forming galaxies. Our tests suggest that the density-morphology relation alone is unlikely to explain the density-SFR relation we observe. For example, we have used the ( inverse) concentration index of SDSS galaxies to classify late-type galaxies and show that the distribution of the star-forming (EW Halpha > 5Angstrom) late-type galaxies is different in dense regions ( within 2 virial radii) compared with similar galaxies in the field. However, at present, we are unable to make definitive statements about the independence of the density-morphology and density-SFR relation. We have tested our work against potential systematic uncertainties including stellar absorption, reddening, SDSS survey strategy, SDSS analysis pipelines, and aperture bias. Our observations are in qualitative agreement with recent simulations of hierarchical galaxy formation that predict a decrease in the SFR of galaxies within the virial radius. Our results are in agreement with recent 2dF Galaxy Redshift Survey results as well as consistent with previous observations of a decrease in the SFR of galaxies in the cores of distant clusters. Taken together, these works demonstrate that the decrease in SFR of galaxies in dense environments is a universal phenomenon over a wide range in density (from 0.08 to 10 h(75)(-2) Mpc(-2)) and redshift (out to z similar or equal to 0.5).

Analysis and removal of emerging contaminants in wastewater and drinking water

Abstract: The occurrence of trace organic contaminants in wastewaters, their behavior during wastewater treatment and production of drinking water are key issues in the re-use of water resources. Elimination of different classes of emerging contaminants, such as surfactant degradates, pharmaceuticals and polar pesticides in wastewater-treatment plants (WWTPs) was found to be rather low, so sewage effluents are one of the main sources of these compounds and their treatment-resistant metabolites. This article reviews the state-of-the-art in the analysis of several groups of emerging contaminants (acidic pharmaceuticals, antibacterial agents, acidic pesticides and surfactant metabolites) in wastewaters. It also discusses the elimination of emerging contaminants in WWTPs applying conventional activated sludge treatment (AST) and advanced treatment processes, such as membrane bioreactors (MBRs) and advanced oxidation processes (AOPs), as well as during production of drinking water.

Conversion Limits in the Reaction of CO2 with Lime

Abstract: The use of calcines of natural limestones as CO2 regenerable sorbents is investigated in this work by studying the decay of the maximum carbonation conversion during many carbonation/calcination cycles. New experimental information is complemented with a compilation of previously published data on this subject. The observed conversion limits in the reaction of CO2 with lime are interpreted in terms of a certain loss in the porosity associated with small pores and a certain increase in the porosity associated with large pores. In the carbonation part of every cycle, the CaCO3 fills up all the available porosity made up of small pores plus a small fraction of the large voids, limited by the thickness of the product layer that marks the onset of the slow carbonation rate. A simple model based on textural changes, observed by scanning electron microscopy, fits equally well all the data from this work and from other authors. The two model parameters are consistent with known mechanism occurring during calcinat...

Perspective: Evolution and detection of genetic robustness.

Abstract: Robustness is the invariance of phenotypes in the face of perturbation. The robustness of phenotypes appears at various levels of biological organization, including gene expression, protein folding, metabolic flux, physiological homeostasis, development, and even organismal fitness. The mechanisms underlying robustness are diverse, ranging from thermodynamic stability at the RNA and protein level to behavior at the organismal level. Phenotypes can be robust either against heritable perturbations (e.g., mutations) or nonheritable perturbations (e.g., the weather). Here we primarily focus on the first kind of robustness-genetic robustness-and survey three growing avenues of research: (1) measuring genetic robustness in nature and in the laboratory; (2) understanding the evolution of genetic robustness; and (3) exploring the implications of genetic robustness for future evolution.

Biopolymer−Clay Nanocomposites Based on Chitosan Intercalated in Montmorillonite

Abstract: The objective of this work is the intercalation of the cationic biopolymer chitosan in Na+−montmorillonite, providing compact and robust three-dimensional nanocomposites with interesting functional properties. CHN chemical analysis, X-ray diffraction, Fourier transform infrared spectroscopy, scanning transmission electron microscopy, energy-dispersion X-ray analysis, and thermal analysis have been employed in the characterization of the nanocomposites, confirming the adsorption in mono- or bilayers of chitosan chains depending on the relative amount of chitosan with respect to the cationic exchange capacity of the clay. The first chitosan layer is adsorbed through a cationic exchange procedure, while the second layer is adsorbed in the acetate salt form. Because the deintercalation of the biopolymer is very difficult, the −NH3+Ac- species belonging to the chitosan second layer act as anionic exchange sites and, in this way, such nanocomposites become suitable systems for the detection of anions. These mat...

A nanoporous molecular magnet with reversible solvent-induced mechanical and magnetic properties

Abstract: A nanoporous molecular magnet with reversible solvent-induced mechanical and magnetic properties

Atmospheric Loss of Exoplanets Resulting from Stellar X-Ray and Extreme-Ultraviolet Heating

Abstract: Past studies addressing the thermal atmospheric escape of hydrogen from hot Jupiters have been based on the planet's effective temperature, which, as we show here, is not physically relevant for loss processes In consequence, these studies led to significant underestimations of the atmospheric escape rate (≤103 g s-1) and to the conclusion of long-term atmospheric stability From more realistic exospheric temperatures, determined from X-ray and extreme-ultraviolet (XUV) irradiation and thermal conduction in the thermosphere, we find that energy-limited escape and atmospheric expansion arise, leading to much higher estimations for the loss rates (≈1012 g s-1) These fluxes are in good agreement with recent determinations for HD 209458b based on observations of its extended exosphere We also show that for young solar-type stars, which emit stronger XUV fluxes, the inferred loss rates are significantly higher Thus, hydrogen-rich giant exoplanets under such strong XUV irradiances may evaporate down to their core sizes or shrink to levels at which heavier atmospheric constituents may prevent hydrodynamic escape These results could explain the apparent paucity of exoplanets so far detected at orbital distances less than 004 AU

Conjugative Plasmid Transfer in Gram-Positive Bacteria

Abstract: Conjugative transfer of bacterial plasmids is the most efficient way of horizontal gene spread, and it is therefore considered one of the major reasons for the increase in the number of bacteria exhibiting multiple-antibiotic resistance. Thus, conjugation and spread of antibiotic resistance represents a severe problem in antibiotic treatment, especially of immunosuppressed patients and in intensive care units. While conjugation in gram-negative bacteria has been studied in great detail over the last decades, the transfer mechanisms of antibiotic resistance plasmids in gram-positive bacteria remained obscure. In the last few years, the entire nucleotide sequences of several large conjugative plasmids from gram-positive bacteria have been determined. Sequence analyses and data bank comparisons of their putative transfer (tra) regions have revealed significant similarities to tra regions of plasmids from gram-negative bacteria with regard to the respective DNA relaxases and their targets, the origins of transfer (oriT), and putative nucleoside triphosphatases NTP-ases with homologies to type IV secretion systems. In contrast, a single gene encoding a septal DNA translocator protein is involved in plasmid transfer between micelle-forming streptomycetes. Based on these clues, we propose the existence of two fundamentally different plasmid-mediated conjugative mechanisms in gram-positive microorganisms, namely, the mechanism taking place in unicellular gram-positive bacteria, which is functionally similar to that in gram-negative bacteria, and a second type that occurs in multicellular gram-positive bacteria, which seems to be characterized by double-stranded DNA transfer.

Arbuscular mycorrhizal symbiosis and alleviation of osmotic stress. New perspectives for molecular studies

Abstract: Water deficit is considered one of the most important abiotic factors limiting plant growth and yield in many areas on earth. Several eco-physiological studies have demonstrated that the arbuscular mycorrhizal (AM) symbiosis often results in altered rates of water movement into, through and out of the host plants, with consequent effects on tissue hydration and plant physiology. It is now accepted that the contribution of AM symbiosis to plant drought tolerance is the result of accumulative physical, nutritional, physiological and cellular effects. This review considers several aspects that should be investigated at a molecular level in order to gain a whole understanding of the different mechanisms by which the AM symbiosis protects the host plants against the detrimental effects of water deficit.

High-yield isolation of murine microglia by mild trypsinization

Abstract: Microglia can be isolated with high purity but low yield by shaking off loosely adherent cells from mixed glial cultures. Here we describe a new technique for isolating microglia with an average yield close to 2,000,000 microglial cells/mouse pup, more than five times higher than that of the shaking method. Confluent mixed glial cultures are subjected to mild trypsinization (0.05-0.12%) in the presence of 0.2-0.5 mM EDTA and 0.5-0.8 mM Ca2+. This results in the detachment of an intact layer of cells containing virtually all the astrocytes, leaving undisturbed a population of firmly attached cells identified as >98% microglia. These almost pure microglial preparations can be kept in culture for weeks and show proliferation and phagocytosis. Treatment with macrophage colony-stimulating factor and lipopolysaccharide, alone or in the presence of interferon gamma, induces typical microglial responses in terms of proliferation, morphological changes, nuclear factor-kappaB translocation, NO, and tumor necrosis alpha release and phagocytosis. This method allows for the preparation of highly enriched mouse or rat microglial cultures with ease and reproducibility. Because of its high yield, it can be especially convenient when high amounts of microglial protein/mRNA are required or in cases in which the starting material is limited, such as microglial cultures from transgenic animals.