The Abisko Polar Prediction School

Polar regions are experiencing rapid climate change, faster than elsewhere on Earth with consequences for the weather and sea ice. This change is opening up new possibilities for businesses such as tourism, shipping, fisheries and oil and gas extraction, but also bringing new risks to delicate polar environments. Effective weather and climate prediction is essential to managing these risks, however our ability to forecast polar environmental conditions over periods from days to decades ahead falls far behind our abilities in the mid-latitudes. In order to meet the growing societal need for young scientists trained in this area, a Polar Prediction School for early career scientists from around the world was held in April 2016

A root phloem pole cell atlas reveals common transcriptional states in protophloem-adjacent cells

The phloem pole atlas has over 10,000 cells, with an unprecedented resolution of the transcriptional dynamics in phloem development. Despite distinct mature transcriptional states, co-expression networks show common states in protophloem-adjacent cells. Single-cell sequencing has recently allowed the generation of exhaustive root cell atlases. However, some cell types are elusive and remain underrepresented. Here we use a second-generation single-cell approach, where we zoom in on the root transcriptome sorting with specific markers to profile the phloem poles at an unprecedented resolution. Our data highlight the similarities among the developmental trajectories and gene regulatory networks common to protophloem sieve element (PSE)-adjacent lineages in relation to PSE enucleation, a key event in phloem biology. As a signature for early PSE-adjacent lineages, we have identified a set of DNA-binding with one finger (DOF) transcription factors, the PINEAPPLEs (PAPL), that act downstream of PHLOEM EARLY DOF (PEAR) genes and are important to guarantee a proper root nutrition in the transition to autotrophy. Our data provide a holistic view of the phloem poles that act as a functional unit in root development.Peer reviewe

Origin of chirality in transition-metal dichalcogenides

Chirality is a ubiquitous phenomenon in which a symmetry between left- and right-handed objects is broken, examples in nature ranging from subatomic particles and molecules to living organisms. In particle physics, the weak force is responsible for the symmetry breaking and parity violation in beta decay, but in condensed matter systems interactions that lead to chirality remain poorly understood. Here, we unravel the mechanism of chiral charge density wave formation in the transition-metal dichalcogenide 1T-TiSe2. Using representation analysis, we show that charge density modulations and ionic displacements, which transform as a continuous scalar field and a vector field on a discrete lattice, respectively, follow different irreducible representations of the space group, despite the fact that they propagate with the same wave-vectors and are strongly coupled to each other. This charge-lattice symmetry frustration is resolved by further breaking of all symmetries not common to both sectors through induced lattice distortions, thus leading to chirality. Our theory is verified using Raman spectroscopy and inelastic x-ray scattering, which reveal that all but translation symmetries are broken at a level not resolved by state-of-the-art diffraction techniques.Comment: 10 pages, 3 figures, 1 tabl

Fast dating using least-squares criteria and algorithms

International audiencePhylogenies provide a useful way to understand the evolutionary history of genetic samples, and data sets with more than a thousand taxa are becoming increasingly common, notably with viruses (e.g., human immunodeficiency virus (HIV)). Dating ancestral events is one of the first, essential goals with such data. However, current sophisticated probabilistic approaches struggle to handle data sets of this size. Here, we present very fast dating algorithms, based on a Gaussian model closely related to the Langley–Fitch molecular-clock model. We show that this model is robust to uncorrelated violations of the molecular clock. Our algorithms apply to serial data, where the tips of the tree have been sampled through times. They estimate the substitution rate and the dates of all ancestral nodes. When the input tree is unrooted, they can provide an estimate for the root position, thus representing a new, practical alternative to the standard rooting methods (e.g., midpoint). Our algorithms exploit the tree (recursive) structure of the problem at hand, and the close relationships between least-squares and linear algebra. We distinguish between an unconstrained setting and the case where the temporal precedence constraint (i.e., an ancestral node must be older that its daughter nodes) is accounted for. With rooted trees, the former is solved using linear algebra in linear computing time (i.e., proportional to the number of taxa), while the resolution of the latter, constrained setting, is based on an active-set method that runs in nearly linear time. With unrooted trees the computing time becomes (nearly) quadratic (i.e., proportional to the square of the number of taxa). In all cases, very large input trees (>10,000 taxa) can easily be processed and transformed into time-scaled trees. We compare these algorithms to standard methods (root-to-tip, r8s version of Langley–Fitch method, and BEAST). Using simulated data, we show that their estimation accuracy is similar to that of the most sophisticated methods, while their computing time is much faster. We apply these algorithms on a large data set comprising 1194 strains of Influenza virus from the pdm09 H1N1 Human pandemic. Again the results show that these algorithms provide a very fast alternative with results similar to those of other computer programs. These algorithms are implemented in the LSD software (least-squares dating), which can be downloaded from http://www.atgc-montpellier.fr/LSD/, along with all our data sets and detailed results. An Online Appendix, providing additional algorithm descriptions, tables, and figures can be found in the Supplementary Material available on Dryad at http://dx.doi.org/10.5061/dryad.968t3

Advancing polar prediction capabilities on daily to seasonal time scales

It is argued that existing polar prediction systems do not yet meet users’ needs; and possible ways forward in advancing prediction capacity in polar regions and beyond are outlined. The polar regions have been attracting more and more attention in recent years, fuelled by the perceptible impacts of anthropogenic climate change. Polar climate change provides new opportunities, such as shorter shipping routes between Europe and East Asia, but also new risks such as the potential for industrial accidents or emergencies in ice-covered seas. Here, it is argued that environmental prediction systems for the polar regions are less developed than elsewhere. There are many reasons for this situation, including the polar regions being (historically) lower priority, with less in situ observations, and with numerous local physical processes that are less well-represented by models. By contrasting the relative importance of different physical processes in polar and lower latitudes, the need for a dedicated polar prediction effort is illustrated. Research priorities are identified that will help to advance environmental polar prediction capabilities. Examples include an improvement of the polar observing system; the use of coupled atmosphere-sea ice-ocean models, even for short-term prediction; and insight into polar-lower latitude linkages and their role for forecasting. Given the enormity of some of the challenges ahead, in a harsh and remote environment such as the polar regions, it is argued that rapid progress will only be possible with a coordinated international effort. More specifically, it is proposed to hold a Year of Polar Prediction (YOPP) from mid-2017 to mid-2019 in which the international research and operational forecasting community will work together with stakeholders in a period of intensive observing, modelling, prediction, verification, user-engagement and educational activities

Globalisation and the spatial concentration of production

Abstract In new trade theory (NTT) models, freer trade tends to increase the spatial concentration of industrial production across countries. While nations with large home markets and central geographical location become increasingly attractive business locations, small peripheral countries gradually deindustrialise. Using data for 26 industries, 20 OECD countries and 20 years, we investigate the empirical validity of this claim. Separating out the role of home market size from geographical factors, and using various panel methods, we find robust evidence in line with theory. Freer trade has indeed magnified the importance of domestic demand and geographical location for the pattern of industrial production across the globe and has therefore exacerbated spatial disparities. Keywords: Home market effect, hub effect, trade liberalisation, trade costs, increasing returns to scale, new trade theory, economic geography. JEL-Codes: F12, F15 * We are grateful to an anonymous referee for helpful suggestions and comments. Parts of this paper were drafted when Niepmann was an intern at the World Bank. We are grateful to Mary Amiti, Michael Boehm, Giancarlo Corsetti, Matthieu Crozet, Benjamin Jung, Wilhelm Kohler, Andreas Kopp, and Davide Sala, as well as to seminar participants at EUI Florence and at the RIEF Meeting 2009 in Aix en Provence for comments and discussion. All remaining errors are ours

Myelinated, synapsing cultures of murine spinal cord – validation as an in vitro model of the central nervous system

Research in central nervous system (CNS) biology and pathology requires in vitro models, which, to recapitulate the CNS in vivo, must have extensive myelin and synapse formation under serum-free (defined) conditions. However, finding such a model has proven difficult. The technique described here produces dense cultures of myelinated axons, with abundant synapses and nodes of Ranvier, that are suitable for both morphological and biochemical analysis. Cellular and molecular events were easily visualised using conventional microscopy. Ultrastructurally, myelin sheaths were of the appropriate thickness relative to axonal diameter (G-ratio). Production of myelinated axons in these cultures was consistent and repeatable, as shown by statistical analysis of multiple experimental repeats. Myelinated axons were so abundant that from one litter of embryonic mice, myelin was produced in amounts sufficient for bulk biochemical analysis. This culture method was assessed for its ability to generate an in vitro model of the CNS that could be used for both neurobiological and neuropathological research. Myelin protein kinetics were investigated using a myelin fraction isolated from the cultures. This fraction was found to be superior, quantitatively and qualitatively, to the fraction recovered from standard cultures of dissociated oligodendrocytes, or from brain slices. The model was also used to investigate the roles of specific molecules in the pathogenesis of inflammatory CNS diseases. Using the defined conditions offered by this culture system, dose-specific, inhibitory effects of inflammatory cytokines on myelin formation were demonstrated, unequivocally. The method is technically quick, easy and reliable, and should have wide application to CNS research

Optical properties of ZnO deposited by atomic layer deposition (ALD) on Si nanowires

International audienceIn this work, we report proof-of-concept results on the synthesis of Si core/ ZnO shell nanowires (SiNWs/ZnO) by combining nanosphere lithography (NSL), metal assisted chemical etching (MACE) and atomic layer deposition (ALD). The structural properties of the SiNWs/ZnO nanostructures prepared were investigated by X-ray diffraction, Raman spectroscopy, scanning and transmission electron microscopies. The X-ray diffraction analysis revealed that all samples have a hexagonal wurtzite structure. The grain sizes are found to be in the range of 7-14 nm. The optical properties of the samples were investigated using reflectance and photoluminescence spectroscopy. The study of photoluminescence (PL) spectra of SiNWs/ZnO samples showed the domination of defect emission bands, pointing to deviations of the stoichiometry of the prepared 3D ZnO nanostructures. Reduction of the PL intensity of the SiNWs/ZnO with the increase of SiNWs etching time was observed, depicting an advanced light scattering with the increase of the nanowire length. These results open up new prospects for the design of electronic and sensing devices

A phosphatase cascade by which rewarding stimuli control nucleosomal response

ArticleInternational audienceDopamine orchestrates motor behaviour and reward-driven learning. Perturbations of dopamine signalling have been implicated in several neurological and psychiatric disorders, and in drug addiction. The actions of dopamine are mediated in part by the regulation of gene expression in the striatum, through mechanisms that are not fully understood. Here we show that drugs of abuse, as well as food reinforcement learning, promote the nuclear accumulation of 32-kDa dopamine-regulated and cyclic-AMP-regulated phosphoprotein (DARPP-32). This accumulation is mediated through a signalling cascade involving dopamine D1 receptors, cAMP-dependent activation of protein phosphatase-2A, dephosphorylation of DARPP-32 at Ser 97 and inhibition of its nuclear export. The nuclear accumulation of DARPP-32, a potent inhibitor of protein phosphatase-1, increases the phosphorylation of histone H3, an important component of nucleosomal response. Mutation of Ser 97 profoundly alters behavioural effects of drugs of abuse and decreases motivation for food, underlining the functional importance of this signalling cascad

A Large Maize (Zea mays L.) SNP Genotyping Array: Development and Germplasm Genotyping, and Genetic Mapping to Compare with the B73 Reference Genome

SNP genotyping arrays have been useful for many applications that require a large number of molecular markers such as high-density genetic mapping, genome-wide association studies (GWAS), and genomic selection. We report the establishment of a large maize SNP array and its use for diversity analysis and high density linkage mapping. The markers, taken from more than 800,000 SNPs, were selected to be preferentially located in genes and evenly distributed across the genome. The array was tested with a set of maize germplasm including North American and European inbred lines, parent/F1 combinations, and distantly related teosinte material. A total of 49,585 markers, including 33,417 within 17,520 different genes and 16,168 outside genes, were of good quality for genotyping, with an average failure rate of 4% and rates up to 8% in specific germplasm. To demonstrate this array's use in genetic mapping and for the independent validation of the B73 sequence assembly, two intermated maize recombinant inbred line populations – IBM (B73×Mo17) and LHRF (F2×F252) – were genotyped to establish two high density linkage maps with 20,913 and 14,524 markers respectively. 172 mapped markers were absent in the current B73 assembly and their placement can be used for future improvements of the B73 reference sequence. Colinearity of the genetic and physical maps was mostly conserved with some exceptions that suggest errors in the B73 assembly. Five major regions containing non-colinearities were identified on chromosomes 2, 3, 6, 7 and 9, and are supported by both independent genetic maps. Four additional non-colinear regions were found on the LHRF map only; they may be due to a lower density of IBM markers in those regions or to true structural rearrangements between lines. Given the array's high quality, it will be a valuable resource for maize genetics and many aspects of maize breeding