World-leading science with SPIRou - the nIR spectropolarimeter / high-precision velocimeter for CFHT

SPIRou is a near-infrared (nIR) spectropolarimeter / velocimeter proposed as a new-generation instrument for CFHT. SPIRou aims in particular at becoming world-leader on two forefront science topics, (i) the quest for habitable Earth-like planets around very- low-mass stars, and (ii) the study of low-mass star and planet formation in the presence of magnetic fields. In addition to these two main goals, SPIRou will be able to tackle many key programs, from weather patterns on brown dwarf to solar-system planet atmospheres, to dynamo processes in fully-convective bodies and planet habitability. The science programs that SPIRou proposes to tackle are forefront (identified as first priorities by most research agencies worldwide), ambitious (competitive and complementary with science programs carried out on much larger facilities, such as ALMA and JWST) and timely (ideally phased with complementary space missions like TESS and CHEOPS). SPIRou is designed to carry out its science mission with maximum efficiency and optimum precision. More specifically, SPIRou will be able to cover a very wide single-shot nIR spectral domain (0.98-2.35 \mu m) at a resolving power of 73.5K, providing unpolarized and polarized spectra of low-mass stars with a ~15% average throughput and a radial velocity (RV) precision of 1 m/s.Comment: 12 pages, 5 figures, conference proceedings of the French Society of Astronomy and Astrophysics meeting 201

A Constrained Fuzzy Knowledge-Based System for the Management of Container Yard Operations

The management of container yard operations is considered by yard operators to be a very challenging task due to the many uncertainties inherent in such operations. The storage of the containers is one of those operations that require proper management for the efficient utilisation of the yard, requiring rapid retrieval time and a minimum number of re-handlings. The main challenge is when containers of a different size, type, or weight need to be stored in a yard that holds a number of pre-existing containers. This challenge becomes even more complex when the date and time for the departure of the containers are unknown, as is the case when the container is collected by a third-party logistics company without any prior notice being given. The aim of this study is to develop a new system for the management of container yard operations that takes into consideration a number of factors and constraints that occur in a real-life situation. One of these factors is the duration of stay for the topmost containers of each stack, when the containers are stored. Because the duration of stay for containers in a yard varies dynamically over time, an ‘ON/OFF’ strategy is proposed to activate/deactivate the duration of stay factor constraint if the length of stay for these containers varies significantly over time. A number of tools and techniques are utilised for developing the proposed system including: discrete event simulation for the modelling of container storage and retrieval operations, a fuzzy know ledge-based model for the stack allocation of containers, and a heuristic algorithm called ‘neighbourhood’ for the container retrieval operation. Results show that by adopting the proposed ‘ON/OFF’ strategy, 5% of the number of re-handlings, 2.5% of the total retrieval time, 6.6% of the total re-handling time and 42% of the average waiting time per truck are reduced

Investigations into, and development of, a lyophilized and formulated recombinant human factor IX produced from CHO cells

Objectives: To develop a recombinant human factor IX (rFIX) formulation equivalent to commercially available products in terms of cake appearance, residual moisture, proportion of soluble aggregates and activity maintenance for 3 months at 4–8 °C. Results: NaCl and low bulking agent/cryoprotectant mass ratio had a negative impact on cake quality upon lyophilisation for a wide range of formulations tested. Particular devised formulations maintained rFIX activity after lyophilization with a similar performance when compared with the rFIX formulated using the excipients reported for a commercially available FIX formulation (Benefix). rFIX remained active after 3 months when stored at 4 °C, though this was not the case with samples stored at 40 °C. Interestingly, particular formulations had an increase in residual moisture after 3 months storage, but not above a 3% threshold. All four formulations tested were equivalent to the Benefix formulation in terms of particle size distribution and cake appearance. Conclusions: Three specific formulations, consisting of surfactant polysorbate-80, sucrose or trehalose as cryoprotectant, mannitol or glycine as bulking agent, l-histidine as buffering agent, and NaCl added in the reconstitution liquid at 0.234% (w/v) were suitable for use with a CHO cell-derived recombinant FIX

DNA methylation patterns of Brachypodium distachyon chromosomes and their alteration by 5-azacytidine treatment

Sequential immunolocalisation of 5-methylcytosine (5-MeC) and fluorescence in situ hybridisation with chromosome-specific BAC clones were performed on Brachypodium distachyon mitotic metaphase chromosomes to determine specific DNA methylation patterns of each chromosome in the complement. In the majority of cells examined, chromosomes Bd4 and Bd5, which bear the loci of 5S and 35S ribosomal DNA, respectively, had characteristic 5-MeC patterns. In contrast, the distribution of 5-MeC along the metacentric chromosome pairs Bd1, Bd2 and Bd3 was more variable. There were numerous differences in distribution of methylated sites between homologous chromosomes as well as between chromosome arms. Some chromosome sites, such as pericentromeric regions, were highly methylated in all chromosomes. Additionally, the influence of a hypomethylating agent, 5-azacytidine, on B. distachyon chromosome methylation patterns was confirmed. It was found that some chromosome pairs underwent demethylation more easily than others, but there was no apparent regularity in demethylation of particular chromosome segments

The Brazilian Program for Biodiversity Research (PPBio) Information System.

The database of the Brazilian Program for Biodiversity Research (PPBio; GIVD ID SA-BR-001) includes data on the environment and biological groups such as plants. It is organized by site, which is usually a grid with 10 to 72 uniformly-distributed plots, and has already surveyed 1,638 relevés across different Brazilian ecosystems. The sampling design is based on the RAPELD system to allow integration of data from diverse taxa and ecosystem processes. RAPELD is a spatially-explicit sampling scheme to monitor biodiversity in long-term ecological research sites and during rapid appraisals of biodiversity that has attracted support from many management agencies, which are using it as their long-term monitoring system. Vegetation surveys include measurements of cover, biomass and number of individuals from woody and herbaceous vascular plants, along with environmental data. We have recently migrated to a metadata catalog and data repository which allows searching for specific groups across all sites. All RAPELD data have been collected since 2001, though the site also allows data from other long-term plots to be archived as associated projects

The Brazilian Program for Biodiversity Research (PPBio) Information System.

The database of the Brazilian Program for Biodiversity Research (PPBio; GIVD ID SA-BR-001) includes data on the environment and biological groups such as plants. It is organized by site, which is usually a grid with 10 to 72 uniformly-distributed plots, and has already surveyed 1,638 relevés across different Brazilian ecosystems. The sampling design is based on the RAPELD system to allow integration of data from diverse taxa and ecosystem processes. RAPELD is a spatially-explicit sampling scheme to monitor biodiversity in long-term ecological research sites and during rapid appraisals of biodiversity that has attracted support from many management agencies, which are using it as their long-term monitoring system. Vegetation surveys include measurements of cover, biomass and number of individuals from woody and herbaceous vascular plants, along with environmental data. We have recently migrated to a metadata catalog and data repository which allows searching for specific groups across all sites. All RAPELD data have been collected since 2001, though the site also allows data from other long-term plots to be archived as associated projects

Hyphal Development in Candida albicans Requires Two Temporally Linked Changes in Promoter Chromatin for Initiation and Maintenance

Phenotypic plasticity is common in development. For Candida albicans, the most common cause of invasive fungal infections in humans, morphological plasticity is its defining feature and is critical for its pathogenesis. Unlike other fungal pathogens that exist primarily in either yeast or hyphal forms, C. albicans is able to switch reversibly between yeast and hyphal growth forms in response to environmental cues. Although many regulators have been found involved in hyphal development, the mechanisms of regulating hyphal development and plasticity of dimorphism remain unclear. Here we show that hyphal development involves two sequential regulations of the promoter chromatin of hypha-specific genes. Initiation requires a rapid but temporary disappearance of the Nrg1 transcriptional repressor of hyphal morphogenesis via activation of the cAMP-PKA pathway. Maintenance requires promoter recruitment of Hda1 histone deacetylase under reduced Tor1 (target of rapamycin) signaling. Hda1 deacetylates a subunit of the NuA4 histone acetyltransferase module, leading to eviction of the NuA4 acetyltransferase module and blockage of Nrg1 access to promoters of hypha-specific genes. Promoter recruitment of Hda1 for hyphal maintenance happens only during the period when Nrg1 is gone. The sequential regulation of hyphal development by the activation of the cAMP-PKA pathway and reduced Tor1 signaling provides a molecular mechanism for plasticity of dimorphism and how C. albicans adapts to the varied host environments in pathogenesis. Such temporally linked regulation of promoter chromatin by different signaling pathways provides a unique mechanism for integrating multiple signals during development and cell fate specification

mTOR: from growth signal integration to cancer, diabetes and ageing

In all eukaryotes, the target of rapamycin (TOR) signalling pathway couples energy and nutrient abundance to the execution of cell growth and division, owing to the ability of TOR protein kinase to simultaneously sense energy, nutrients and stress and, in metazoans, growth factors. Mammalian TOR complex 1 (mTORC1) and mTORC2 exert their actions by regulating other important kinases, such as S6 kinase (S6K) and Akt. In the past few years, a significant advance in our understanding of the regulation and functions of mTOR has revealed the crucial involvement of this signalling pathway in the onset and progression of diabetes, cancer and ageing.National Institutes of Health (U.S.)Howard Hughes Medical InstituteWhitehead Institute for Biomedical ResearchJane Coffin Childs Memorial Fund for Medical Research (Postdoctoral Fellowship)Human Frontier Science Program (Strasbourg, France

Long-term decline of the Amazon carbon sink

Atmospheric carbon dioxide records indicate that the land surface has acted as a strong global carbon sink over recent decades1, 2, with a substantial fraction of this sink probably located in the tropics3, particularly in the Amazon4. Nevertheless, it is unclear how the terrestrial carbon sink will evolve as climate and atmospheric composition continue to change. Here we analyse the historical evolution of the biomass dynamics of the Amazon rainforest over three decades using a distributed network of 321 plots. While this analysis confirms that Amazon forests have acted as a long-term net biomass sink, we find a long-term decreasing trend of carbon accumulation. Rates of net increase in above-ground biomass declined by one-third during the past decade compared to the 1990s. This is a consequence of growth rate increases levelling off recently, while biomass mortality persistently increased throughout, leading to a shortening of carbon residence times. Potential drivers for the mortality increase include greater climate variability, and feedbacks of faster growth on mortality, resulting in shortened tree longevity5. The observed decline of the Amazon sink diverges markedly from the recent increase in terrestrial carbon uptake at the global scale1, 2, and is contrary to expectations based on models6