Showing papers by "Centre national de la recherche scientifique published in 2008"
TL;DR: The state-of-the-art on hybrid porous solids, their advantages, their new routes of synthesis, the structural concepts useful for their 'design', aiming at reaching very large pores are presented.
Abstract: This critical review will be of interest to the experts in porous solids (including catalysis), but also solid state chemists and physicists. It presents the state-of-the-art on hybrid porous solids, their advantages, their new routes of synthesis, the structural concepts useful for their ‘design’, aiming at reaching very large pores. Their dynamic properties and the possibility of predicting their structure are described. The large tunability of the pore size leads to unprecedented properties and applications. They concern adsorption of species, storage and delivery and the physical properties of the dense phases. (323 references)
5,187 citations
TL;DR: The Phylogeny.fr platform transparently chains programs to automatically perform phylogenetic analyses and can also meet the needs of specialists; the first ones will find up-to-date tools chained in a phylogeny pipeline to analyze their data in a simple and robust way, while the specialists will be able to easily build and run sophisticated analyses.
Abstract: Phylogenetic analyses are central to many research areas in biology and typically involve the identification of homologous sequences, their multiple alignment, the phylogenetic reconstruction and the graphical representation of the inferred tree. The Phylogeny.fr platform transparently chains programs to automatically perform these tasks. It is primarily designed for biologists with no experience in phylogeny, but can also meet the needs of specialists; the first ones will find up-to-date tools chained in a phylogeny pipeline to analyze their data in a simple and robust way, while the specialists will be able to easily build and run sophisticated analyses. Phylogeny.fr offers three main modes. The ‘One Click’ mode targets non-specialists and provides a ready-to-use pipeline chaining programs with recognized accuracy and speed: MUSCLE for multiple alignment, PhyML for tree building, and TreeDyn for tree rendering. All parameters are set up to suit most studies, and users only have to provide their input sequences to obtain a ready-to-print tree. The ‘Advanced’ mode uses the same pipeline but allows the parameters of each program to be customized by users. The ‘A la Carte’ mode offers more flexibility and sophistication, as users can build their own pipeline by selecting and setting up the required steps from a large choice of tools to suit their specific needs. Prior to phylogenetic analysis, users can also collect neighbors of a query sequence by running BLAST on general or specialized databases. A guide tree then helps to select neighbor sequences to be used as input for the phylogeny pipeline. Phylogeny.fr is available at: http://www.phylogeny.fr/
4,364 citations
TL;DR: Although NK cells might appear to be redundant in several conditions of immune challenge in humans, NK cell manipulation seems to hold promise in efforts to improve hematopoietic and solid organ transplantation, promote antitumor immunotherapy and control inflammatory and autoimmune disorders.
Abstract: Natural killer (NK) cells are effector lymphocytes of the innate immune system that control several types of tumors and microbial infections by limiting their spread and subsequent tissue damage. Recent research highlights the fact that NK cells are also regulatory cells engaged in reciprocal interactions with dendritic cells, macrophages, T cells and endothelial cells. NK cells can thus limit or exacerbate immune responses. Although NK cells might appear to be redundant in several conditions of immune challenge in humans, NK cell manipulation seems to hold promise in efforts to improve hematopoietic and solid organ transplantation, promote antitumor immunotherapy and control inflammatory and autoimmune disorders.
3,108 citations
TL;DR: The Bodipy family, first developed as luminescent tags and laser dyes, has become a cornerstone for these new applications and the near future looks extremely bright for "porphyrin's little sister".
Abstract: The world of organic luminophores has been confined for a long time to fairly standard biological labeling applications and to certain analytical tests. Recently, however, the field has undergone a major change of direction, driven by the dual needs to develop novel organic electronic materials and to fuel the rapidly emerging nanotechnologies. Among the many diverse fluorescent molecules, the Bodipy family, first developed as luminescent tags and laser dyes, has become a cornerstone for these new applications. The near future looks extremely bright for "porphyrin's little sister".
2,705 citations
TL;DR: It is shown that the inclusion of isolated populations that underwent a strong bottleneck can lead to a high rate of false positives, and it is demonstrated that it is possible to avoid them by carefully choosing the populations that should be included in the analysis.
Abstract: Identifying loci under natural selection from genomic surveys is of great interest in different research areas. Commonly used methods to separate neutral effects from adaptive effects are based on locus-specific population differentiation coefficients to identify outliers. Here we extend such an approach to estimate directly the probability that each locus is subject to selection using a Bayesian method. We also extend it to allow the use of dominant markers like AFLPs. It has been shown that this model is robust to complex demographic scenarios for neutral genetic differentiation. Here we show that the inclusion of isolated populations that underwent a strong bottleneck can lead to a high rate of false positives. Nevertheless, we demonstrate that it is possible to avoid them by carefully choosing the populations that should be included in the analysis. We analyze two previously published data sets: a human data set of codominant markers and a Littorina saxatilis data set of dominant markers. We also perform a detailed sensitivity study to compare the power of the method using amplified fragment length polymorphism (AFLP), SNP, and microsatellite markers. The method has been implemented in a new software available at our website (http://www-leca.ujf-grenoble.fr/logiciels.htm).
2,366 citations
TL;DR: It is found that atmospheric carbon dioxide is strongly correlated with Antarctic temperature throughout eight glacial cycles but with significantly lower concentrations between 650,000 and 750,000 yr before present, which extends the pre-industrial range of carbon dioxide concentrations during the late Quaternary by about 10 p.p.m.v.
Abstract: Changes in past atmospheric carbon dioxide concentrations can be determined by measuring the composition of air trapped in ice cores from Antarctica. So far, the Antarctic Vostok and EPICA Dome C ice cores have provided a composite record of atmospheric carbon dioxide levels over the past 650,000 years. Here we present results of the lowest 200 m of the Dome C ice core, extending the record of atmospheric carbon dioxide concentration by two complete glacial cycles to 800,000 yr before present. From previously published data and the present work, we find that atmospheric carbon dioxide is strongly correlated with Antarctic temperature throughout eight glacial cycles but with significantly lower concentrations between 650,000 and 750,000 yr before present. Carbon dioxide levels are below 180 parts per million by volume (p.p.m.v.) for a period of 3,000 yr during Marine Isotope Stage 16, possibly reflecting more pronounced oceanic carbon storage. We report the lowest carbon dioxide concentration measured in an ice core, which extends the pre-industrial range of carbon dioxide concentrations during the late Quaternary by about 10 p.p.m.v. to 172-300 p.p.m.v.
1,977 citations
TL;DR: In several species examined, the fine structure of the peptidoglycan significantly varies with the growth conditions, and the different models for the architecture are discussed with respect to structural and physical parameters.
Abstract: The peptidoglycan (murein) sacculus is a unique and essential structural element in the cell wall of most bacteria. Made of glycan strands cross-linked by short peptides, the sacculus forms a closed, bag-shaped structure surrounding the cytoplasmic membrane. There is a high diversity in the composition and sequence of the peptides in the peptidoglycan from different species. Furthermore, in several species examined, the fine structure of the peptidoglycan significantly varies with the growth conditions. Limited number of biophysical data on the thickness, elasticity and porosity of peptidoglycan are available. The different models for the architecture of peptidoglycan are discussed with respect to structural and physical parameters.
1,876 citations
TL;DR: Evidence is presented that carotenoid cleavage dioxygenase 8 shoot branching mutants of pea are strigolactone deficient and that strigOLactone application restores the wild-type branching phenotype to ccd8 mutants, and that other branching mutants previously characterized as lacking a response to the branching inhibition signal also lack striglactone response.
Abstract: A carotenoid-derived hormonal signal that inhibits shoot branching in plants has long escaped identification. Strigolactones are compounds thought to be derived from carotenoids and are known to trigger the germination of parasitic plant seeds and stimulate symbiotic fungi. Here we present evidence that carotenoid cleavage dioxygenase 8 shoot branching mutants of pea are strigolactone deficient and that strigolactone application restores the wild-type branching phenotype to ccd8 mutants. Moreover, we show that other branching mutants previously characterized as lacking a response to the branching inhibition signal also lack strigolactone response, and are not deficient in strigolactones. These responses are conserved in Arabidopsis. In agreement with the expected properties of the hormonal signal, exogenous strigolactone can be transported in shoots and act at low concentrations. We suggest that endogenous strigolactones or related compounds inhibit shoot branching in plants. Furthermore, ccd8 mutants demonstrate the diverse effects of strigolactones in shoot branching, mycorrhizal symbiosis and parasitic weed interaction.
1,873 citations
TL;DR: A practical secure communication protocol is developed, which uses a four-step procedure to ensure wireless information-theoretic security and is shown that the protocol is effective in secure key renewal-even in the presence of imperfect channel state information.
Abstract: This paper considers the transmission of confidential data over wireless channels. Based on an information-theoretic formulation of the problem, in which two legitimates partners communicate over a quasi-static fading channel and an eavesdropper observes their transmissions through a second independent quasi-static fading channel, the important role of fading is characterized in terms of average secure communication rates and outage probability. Based on the insights from this analysis, a practical secure communication protocol is developed, which uses a four-step procedure to ensure wireless information-theoretic security: (i) common randomness via opportunistic transmission, (ii) message reconciliation, (iii) common key generation via privacy amplification, and (iv) message protection with a secret key. A reconciliation procedure based on multilevel coding and optimized low-density parity-check (LDPC) codes is introduced, which allows to achieve communication rates close to the fundamental security limits in several relevant instances. Finally, a set of metrics for assessing average secure key generation rates is established, and it is shown that the protocol is effective in secure key renewal-even in the presence of imperfect channel state information.
1,759 citations
TL;DR: An observer on SO(3), termed the explicit complementary filter, that requires only accelerometer and gyro outputs; is suitable for implementation on embedded hardware; and provides good attitude estimates as well as estimating the gyro biases online.
Abstract: This paper considers the problem of obtaining good attitude estimates from measurements obtained from typical low cost inertial measurement units. The outputs of such systems are characterized by high noise levels and time varying additive biases. We formulate the filtering problem as deterministic observer kinematics posed directly on the special orthogonal group SO (3) driven by reconstructed attitude and angular velocity measurements. Lyapunov analysis results for the proposed observers are derived that ensure almost global stability of the observer error. The approach taken leads to an observer that we term the direct complementary filter. By exploiting the geometry of the special orthogonal group a related observer, termed the passive complementary filter, is derived that decouples the gyro measurements from the reconstructed attitude in the observer inputs. Both the direct and passive filters can be extended to estimate gyro bias online. The passive filter is further developed to provide a formulation in terms of the measurement error that avoids any algebraic reconstruction of the attitude. This leads to an observer on SO(3), termed the explicit complementary filter, that requires only accelerometer and gyro outputs; is suitable for implementation on embedded hardware; and provides good attitude estimates as well as estimating the gyro biases online. The performance of the observers are demonstrated with a set of experiments performed on a robotic test-bed and a radio controlled unmanned aerial vehicle.
1,581 citations
TL;DR: The results demonstrate that old-growth forests can continue to accumulate carbon, contrary to the long-standing view that they are carbon neutral, and suggest that 15 per cent of the global forest area, which is currently not considered when offsetting increasing atmospheric carbon dioxide concentrations, provides at least 10 per cent the global net ecosystem productivity.
Abstract: Old-growth forests remove carbon dioxide from the atmosphere at rates that vary with climate and nitrogen deposition. The sequestered carbon dioxide is stored in live woody tissues and slowly decomposing organic matter in litter and soil. Old-growth forests therefore serve as a global carbon dioxide sink, but they are not protected by international treaties, because it is generally thought that ageing forests cease to accumulate carbon. Here we report a search of literature and databases for forest carbon-flux estimates. We find that in forests between 15 and 800 years of age, net ecosystem productivity (the net carbon balance of the forest including soils) is usually positive. Our results demonstrate that old-growth forests can continue to accumulate carbon, contrary to the long-standing view that they are carbon neutral. Over 30 per cent of the global forest area is unmanaged primary forest, and this area contains the remaining old-growth forests. Half of the primary forests (6 times 10 8 hectares) are located in the boreal and temperate regions of the Northern Hemisphere. On the basis of our analysis, these forests alone sequester about 1.3 plusminus 0.5 gigatonnes of carbon per year. Thus, our findings suggest that 15 per cent of the global forest area, which is currently not considered when offsetting increasing atmospheric carbon dioxide concentrations, provides at least 10 per cent of the global net ecosystem productivity. Old-growth forests accumulate carbon for centuries and contain large quantities of it. We expect, however, that much of this carbon, even soil carbon, will move back to the atmosphere if these forests are disturbed
TL;DR: In each case, the very slow and complete delivery of Ibuprofen was achieved under physiological conditions after 3 weeks with a predictable zero-order kinetics, which highlights the unique properties of flexible hybrid solids for adapting their pore opening to optimize the drug-matrix interactions.
Abstract: Flexible nanoporous chromium or iron terephtalates (BDC) MIL-53(Cr, Fe) or M(OH)[BDC] have been used as matrices for the adsorption and in vitro drug delivery of Ibuprofen (or alpha- p-isobutylphenylpropionic acid). Both MIL-53(Cr) and MIL-53(Fe) solids adsorb around 20 wt % of Ibuprofen (Ibuprofen/dehydrated MIL-53 molar ratio = 0.22(1)), indicating that the amount of inserted drug does not depend on the metal (Cr, Fe) constitutive of the hybrid framework. Structural and spectroscopic characterizations are provided for the solid filled with Ibuprofen. In each case, the very slow and complete delivery of Ibuprofen was achieved under physiological conditions after 3 weeks with a predictable zero-order kinetics, which highlights the unique properties of flexible hybrid solids for adapting their pore opening to optimize the drug-matrix interactions.
TL;DR: Analysis provides evidence that plant miRNA–guided silencing has a widespread translational inhibitory component that is genetically separable from endonucleolytic cleavage, and shows that the same is true of silencing mediated by small interfering RNA (siRNA) populations.
Abstract: High complementarity between plant microRNAs (miRNAs) and their messenger RNA targets is thought to cause silencing, prevalently by endonucleolytic cleavage. We have isolated Arabidopsis mutants defective in miRNA action. Their analysis provides evidence that plant miRNA-guided silencing has a widespread translational inhibitory component that is genetically separable from endonucleolytic cleavage. We further show that the same is true of silencing mediated by small interfering RNA (siRNA) populations. Translational repression is effected in part by the ARGONAUTE proteins AGO1 and AGO10. It also requires the activity of the microtubule-severing enzyme katanin, implicating cytoskeleton dynamics in miRNA action, as recently suggested from animal studies. Also as in animals, the decapping component VARICOSE (VCS)/Ge-1 is required for translational repression by miRNAs, which suggests that the underlying mechanisms in the two kingdoms are related.
University of Oldenburg1, University of Groningen2, University of Sheffield3, OFFIS4, University of Regensburg5, Radboud University Nijmegen6, Helmholtz Centre for Environmental Research - UFZ7, Katholieke Universiteit Leuven8, Ghent University9, Wageningen University and Research Centre10, VU University Amsterdam11, Stockholm University12, Centre national de la recherche scientifique13, Autonomous University of Madrid14
TL;DR: The LEDA Traitbase is useful for large-scale analyses of functional responses of communities to environmental change, effects of community trait composition on ecosystem properties and patterns of rarity and invasiveness, as well as linkages between traits as expressions of fundamental trade-offs in plants.
Abstract: Summary 1. An international group of scientists has built an open internet data base of life-history traits of the Northwest European flora (the LEDA-Traitbase) that can be used as a data source for fundamental research on plant biodiversity and coexistence, macro-ecological patterns and plant functional responses. 2. The species-trait matrix comprises referenced information under the control of an editorial board, for ca. 3000 species of the Northwest European flora, combining existing information and additional measurements. The data base currently contains data on 26 plant traits that describe three key features of plant dynamics: persistence, regeneration and dispersal. The LEDA-Traitbase is freely available at www.leda-traitbase.org. 3. We present the structure of the data base and an overview of the trait information available. 4. Synthesis. The LEDA Traitbase is useful for large-scale analyses of functional responses of communities to environmental change, effects of community trait composition on ecosystem properties and patterns of rarity and invasiveness, as well as linkages between traits as expressions of fundamental trade-offs in plants.
TL;DR: This work directly image the atomic density profiles as a function of time, and finds that weak disorder can stop the expansion and lead to the formation of a stationary, exponentially localized wavefunction—a direct signature of Anderson localization.
Abstract: Anderson localization (AL) is a phenomenon in wave physics, occurring when interference between multiple scattering paths causes diffusion to cease. Experimentally, localization has been reported for light waves, microwaves, sound waves and electron gases, but there has been no direct observation of AL for matter waves of any type. The paper reports AL in a Bose–Einstein condensate as it expands in a one-dimensional disordered optical potential. The authors image directly the atomic density profiles as a function of time, and find that weak disorder can stop the expansion and lead to the formation of a stationary exponentially localized wave function — a direct signature of AL. The method can be extended to localization of atomic quantum gases in higher dimensions, and with controlled interactions. In 1958, Anderson predicted the localization1 of electronic wavefunctions in disordered crystals and the resulting absence of diffusion. It is now recognized that Anderson localization is ubiquitous in wave physics2 because it originates from the interference between multiple scattering paths. Experimentally, localization has been reported for light waves3,4,5,6,7, microwaves8,9, sound waves10 and electron gases11. However, there has been no direct observation of exponential spatial localization of matter waves of any type. Here we observe exponential localization of a Bose–Einstein condensate released into a one-dimensional waveguide in the presence of a controlled disorder created by laser speckle12. We operate in a regime of pure Anderson localization, that is, with weak disorder—such that localization results from many quantum reflections of low amplitude—and an atomic density low enough to render interactions negligible. We directly image the atomic density profiles as a function of time, and find that weak disorder can stop the expansion and lead to the formation of a stationary, exponentially localized wavefunction—a direct signature of Anderson localization. We extract the localization length by fitting the exponential wings of the profiles, and compare it to theoretical calculations. The power spectrum of the one-dimensional speckle potentials has a high spatial frequency cutoff, causing exponential localization to occur only when the de Broglie wavelengths of the atoms in the expanding condensate are greater than an effective mobility edge corresponding to that cutoff. In the opposite case, we find that the density profiles decay algebraically, as predicted in ref. 13. The method presented here can be extended to localization of atomic quantum gases in higher dimensions, and with controlled interactions.
TL;DR: The room-temperature manipulation of magnetization by an electric field using the multiferroic BiFeO3 represents an essential step towards the magnetoelectric control of spintronics devices.
Abstract: The room-temperature manipulation of magnetization by an electric field using the multiferroic BiFeO3 represents an essential step towards the magnetoelectric control of spintronics devices.
Stephen Richards1, Richard A. Gibbs1, George M. Weinstock1, Susan J. Brown2 +187 more•Institutions (47)
TL;DR: Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural products.
Abstract: Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved the ability to interact with a diverse chemical environment, as shown by large expansions in odorant and gustatory receptors, as well as P450 and other detoxification enzymes. Development in Tribolium is more representative of other insects than is Drosophila, a fact reflected in gene content and function. For example, Tribolium has retained more ancestral genes involved in cell-cell communication than Drosophila, some being expressed in the growth zone crucial for axial elongation in short-germ development. Systemic RNA interference in T. castaneum functions differently from that in Caenorhabditis elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control.
TL;DR: A novel approach, based on the limited persistence of DNA in the environment, to detect the presence of a species in fresh water, using specific primers that amplify short mitochondrial DNA sequences to track the existence of a frog in controlled environments and natural wetlands.
Abstract: The assessment of species distribution is a first critical phase of biodiversity studies and is necessary to many disciplines such as biogeography, conservation biology and ecology. However, several species are difficult to detect, especially during particular time periods or developmental stages, potentially biasing study outcomes. Here we present a novel approach, based on the limited persistence of DNA in the environment, to detect the presence of a species in fresh water. We used specific primers that amplify short mitochondrial DNA sequences to track the presence of a frog (Rana catesbeiana) in controlled environments and natural wetlands. A multi-sampling approach allowed for species detection in all environments where it was present, even at low densities. The reliability of the results was demonstrated by the identification of amplified DNA fragments, using traditional sequencing and parallel pyrosequencing techniques. As the environment can retain the molecular imprint of inhabiting species, our approach allows the reliable detection of secretive organisms in wetlands without direct observation. Combined with massive sequencing and the development of DNA barcodes that enable species identification, this approach opens new perspectives for the assessment of current biodiversity from environmental samples.
TL;DR: In this paper, the authors test the ability of five Dynamic Global Vegetation Models (DGVMs), forced with observed climatology and atmospheric CO2, to model the contemporary global carbon cycle.
Abstract: This study tests the ability of five Dynamic Global Vegetation Models (DGVMs), forced with observed climatology and atmospheric CO2, to model the contemporary global carbon cycle. The DGVMs are also coupled to a fast ‘climate analogue model’, based on the Hadley Centre General Circulation Model (GCM), and run into the future for four Special Report Emission Scenarios (SRES): A1FI, A2, B1, B2. Results show that all DGVMs are consistent with the contemporary global land carbon budget. Under the more extreme projections of future environmental change, the responses of the DGVMs diverge markedly. In particular, large uncertainties are associated with the response of tropical vegetation to drought and boreal ecosystems to elevated temperatures and changing soil moisture status. The DGVMs show more divergence in their response to regional changes in climate than to increases in atmospheric CO2 content. All models simulate a release of land carbon in response to climate, when physiological effects of elevated atmospheric CO2 on plant production are not considered, implying a positive terrestrial climate-carbon cycle feedback. All DGVMs simulate a reduction in global net primary production (NPP) and a decrease in soil residence time in the tropics and extra-tropics in response to future climate. When both counteracting effects of climate and atmospheric CO2 on ecosystem function are considered, all the DGVMs simulate cumulative net land carbon uptake over the 21st century for the four SRES emission scenarios. However, for the most extreme A1FI emissions scenario, three out of five DGVMs simulate an annual net source of CO2 from the land to the atmosphere in the final decades of the 21st century. For this scenario, cumulative land uptake differs by 494 Pg C among DGVMs over the 21st century. This uncertainty is equivalent to over 50 years of anthropogenic emissions at current levels.
TL;DR: The relevance of macrophage polarization in three domains of infectious diseases: resistance to infection, infectious pathogenesis, and chronic evolution of infectious disease is discussed.
Abstract: Converging studies have shown that M1 and M2 macrophages are functionally polarized in response to microorganisms and host mediators. Gene expression profiling of macrophages reveals that various Gram-negative and Gram-positive bacteria induce the transcriptional activity of a "common host response," which includes genes belonging to the M1 program. However, excessive or prolonged M1 polarization can lead to tissue injury and contribute to pathogenesis. The so-called M2 macrophages play a critical role in the resolution of inflammation by producing anti-inflammatory mediators. These M2 cells cover a continuum of cells with different phenotypic and functional properties. In addition, some bacterial pathogens induce specific M2 programs in macrophages. In this review, we discuss the relevance of macrophage polarization in three domains of infectious diseases: resistance to infection, infectious pathogenesis, and chronic evolution of infectious diseases.
15 Mar 2008
TL;DR: In this paper, a general definition and terminology for the Determination of Isotherm Isotherms is defined and a methodology for the determination of the isotherm is presented.
Abstract: The sections in this article are
Introduction
General Definitions and Terminology
Methodology
Methods for the Determination of Adsorption Isotherms
Operational Definitions of Adsorption
Experimental Procedures
Outgassing the Adsorbent
Determination of the Adsorption Isotherm
Evaluation of Adsorption Data
Presentation of Primary Data
Classification of Adsorption Isotherms
Adsorption Hysteresis
Determination of Surface Area
Application of the BET Method
Empirical Procedures for Isotherm Analysis
Assessment of Mesoporosity
Properties of Porous Materials
Application of the Kelvin Equation
Computation of Mesopore Size Distribution
Assessment of Microporosity
Terminology
Concept of Surface Area
Assessment of Micropore Volume
General Conclusions and Recommendations
Keywords:
physisorption data;
IUPAC;
adsorption isotherms;
surface area;
BET isotherm
TL;DR: Using a 47-year population study of the great tit in the United Kingdom, it is shown that individual adjustment of behavior in response to the environment has enabled the population to track a rapidly changing environment very closely.
Abstract: Rapid climate change has been implicated as a cause of evolution in poorly adapted populations. However, phenotypic plasticity provides the potential for organisms to respond rapidly and effectively to environmental change. Using a 47-year population study of the great tit (Parus major) in the United Kingdom, we show that individual adjustment of behavior in response to the environment has enabled the population to track a rapidly changing environment very closely. Individuals were markedly invariant in their response to environmental variation, suggesting that the current response may be fixed in this population. Phenotypic plasticity can thus play a central role in tracking environmental change; understanding the limits of plasticity is an important goal for future research.
Delaware Biotechnology Institute1, Pennsylvania State University2, Rice University3, Massachusetts Institute of Technology4, University of Cambridge5, Monash University6, Chinese Academy of Sciences7, Oregon State University8, University of California, Riverside9, University of Manchester10, University of California, Los Angeles11, Institut national de la recherche agronomique12, Cold Spring Harbor Laboratory13, University of Pennsylvania14, Centre national de la recherche scientifique15, University of Tokyo16, Max Planck Society17
TL;DR: The specific criteria required for the annotation of plant miRNAs are updated, including experimental and computational data, as well as refinements to standard nomenclature.
Abstract: MicroRNAs (miRNAs) are ∼21 nucleotide noncoding RNAs produced by Dicer-catalyzed excision from stem-loop precursors. Many plant miRNAs play critical roles in development, nutrient homeostasis, abiotic stress responses, and pathogen responses via interactions with specific target mRNAs. miRNAs are not the only Dicer-derived small RNAs produced by plants: A substantial amount of the total small RNA abundance and an overwhelming amount of small RNA sequence diversity is contributed by distinct classes of 21- to 24-nucleotide short interfering RNAs. This fact, coupled with the rapidly increasing rate of plant small RNA discovery, demands an increased rigor in miRNA annotations. Herein, we update the specific criteria required for the annotation of plant miRNAs, including experimental and computational data, as well as refinements to standard nomenclature.
TL;DR: It is shown that single-stranded DNA derived from endogenous retroelements accumulates in Trex1-deficient cells, and thatTrex1 can metabolize reverse-transcribed DNA, and suggest an unanticipated contribution of endogenous Retroelements to autoimmunity.
French Institute of Health and Medical Research1, Institut Gustave Roussy2, University of Naples Federico II3, University of Paris-Sud4, University of Rome Tor Vergata5, Boston Children's Hospital6, Centre national de la recherche scientifique7, University of Gothenburg8, Foundation for Research & Technology – Hellas9, University of Ferrara10, Stony Brook University11, University of Graz12, University College London13
TL;DR: Evidence is provided of a key signalling pathway that links autophagy to the cancer-associated dysregulation of p53, which improved the survival of p 53-deficient cancer cells under conditions of hypoxia and nutrient depletion, allowing them to maintain high ATP levels.
Abstract: Multiple cellular stressors, including activation of the tumour suppressor p53, can stimulate autophagy. Here we show that deletion, depletion or inhibition of p53 can induce autophagy in human, mouse and nematode cells subjected to knockout, knockdown or pharmacological inhibition of p53. Enhanced autophagy improved the survival of p53-deficient cancer cells under conditions of hypoxia and nutrient depletion, allowing them to maintain high ATP levels. Inhibition of p53 led to autophagy in enucleated cells, and cytoplasmic, not nuclear, p53 was able to repress the enhanced autophagy of p53(-/-) cells. Many different inducers of autophagy (for example, starvation, rapamycin and toxins affecting the endoplasmic reticulum) stimulated proteasome-mediated degradation of p53 through a pathway relying on the E3 ubiquitin ligase HDM2. Inhibition of p53 degradation prevented the activation of autophagy in several cell lines, in response to several distinct stimuli. These results provide evidence of a key signalling pathway that links autophagy to the cancer-associated dysregulation of p53.
TL;DR: It is speculated that IL-33 may function, similarly to the prototype ‘alarmin’ HMGB1, as an endogenous ‘danger’ signal to alert the immune system after endothelial or epithelial cell damage during trauma or infection.
Abstract: Background
Interleukin-33 (IL-33) is an IL-1-like cytokine ligand for the IL-1 receptor-related protein ST2, that activates mast cells and Th2 lymphocytes, and induces production of Th2-associated cytokines in vivo. We initially discovered IL-33 as a nuclear factor (NF-HEV) abundantly expressed in high endothelial venules from lymphoid organs, that associates with chromatin and exhibits transcriptional regulatory properties. This suggested that, similarly to IL-1α and chromatin-associated cytokine HMGB1, IL-33 may act as both a cytokine and a nuclear factor. Although the activity of recombinant IL-33 has been well characterized, little is known yet about the expression pattern of endogenous IL-33 in vivo.
Methodology/Principal Findings
Here, we show that IL-33 is constitutively and abundantly expressed in normal human tissues. Using a combination of human tissue microarrays and IL-33 monoclonal and polyclonal antibodies, we found that IL-33 is a novel nuclear marker of the endothelium widely expressed along the vascular tree. We observed abundant nuclear expression of IL-33 in endothelial cells from both large and small blood vessels in most normal human tissues, as well as in human tumors. In addition to endothelium, we also found constitutive nuclear expression of IL-33 in fibroblastic reticular cells of lymphoid tissues, and epithelial cells of tissues exposed to the environment, including skin keratinocytes and epithelial cells of the stomach, tonsillar crypts and salivary glands.
Conclusions/Significance
Together, our results indicate that, unlike inducible cytokines, IL-33 is constitutively expressed in normal human tissues. In addition, they reveal that endothelial cells and epithelial cells constitute major sources of IL-33 in vivo. Based on these findings, we speculate that IL-33 may function, similarly to the prototype ‘alarmin’ HMGB1, as an endogenous ‘danger’ signal to alert the immune system after endothelial or epithelial cell damage during trauma or infection.
Centre national de la recherche scientifique1, Institut national de la recherche agronomique2, University of Évry Val d'Essonne3, University of Dundee4, University of Provence5, University of Rennes6, Woods Hole Oceanographic Institution7, North Carolina State University8, Iowa State University9, École normale supérieure de Lyon10, Queen's University Belfast11, University of Bari12, Swiss Institute of Bioinformatics13, University of Lausanne14, Wageningen University and Research Centre15, University of Edinburgh16, French Institute of Health and Medical Research17
TL;DR: The draft genome sequence of the root-knot nematode Meloidogyne incognita, a biotrophic parasite of many crops, is reported, providing insights into the adaptations required by metazoans to successfully parasitize immunocompetent plants, and open the way for discovering new antiparasitic strategies.
Abstract: Plant-parasitic nematodes are major agricultural pests worldwide and novel approaches to control them are sorely needed. We report the draft genome sequence of the root-knot nematode Meloidogyne incognita, a biotrophic parasite of many crops, including tomato, cotton and coffee. Most of the assembled sequence of this asexually reproducing nematode, totaling 86 Mb, exists in pairs of homologous but divergent segments. This suggests that ancient allelic regions in M. incognita are evolving toward effective haploidy, permitting new mechanisms of adaptation. The number and diversity of plant cell wall-degrading enzymes in M. incognita is unprecedented in any animal for which a genome sequence is available, and may derive from multiple horizontal gene transfers from bacterial sources. Our results provide insights into the adaptations required by metazoans to successfully parasitize immunocompetent plants, and open the way for discovering new antiparasitic strategies.
TL;DR: The shape and size distribution of crystalline nanoparticles resulting from the sulfuric acid hydrolysis of cellulose from cotton, Avicel, and tunicate were investigated using transmission electron microscopy and atomic force microscopy as well as small- and wide-angle X-ray scattering.
TL;DR: In this paper, a technique based on jet areas is proposed to provide jet-by-jet corrections for pileup and underlying-event effects, which can be used with any jet algorithm that can be sensibly defined.
Centre national de la recherche scientifique1, Max Planck Society2, University of Antwerp3, Laval University4, Peking University5, Environment Canada6, Princeton University7, Swedish University of Agricultural Sciences8, United States Forest Service9, Finnish Meteorological Institute10, Lund University11, University of New Hampshire12, University of Helsinki13
TL;DR: Simulation and observations indicate that northern terrestrial ecosystems may currently lose carbon dioxide in response to autumn warming, with a sensitivity of about 0.2 PgC °C-1, offsetting 90% of the increased carbon dioxide uptake during spring.
Abstract: The carbon balance of terrestrial ecosystems is particularly sensitive to climatic changes in autumn and spring(1-4), with spring and autumn temperatures over northern latitudes having risen by about 1.1 degrees C and 0.8 degrees C, respectively, over the past two decades(5). A simultaneous greening trend has also been observed, characterized by a longer growing season and greater photosynthetic activity(6,7). These observations have led to speculation that spring and autumn warming could enhance carbon sequestration and extend the period of net carbon uptake in the future(8). Here we analyse interannual variations in atmospheric carbon dioxide concentration data and ecosystem carbon dioxide fluxes. We find that atmospheric records from the past 20 years show a trend towards an earlier autumn- to- winter carbon dioxide build- up, suggesting a shorter net carbon uptake period. This trend cannot be explained by changes in atmospheric transport alone and, together with the ecosystem flux data, suggest increasing carbon losses in autumn. We use a process- based terrestrial biosphere model and satellite vegetation greenness index observations to investigate further the observed seasonal response of northern ecosystems to autumnal warming. We find that both photosynthesis and respiration increase during autumn warming, but the increase in respiration is greater. In contrast, warming increases photosynthesis more than respiration in spring. Our simulations and observations indicate that northern terrestrial ecosystems may currently lose carbon dioxide in response to autumn warming, with a sensitivity of about 0.2 PgC degrees C-1, offsetting 90% of the increased carbon dioxide uptake during spring. If future autumn warming occurs at a faster rate than in spring, the ability of northern ecosystems to sequester carbon may be diminished earlier than previously suggested(9,10).