Showing papers by "Commissariat à l'énergie atomique et aux énergies alternatives published in 2017"
Peking University1, Nanjing Agricultural University2, Stanford University3, Chinese Academy of Sciences4, University of Sassari5, Commissariat à l'énergie atomique et aux énergies alternatives6, Institut national de la recherche agronomique7, University of Chicago8, University of Bonn9, University of Antwerp10, International Rice Research Institute11, Potsdam Institute for Climate Impact Research12, Goddard Institute for Space Studies13, University of Florida14
TL;DR: Investigating the impacts of temperature on yields of the four crops by compiling extensive published results from four analytical methods consistently showed negative temperature impacts on crop yield at the global scale, generally underpinned by similar impacts at country and site scales.
Abstract: Wheat, rice, maize, and soybean provide two-thirds of human caloric intake. Assessing the impact of global temperature increase on production of these crops is therefore critical to maintaining global food supply, but different studies have yielded different results. Here, we investigated the impacts of temperature on yields of the four crops by compiling extensive published results from four analytical methods: global grid-based and local point-based models, statistical regressions, and field-warming experiments. Results from the different methods consistently showed negative temperature impacts on crop yield at the global scale, generally underpinned by similar impacts at country and site scales. Without CO2 fertilization, effective adaptation, and genetic improvement, each degree-Celsius increase in global mean temperature would, on average, reduce global yields of wheat by 6.0%, rice by 3.2%, maize by 7.4%, and soybean by 3.1%. Results are highly heterogeneous across crops and geographical areas, with some positive impact estimates. Multimethod analyses improved the confidence in assessments of future climate impacts on global major crops and suggest crop- and region-specific adaptation strategies to ensure food security for an increasing world population.
1,442 citations
University of California, Irvine1, Goddard Space Flight Center2, University of Maryland, College Park3, VU University Amsterdam4, Duke University5, Columbia University6, Karlsruhe Institute of Technology7, Max Planck Society8, Oregon State University9, Chinese Academy of Sciences10, Imperial College London11, Environment Canada12, Commissariat à l'énergie atomique et aux énergies alternatives13
TL;DR: Assessing long-term fire trends using multiple satellite data sets found that global burned area declined by 24.3 ± 8.8% over the past 18 years, and the estimated decrease in burned area remained robust after adjusting for precipitation variability and was largest in savannas.
Abstract: Fire is an essential Earth system process that alters ecosystem and atmospheric composition. Here we assessed long-term fire trends using multiple satellite data sets. We found that global burned area declined by 24.3 ± 8.8% over the past 18 years. The estimated decrease in burned area remained robust after adjusting for precipitation variability and was largest in savannas. Agricultural expansion and intensification were primary drivers of declining fire activity. Fewer and smaller fires reduced aerosol concentrations, modified vegetation structure, and increased the magnitude of the terrestrial carbon sink. Fire models were unable to reproduce the pattern and magnitude of observed declines, suggesting that they may overestimate fire emissions in future projections. Using economic and demographic variables, we developed a conceptual model for predicting fire in human-dominated landscapes.
625 citations
TL;DR: This paper presents a short overview of the changes to the trigger and data acquisition systems during the first long shutdown of the LHC and shows the performance of the trigger system and its components based on the 2015 proton–proton collision data.
Abstract: During 2015 the ATLAS experiment recorded 3.8 fb(-1) of proton-proton collision data at a centre-of-mass energy of 13 TeV. The ATLAS trigger system is a crucial component of the experiment, respons ...
488 citations
TL;DR: Topological cell clustering is established as a well-performing calorimeter signal definition for jet and missing transverse momentum reconstruction in ATLAS and is exploited to apply a local energy calibration and corrections depending on the nature of the cluster.
Abstract: The reconstruction of the signal from hadrons and jets emerging from the proton–proton collisions at the Large Hadron Collider (LHC) and entering the ATLAS calorimeters is based on a three-dimensional topological clustering of individual calorimeter cell signals. The cluster formation follows cell signal-significance patterns generated by electromagnetic and hadronic showers. In this, the clustering algorithm implicitly performs a topological noise suppression by removing cells with insignificant signals which are not in close proximity to cells with significant signals. The resulting topological cell clusters have shape and location information, which is exploited to apply a local energy calibration and corrections depending on the nature of the cluster. Topological cell clustering is established as a well-performing calorimeter signal definition for jet and missing transverse momentum reconstruction in ATLAS.
438 citations
Jamia Millia Islamia1, Hanoi University of Science2, Vietnam Academy of Science and Technology3, Saitama University4, Aarhus University5, University of California, Santa Barbara6, Commissariat à l'énergie atomique et aux énergies alternatives7, University of Münster8, University of Connecticut9, University of Manchester10, Indian Institute of Technology Guwahati11, Leiden University12, Northwestern University13, Federal University of Paraíba14, Centre national de la recherche scientifique15, Universidade Federal do ABC16, University of Southampton17, Argonne National Laboratory18, Karlsruhe Institute of Technology19, University of Mainz20, Technische Universität München21, Max Planck Society22, Heidelberg University23, University of Tübingen24, Massachusetts Institute of Technology25, Durham University26, University of California, San Diego27, C. N. Yang Institute for Theoretical Physics28, Moscow Institute of Physics and Technology29, Russian Academy of Sciences30, University of Sydney31, University of Copenhagen32, Université libre de Bruxelles33, Paris Diderot University34, Niels Bohr Institute35, Estácio S.A.36, CERN37, University of California, Santa Cruz38, Institute on Taxation and Economic Policy39, University of Bern40, Institute for Advanced Study41, RWTH Aachen University42, Chinese Academy of Sciences43, East China University of Science and Technology44, University of Chicago45, Autonomous University of Madrid46, King's College London47, INAF48, Lawrence Berkeley National Laboratory49, Istituto Nazionale di Fisica Nucleare50, University of Bari51, University of Geneva52, Petersburg Nuclear Physics Institute53, University of Genoa54, Kapteyn Astronomical Institute55, Fermilab56, Spanish National Research Council57, Oak Ridge National Laboratory58, University of California, Berkeley59, École Polytechnique Fédérale de Lausanne60, University of Paris61, University of Zurich62, Mitchell Institute63, Tohoku University64, Princeton University65, Shimane University66, University of Maryland, College Park67, Dresden University of Technology68
TL;DR: A comprehensive review of keV-scale neutrino Dark Matter can be found in this paper, where the role of active neutrinos in particle physics, astrophysics, and cosmology is reviewed.
Abstract: We present a comprehensive review of keV-scale sterile neutrino Dark Matter, collecting views and insights from all disciplines involved—cosmology, astrophysics, nuclear, and particle physics—in each case viewed from both theoretical and experimental/observational perspectives. After reviewing the role of active neutrinos in particle physics, astrophysics, and cosmology, we focus on sterile neutrinos in the context of the Dark Matter puzzle. Here, we first review the physics motivation for sterile neutrino Dark Matter, based on challenges and tensions in purely cold Dark Matter scenarios. We then round out the discussion by critically summarizing all known constraints on sterile neutrino Dark Matter arising from astrophysical observations, laboratory experiments, and theoretical considerations. In this context, we provide a balanced discourse on the possibly positive signal from X-ray observations. Another focus of the paper concerns the construction of particle physics models, aiming to explain how sterile neutrinos of keV-scale masses could arise in concrete settings beyond the Standard Model of elementary particle physics. The paper ends with an extensive review of current and future astrophysical and laboratory searches, highlighting new ideas and their experimental challenges, as well as future perspectives for the discovery of sterile neutrinos.
398 citations
TL;DR: It is argued that despite their recent successes, current machines are still mostly implementing computations that reflect unconscious processing in the human brain, and the word “consciousness” conflates two different types of information-processing computations in the brain.
Abstract: The controversial question of whether machines may ever be conscious must be based on a careful consideration of how consciousness arises in the only physical system that undoubtedly possesses it: the human brain. We suggest that the word “consciousness” conflates two different types of information-processing computations in the brain: the selection of information for global broadcasting, thus making it flexibly available for computation and report (C1, consciousness in the first sense), and the self-monitoring of those computations, leading to a subjective sense of certainty or error (C2, consciousness in the second sense). We argue that despite their recent successes, current machines are still mostly implementing computations that reflect unconscious processing (C0) in the human brain. We review the psychological and neural science of unconscious (C0) and conscious computations (C1 and C2) and outline how they may inspire novel machine architectures.
395 citations
TL;DR: In this article, a search for new resonant and non-resonant high-mass phenomena in dielectron and dimuon fi nal states was conducted using 36 : 1 fb(-1) of proton-proton collision data.
Abstract: A search is conducted for new resonant and non-resonant high-mass phenomena in dielectron and dimuon fi nal states. The search uses 36 : 1 fb(-1) of proton-proton collision data, collected at root ...
329 citations
TL;DR: It is shown that the microalga Chlorella variabilis NC64A harbors a photoenzyme that acts in lipid metabolism that may be useful in light-driven, bio-based production of hydrocarbons, which is named fatty acid photodecarboxylase.
Abstract: Although many organisms capture or respond to sunlight, few enzymes are known to be driven by light. Among these are DNA photolyases and the photosynthetic reaction centers. Here, we show that the microalga Chlorella variabilis NC64A harbors a photoenzyme that acts in lipid metabolism. This enzyme belongs to an algae-specific clade of the glucose-methanol-choline oxidoreductase family and catalyzes the decarboxylation of free fatty acids to n-alkanes or -alkenes in response to blue light. Crystal structure of the protein reveals a fatty acid–binding site in a hydrophobic tunnel leading to the light-capturing flavin adenine dinucleotide (FAD) cofactor. The decarboxylation is initiated through electron abstraction from the fatty acid by the photoexcited FAD with a quantum yield >80%. This photoenzyme, which we name fatty acid photodecarboxylase, may be useful in light-driven, bio-based production of hydrocarbons.
271 citations
20 Feb 2017
TL;DR: In this article, the authors report on several fibers with a hypocycloid core contour and a cladding structure made of a single ring from a tubular amorphous lattice, including one with a record transmission loss of 7.7 dB/km at ∼ 750 nm (only a factor ∼2 above the SRSL).
Abstract: Attenuation in photonic bandgap guiding hollow-core photonic crystal fiber (HC-PCF) has not beaten the fundamental silica Rayleigh scattering limit (SRSL) of conventional step-index fibers due to strong core-cladding optical overlap, surface roughness at the silica cladding struts, and the presence of interface modes. Hope has been revived recently by the introduction of hypocycloid core contour (i.e., negative curvature) in inhibited-coupling guiding HC-PCF. We report on several fibers with a hypocycloid core contour and a cladding structure made of a single ring from a tubular amorphous lattice, including one with a record transmission loss of 7.7 dB/km at ∼750 nm (only a factor ∼2 above the SRSL) and a second with an ultrabroad fundamental band with loss in the range of 10–20 dB/km, spanning from 600 to 1200 nm. The reduction in confinement loss makes these fibers serious contenders for light transmission below the SRSL in the UV–VIS–NIR spectral range and could find application in high-energy pulse laser beam delivery or gas-based coherent and nonlinear optics.
245 citations
TL;DR: This work genetically uncouple two Pi sensing pathways in the root apex of Arabidopsis thaliana and uncovers STOP1 and ALMT1 as a signalling pathway of low Pi availability and exuded malate as an unexpected apoplastic inhibitor of root cell wall expansion.
Abstract: Environmental cues profoundly modulate cell proliferation and cell elongation to inform and direct plant growth and development. External phosphate (Pi) limitation inhibits primary root growth in many plant species. However, the underlying Pi sensory mechanisms are unknown. Here we genetically uncouple two Pi sensing pathways in the root apex of Arabidopsis thaliana. First, the rapid inhibition of cell elongation in the transition zone is controlled by transcription factor STOP1, by its direct target, ALMT1, encoding a malate channel, and by ferroxidase LPR1, which together mediate Fe and peroxidase-dependent cell wall stiffening. Second, during the subsequent slow inhibition of cell proliferation in the apical meristem, which is mediated by LPR1-dependent, but largely STOP1-ALMT1-independent, Fe and callose accumulate in the stem cell niche, leading to meristem reduction. Our work uncovers STOP1 and ALMT1 as a signalling pathway of low Pi availability and exuded malate as an unexpected apoplastic inhibitor of root cell wall expansion.
226 citations
Goddard Space Flight Center1, University of Exeter2, Jet Propulsion Laboratory3, University of Maryland, College Park4, University of Edinburgh5, Commissariat à l'énergie atomique et aux énergies alternatives6, Columbia University7, Goddard Institute for Space Studies8, Space Telescope Science Institute9, University of California, Santa Cruz10, California Institute of Technology11
TL;DR: HAT-P-26b’s atmosphere is primordial and obtained its gaseous envelope late in its disk lifetime, with little contamination from metal-rich planetesimals, according to a detailed atmospheric study of the transiting Neptune-mass exoplanet.
Abstract: A correlation between giant-planet mass and atmospheric heavy elemental abundance was first noted in the past century from observations of planets in our own Solar System and has served as a cornerstone of planet-formation theory. Using data from the Hubble and Spitzer Space Telescopes from 0.5 to 5 micrometers, we conducted a detailed atmospheric study of the transiting Neptune-mass exoplanet HAT-P-26b. We detected prominent H 2 O absorption bands with a maximum base-to-peak amplitude of 525 parts per million in the transmission spectrum. Using the water abundance as a proxy for metallicity, we measured HAT-P-26b’s atmospheric heavy element content ( 4.8 − 4.0 + 21.5 times solar). This likely indicates that HAT-P-26b’s atmosphere is primordial and obtained its gaseous envelope late in its disk lifetime, with little contamination from metal-rich planetesimals.
TL;DR: It is revealed that ribosomal RNA 2′-O-methylation can be modulated in human ribosomes, including at key functional sites for translation, and that changes in the 2′'-O- methylation pattern control the intrinsic capabilities of ribosome to translate mRNAs.
Abstract: Ribosomal RNAs (rRNAs) are main effectors of messenger RNA (mRNA) decoding, peptide-bond formation, and ribosome dynamics during translation. Ribose 2′-O-methylation (2′-O-Me) is the most abundant rRNA chemical modification, and displays a complex pattern in rRNA. 2′-O-Me was shown to be essential for accurate and efficient protein synthesis in eukaryotic cells. However, whether rRNA 2′-O-Me is an adjustable feature of the human ribosome and a means of regulating ribosome function remains to be determined. Here we challenged rRNA 2′-O-Me globally by inhibiting the rRNA methyl-transferase fibrillarin in human cells. Using RiboMethSeq, a nonbiased quantitative mapping of 2′-O-Me, we identified a repertoire of 2′-O-Me sites subjected to variation and demonstrate that functional domains of ribosomes are targets of 2′-O-Me plasticity. Using the cricket paralysis virus internal ribosome entry site element, coupled to in vitro translation, we show that the intrinsic capability of ribosomes to translate mRNAs is modulated through a 2′-O-Me pattern and not by nonribosomal actors of the translational machinery. Our data establish rRNA 2′-O-Me plasticity as a mechanism providing functional specificity to human ribosomes.
TL;DR: The generation of a comprehensive nanopore sequencing data set with a median read length of 11,979 bp for a self-compatible accession of the wild tomato species Solanum pennellii indicates that such long read sequencing data can be used to affordably sequence and assemble gigabase-sized plant genomes.
Abstract: Updates in nanopore technology have made it possible to obtain gigabases of sequence data. Prior to this, nanopore sequencing technology was mainly used to analyze microbial samples. Here, we describe the generation of a comprehensive nanopore sequencing data set with a median read length of 11,979 bp for a self-compatible accession of the wild tomato species Solanum pennellii. We describe the assembly of its genome to a contig N50 of 2.5 MB. The assembly pipeline comprised initial read correction with Canu and assembly with SMARTdenovo. The resulting raw nanopore-based de novo genome is structurally highly similar to that of the reference S. pennellii LA716 accession but has a high error rate and was rich in homopolymer deletions. After polishing the assembly with Illumina reads, we obtained an error rate of <0.02% when assessed versus the same Illumina data. We obtained a gene completeness of 96.53%, slightly surpassing that of the reference S. pennellii. Taken together, our data indicate that such long read sequencing data can be used to affordably sequence and assemble gigabase-sized plant genomes.
University of Freiburg1, University Medical Center Groningen2, Lund University3, University of Bonn4, Commissariat à l'énergie atomique et aux énergies alternatives5, Centre national de la recherche scientifique6, German Center for Neurodegenerative Diseases7, University Hospital Bonn8, Katholieke Universiteit Leuven9, University of Amsterdam10, University of Erlangen-Nuremberg11, Vita-Salute San Raffaele University12, Indiana University13, Braunschweig University of Technology14, Pfizer15, Ludwig Maximilian University of Munich16
TL;DR: The principal cellular and molecular players in inflammation as they pertain to AD are described, modifying factors are examined, and potential future therapeutic targets are discussed.
Abstract: Over the past few decades, research on Alzheimer's disease (AD) has focused on pathomechanisms linked to two of the major pathological hallmarks of extracellular deposition of beta-amyloid peptides and intra-neuronal formation of neurofibrils. Recently, a third disease component, the neuroinflammatory reaction mediated by cerebral innate immune cells, has entered the spotlight, prompted by findings from genetic, pre-clinical, and clinical studies. Various proteins that arise during neurodegeneration, including beta-amyloid, tau, heat shock proteins, and chromogranin, among others, act as danger-associated molecular patterns, that-upon engagement of pattern recognition receptors-induce inflammatory signaling pathways and ultimately lead to the production and release of immune mediators. These may have beneficial effects but ultimately compromise neuronal function and cause cell death. The current review, assembled by participants of the Chiclana Summer School on Neuroinflammation 2016, provides an overview of our current understanding of AD-related immune processes. We describe the principal cellular and molecular players in inflammation as they pertain to AD, examine modifying factors, and discuss potential future therapeutic targets.
TL;DR: Several HTS/HCA methods are being validated and applied for NM testing in the FP7 project NANoREG, including Label‐free cellular screening of NM uptake, HTS, HCA, High throughput flow cytometry, Impedance‐based monitoring, Multiplex analysis of secreted products, and genotoxicity methods.
Abstract: With the growing numbers of nanomaterials (NMs), there is a great demand for rapid and reliable ways of testing NM safety-preferably using in vitro approaches, to avoid the ethical dilemmas associated with animal research. Data are needed for developing intelligent testing strategies for risk assessment of NMs, based on grouping and read-across approaches. The adoption of high throughput screening (HTS) and high content analysis (HCA) for NM toxicity testing allows the testing of numerous materials at different concentrations and on different types of cells, reduces the effect of inter-experimental variation, and makes substantial savings in time and cost. HTS/HCA approaches facilitate the classification of key biological indicators of NM-cell interactions. Validation of in vitro HTS tests is required, taking account of relevance to in vivo results. HTS/HCA approaches are needed to assess dose- and time-dependent toxicity, allowing prediction of in vivo adverse effects. Several HTS/HCA methods are being validated and applied for NM testing in the FP7 project NANoREG, including Label-free cellular screening of NM uptake, HCA, High throughput flow cytometry, Impedance-based monitoring, Multiplex analysis of secreted products, and genotoxicity methods-namely High throughput comet assay, High throughput in vitro micronucleus assay, and γH2AX assay. There are several technical challenges with HTS/HCA for NM testing, as toxicity screening needs to be coupled with characterization of NMs in exposure medium prior to the test; possible interference of NMs with HTS/HCA techniques is another concern. Advantages and challenges of HTS/HCA approaches in NM safety are discussed. WIREs Nanomed Nanobiotechnol 2017, 9:e1413. doi: 10.1002/wnan.1413 For further resources related to this article, please visit the WIREs website.
TL;DR: The first Gaia Data Release contains the Tycho-Gaia Astrometric Solution (TGAS) component by means of the astrometric data for open clusters as discussed by the authors, which is a subset of about 2 million stars for which, besides the position and photometry, the proper motion and parallax are calculated using Hipparcos and Tycho 2 positions in 1991.
Abstract: Context. The first Gaia Data Release contains the Tycho-Gaia Astrometric Solution (TGAS). This is a subset of about 2 million stars for which, besides the position and photometry, the proper motion and parallax are calculated using Hipparcos and Tycho-2 positions in 1991.25 as prior information. Aims. We investigate the scientific potential and limitations of the TGAS component by means of the astrometric data for open clusters. Methods. Mean cluster parallax and proper motion values are derived taking into account the error correlations within the astrometric solutions for individual stars, an estimate of the internal velocity dispersion in the cluster, and, where relevant, the effects of the depth of the cluster along the line of sight. Internal consistency of the TGAS data is assessed. Results. Values given for standard uncertainties are still inaccurate and may lead to unrealistic unit-weight standard deviations of least squares solutions for cluster parameters. Reconstructed mean cluster parallax and proper motion values are generally in very good agreement with earlier Hipparcos-based determination, although the Gaia mean parallax for the Pleiades is a significant exception. We have no current explanation for that discrepancy. Most clusters are observed to extend to nearly 15 pc from the cluster centre, and it will be up to future Gaia releases to establish whether those potential cluster-member stars are still dynamically bound to the clusters. Conclusions. The Gaia DR1 provides the means to examine open clusters far beyond their more easily visible cores, and can provide membership assessments based on proper motions and parallaxes. A combined HR diagram shows the same features as observed before using the Hipparcos data, with clearly increased luminosities for older A and F dwarfs.
TL;DR: The net effect of migration in China has been a reduction of PM2.5 exposure, primarily because of an unequal distribution of RTC energy mixes between urban and rural areas, and people have switched to cleaner fuel types, which considerably lessened regional emissions.
Abstract: Direct residential and transportation energy consumption (RTC) contributes significantly to ambient fine particulate matter with a diameter smaller than 2.5 μm (PM2.5) in China. During massive rural-urban migration, population and pollutant emissions from RTC have evolved in terms of magnitude and geographic distribution, which was thought to worsen PM2.5 levels in cities but has not been quantitatively addressed. We quantify the temporal trends and spatial patterns of migration to cities and evaluate their associated pollutant emissions from RTC and subsequent health impact from 1980 to 2030. We show that, despite increased urban RTC emissions due to migration, the net effect of migration in China has been a reduction of PM2.5 exposure, primarily because of an unequal distribution of RTC energy mixes between urban and rural areas. After migration, people have switched to cleaner fuel types, which considerably lessened regional emissions. Consequently, the national average PM2.5 exposure concentration in 2010 was reduced by 3.9 μg/m3 (90% confidence interval, 3.0 to 5.4 μg/m3) due to migration, corresponding to an annual reduction of 36,000 (19,000 to 47,000) premature deaths. This reduction was the result of an increase in deaths by 142,000 (78,000 to 181,000) due to migrants swarming into cities and decreases in deaths by 148,000 (76,000 to 194,000) and 29,000 (15,000 to 39,000) due to transitions to a cleaner energy mix and lower urban population densities, respectively. Locally, however, megacities such as Beijing and Shanghai experienced increases in PM2.5 exposure associated with migration because these cities received massive immigration, which has driven a large increase in local emissions.
TL;DR: In this article, the influence of LED size on the radiative and non-radiative recombination was investigated, showing that coefficient A is strongly dependent on LED size, indicating a drastic effect of sidewall defects on the performance of LEDs.
Abstract: GaN-based micro light-emitting diode (μLED) arrays are very promising devices for display applications. In these arrays, each μLED works as a single pixel of a whole image. The electro-optical performance of these μLEDs is an important subject to study. Here, we investigate the influence of LED size on the radiative and non-radiative recombination. The standard ABC model has been widely used to describe the efficiency of GaN based LEDs. Using this model, we extract A, B, and C coefficients for various LED sizes, showing how the competition between radiative and non-radiative recombination processes varies with the LED geometry. Time-resolved photoluminescence allows us to determine coefficient B, related to radiative recombination. Through current-voltage-luminance characterizations, we determine parameters A and C related to Shockley-Read-Hall and Auger recombination. We find that coefficient A is strongly dependent on LED size, indicating a drastic effect of sidewall defects on the performance of LEDs. ...
TL;DR: The high-resolution structure of channelrhodopsin 2, the most widely used optogenetics tool, as well as the structure of a mutant with a longer open-state lifetime are described, providing a basis for designing better optogenetic tools.
Abstract: INTRODUCTION Ion channels are integral membrane proteins that upon stimulation modulate the flow of ions across the cell or organelle membrane. The resulting electrical signals are involved in biological functions such as electrochemical transmission and information processing in neurons. Channelrhodopsins (ChRs) appear to be unusual channels. They belong to the large family of microbial rhodopsins, seven-helical transmembrane proteins containing retinal as chromophore. Photon absorption initiates retinal isomerization resulting in a photocycle, with different spectroscopically distinguishable intermediates, thereby controlling the opening and closing of the channel. In 2003, it was demonstrated that light-induced currents by heterologously expressed ChR2 can be used to change a host’s membrane potential. The concept was further applied to precisely control muscle and neural activity by using light-induced depolarization to trigger an action potential in neurons expressing ChR2. This optogenetic approach with ChR2 and other ChRs has been widely used for remote control of neural cells in culture and in living animals with high spatiotemporal resolution. It is also used in biomedical studies aimed to cure severe diseases. RATIONALE Despite the wealth of biochemical and biophysical data, a high-resolution structure and structural mechanisms of a native ChR2 (and other ChRs) have not yet been known. A step forward was the structure of a chimera (C1C2). However, recent electrophysiological and Fourier transform infrared data showed that C1C2 exhibits light-induced responses that are functionally and mechanistically different from ChR2. Given that ChR2 is the most frequently used tool in optogenetics, a high-resolution structure of ChR2 is of high importance. Deciphering the structure of the native channel would shed light on how the light-induced changes at the retinal Schiff base (RSB) are linked to the channel operation and may make engineering of enhanced optogenetic tools more efficient. RESULTS We expressed ChR2 in LEXSY and used in the meso crystallization approach to determine the crystal structure of the wild-type ChR2 and C128T slow mutant at 2.4 and 2.7 A, respectively (C, cysteine; T, threonine). Two different dark-state conformations of ChR2 in the two protomers in the asymmetric unit were resolved. The overall structure alignment of the protomers does not show a visible difference in backbone conformation. However, the conformation of some amino acids and the position of water molecules are not the same. The dimerization is strong and provided mainly through the interaction of helices 3 and 4 and the N termini. In addition, the protomers are connected with a disulfide bond, C34/C36′. In both protomers, we identified ion conduction pathway comprising four cavities [extracellular cavity 1 (EC1), EC2, intracellular cavity 1 (IC1), and IC2] that are separated by three gates [extracellular gate (ECG), central gate (CG), and intracellular gate (ICG)] (figure, panel A). Arginines R120 and R268 are the cores of ECG and ICG, respectively, in all ChRs. The Schiff base is hydrogen-bond–connected to E123 and D253 amino acids (E, glutamic acid; D, aspartic acid) and is a key part of the CG that is further connected with two other gates through an extended H-bond network mediated by numerous water molecules (figure, panel B). The DC gate is separate from the gates in the channel pathway and is bridged by hydrogen bonds through the water molecule w5. Hydrogen bonding of the DC pair (C128 and D156) has two important consequences. It stabilizes helices 3 and 4 and provides connection from D156, a possible proton donor, to the RSB. The presence of the hydrogen bonds provides structural insights into how the DC gate controls ChR2 gating lifetime. CONCLUSION The determined structures of ChR2 and its C128T mutant present the molecular basis for the understanding of ChR functioning. They provide insights into mechanisms of channel opening and closing. A plausible scenario is that the disruption of the H-bonds between E123 and D253 and the Schiff base and the protonation of D253 upon retinal isomerization trigger rearrangements in the extended hydrogen-bonded networks, stabilizing the ECG and CG and also rearranging the H-bonding network in the cavities. Upon retinal isomerization, these two gates are opened and the network is broken. This leads to the reorientation of helix 2. Additional changes in helices 6 and 7 induced by the isomerization could help with opening the ICG and channel pore formation.
TL;DR: The discovery of FeH5 suggests a low-pressure path to make materials that approach bulk dense atomic hydrogen, and provides an opportunity to investigate special electrical properties expected from atomic hydrogen bonding, such as superconductivity.
Abstract: High pressure promotes the formation of polyhydrides with unusually high hydrogen-to-metal ratios. These polyhydrides have complex hydrogenic sublattices. We synthesized iron pentahydride (FeH5) by a direct reaction between iron and H2 above 130 gigapascals in a laser-heated diamond anvil cell. FeH5 exhibits a structure built of atomic hydrogen only. It consists of intercalated layers of quasicubic FeH3 units and four-plane slabs of thin atomic hydrogen. The distribution of the valence electron density indicates a bonding between hydrogen and iron atoms but none between hydrogen atoms, presenting a two-dimensional metallic character. The discovery of FeH5 suggests a low-pressure path to make materials that approach bulk dense atomic hydrogen.
TL;DR: The analyses show that the Oxford Nanopore technology is already usable for de novo sequencing and assembly; however, non-random errors in homopolymers require polishing the consensus using an alternate sequencing technology.
Abstract: Background Oxford Nanopore Technologies Ltd (Oxford, UK) have recently commercialized MinION, a small single-molecule nanopore sequencer, that offers the possibility of sequencing long DNA fragments from small genomes in a matter of seconds. The Oxford Nanopore technology is truly disruptive; it has the potential to revolutionize genomic applications due to its portability, low cost, and ease of use compared with existing long reads sequencing technologies. The MinION sequencer enables the rapid sequencing of small eukaryotic genomes, such as the yeast genome. Combined with existing assembler algorithms, near complete genome assemblies can be generated and comprehensive population genomic analyses can be performed. Results Here, we resequenced the genome of the Saccharomyces cerevisiae S288C strain to evaluate the performance of nanopore-only assemblers. Then we de novo sequenced and assembled the genomes of 21 isolates representative of the S. cerevisiae genetic diversity using the MinION platform. The contiguity of our assemblies was 14 times higher than the Illumina-only assemblies and we obtained one or two long contigs for 65 % of the chromosomes. This high contiguity allowed us to accurately detect large structural variations across the 21 studied genomes. Conclusion Because of the high completeness of the nanopore assemblies, we were able to produce a complete cartography of transposable elements insertions and inspect structural variants that are generally missed using a short-read sequencing strategy. Our analyses show that the Oxford Nanopore technology is already usable for de novo sequencing and assembly; however, non-random errors in homopolymers require polishing the consensus using an alternate sequencing technology.
TL;DR: The parkinsonism-associated protein DJ-1 and its prokaryotic homologs constitute a major nucleotide repair system that is named guanine glycation repair, and is associated with increased mutation frequency, DNA strand breaks, and cytotoxicity.
Abstract: DNA damage induced by reactive carbonyls (mainly methylglyoxal and glyoxal), called DNA glycation, is quantitatively as important as oxidative damage. DNA glycation is associated with increased mutation frequency, DNA strand breaks, and cytotoxicity. However, in contrast to guanine oxidation repair, how glycated DNA is repaired remains undetermined. Here, we found that the parkinsonism-associated protein DJ-1 and its bacterial homologs Hsp31, YhbO, and YajL could repair methylglyoxal- and glyoxal-glycated nucleotides and nucleic acids. DJ-1–depleted cells displayed increased levels of glycated DNA, DNA strand breaks, and phosphorylated p53. Deglycase-deficient bacterial mutants displayed increased levels of glycated DNA and RNA and exhibited strong mutator phenotypes. Thus, DJ-1 and its prokaryotic homologs constitute a major nucleotide repair system that we name guanine glycation repair.
Cybercast News Service1, Commissariat à l'énergie atomique et aux énergies alternatives2, Spanish National Research Council3, École Normale Supérieure4, European Bioinformatics Institute5, Technical University of Madrid6, Centre national de la recherche scientifique7, University of Paris8, University of the South, Toulon-Var9, Bigelow Laboratory For Ocean Sciences10, University of Arizona11, University of Évry Val d'Essonne12, University of Chile13, Wellcome Trust14, Kyoto University15, University of Michigan16, Massachusetts Institute of Technology17, Stazione Zoologica Anton Dohrn18, University of Maine19, French Alternative Energies and Atomic Energy Commission20
TL;DR: Detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, are provided and registries of genomics datasets available at the European Nucleotide Archive are described.
Abstract: A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009-2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world's planktonic ecosystems.
TL;DR: The algorithm removes calorimeter energy deposits due to charged hadrons from consideration during jet reconstruction, instead using measurements of their momenta from the inner tracker, which improves the accuracy of the charged-hadron measurement, while retaining the calorimeters' measurements of neutral-particle energies.
Abstract: This paper describes the implementation and performance of a particle flow algorithm applied to 20.2 fb(-1) of ATLAS data from 8 TeV proton-proton collisions in Run 1 of the LHC. The algorithm remo ...
TL;DR: In this article, the authors present the potential sensitivity of a future recoil detector for the first detection of coherent elastic neutrino nucleus scattering (CEνNS) using the Chooz reactor complex in France as a luminous source of reactor neutrinos.
Abstract: We present the potential sensitivity of a future recoil detector for a first detection of the process of coherent elastic neutrino nucleus scattering (CEνNS). We use the Chooz reactor complex in France as our luminous source of reactor neutrinos. Leveraging the ability to cleanly separate the rate correlated with the reactor thermal power against (uncorrelated) backgrounds, we show that a 10 kg cryogenic bolometric array with 100 eV threshold should be able to extract a CEνNS signal within one year of running.
TL;DR: Activation of macaque retinas, up to 6 months post-injection, using channelrhodopsin-Ca2+-permeable channelr Rhodopsin (CatCh) at safe light intensities is reported, suggesting that the inclusion of optimized promoters is key in the path to clinical translation of optogenetics.
Goddard Space Flight Center1, University of Exeter2, Jet Propulsion Laboratory3, University of Maryland, College Park4, University of Edinburgh5, Commissariat à l'énergie atomique et aux énergies alternatives6, Columbia University7, Goddard Institute for Space Studies8, Space Telescope Science Institute9, University of California, Santa Cruz10, California Institute of Technology11
TL;DR: In this paper, the authors conducted a detailed atmospheric study of the transiting Neptune-mass exoplanet HAT-P-26b and detected prominent H2O absorption bands with a maximum base-to-peak amplitude of 525ppm in the transmission spectrum.
Abstract: A correlation between giant-planet mass and atmospheric heavy elemental abundance was first noted in the past century from observations of planets in our own Solar System, and has served as a cornerstone of planet formation theory. Using data from the Hubble and Spitzer Space Telescopes from 0.5 to 5 microns, we conducted a detailed atmospheric study of the transiting Neptune-mass exoplanet HAT-P-26b. We detected prominent H2O absorption bands with a maximum base-to-peak amplitude of 525ppm in the transmission spectrum. Using the water abundance as a proxy for metallicity, we measured HAT-P-26b's atmospheric heavy element content [4.8 (-4.0 +21.5) times solar]. This likely indicates that HAT-P-26b's atmosphere is primordial and obtained its gaseous envelope late in its disk lifetime, with little contamination from metal-rich planetesimals.
TL;DR: The first measurement of transverse-spin-dependent azimuthal asymmetries in the pion-induced Drell-Yan (DY) process is reported and the observed sign of the Sivers asymmetry is found to be consistent with the fundamental prediction of quantum chromodynamics (QCD) that the Siver TMD PDFs extracted from DY have a sign opposite to the one extracted from semi-inclusive deep-inelastic scattering (SIDIS) data.
Abstract: The first measurement of transverse-spin-dependent azimuthal asymmetries in the pion-induced Drell-Yan (DY) process is reported. We use the CERN SPS 190 GeV/c pi(-) beam and a transversely polarize ...
TL;DR: Results of a search for physics beyond the Standard Model in events containing an energetic photon and large missing transverse momentum with the ATLAS detector at the Large Hadron Collider are reported, with model-independent limits set on the fiducial cross section.
Abstract: Results of a search for physics beyond the Standard Model in events containing an energetic photon and large missing transverse momentum with the ATLAS detector at the Large Hadron Collider are rep ...
TL;DR: An ionic liquid/water electrolyte promotes excellent selectivity for CO2 electroreduction to formic acid at a porous dendritic copper electrode material.
Abstract: Copper is currently extensively studied because it provides promising electrodes for carbon dioxide electroreduction. The original combination, reported here, of a nanostructured porous dendritic Cu-based material, characterized by electron microcopy (SEM, TEM) and X-ray diffraction methods, and a water/ionic liquid mixture as the solvent, contributing to CO2 solubilization and activation, results in a remarkably efficient (large current densities at low overpotentials), stable and selective (large faradic yields) electrocatalytic system for the conversion of CO2 into formic acid, a product with a variety of uses. These results provide new directions for the further improvement of Cu electrodes.