Éditeur(s) : HAL CCSD Landes Bioscience
Résumé : International audience
In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
Autophagy

hal-00735751
https://hal.archives-ouvertes.fr/hal-00735751
PUBMED : 22966490

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : While Amazonian forests are extraordinarily diverse, the abundance of trees is skewed strongly towards relatively few 'hyperdominant' species. In addition to their diversity, Amazonian trees are a key component of the global carbon cycle, assimilating and storing more carbon than any other ecosystem on Earth. Here we ask, using a unique data set of 530 forest plots, if the functions of storing and producing woody carbon are concentrated in a small number of tree species, whether the most abundant species also dominate carbon cycling, and whether dominant species are characterized by specific functional traits. We find that dominance of forest function is even more concentrated in a few species than is dominance of tree abundance, with only ≈1% of Amazon tree species responsible for 50% of carbon storage and productivity. Although those species that contribute most to biomass and productivity are often abundant, species maximum size is also influential, while the identity and ranking of dominant species varies by function and by region.
ISSN: 2041-1723

hal-01204225
https://hal.archives-ouvertes.fr/hal-01204225
DOI : 10.1038/ncomms7857
PRODINRA : 305614
PUBMED : 25919449

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
This work shows the preparation and separation performance assessment of carbon membranes derived from phenolic resin by a vacuum-assisted method and carbonisation in an inert atmosphere. The vacuum time played an important role in tailoring the structure of the membranes. For instance, pore volumes and surface areas increased from 0.81 and 834 to 2.2 cm3g−1and 1910 m2g−1, respectively, as the vacuum time exposure increased from 0 to 1200 s. The significant structural changes correlated very well with water permeation, as fluxes increased by 91% as the vacuum time increased from 0 to 1200 s reaching up to 169 L m−2h−1at 5 bar. Molecular weight cut-off tests showed no rejection for the smaller glucose and sucrose molecules, though this increased to ~ 80% and full rejection for 36 kDa and 400 kDa polyvinyl pyrrolidine. Interestingly, FTIR spectra showed that the peaks of C–H stretching vibration (2800–3200 cm−1) and C–O stretching (1030 cm−1) became more pronounced as a function of increasing vacuum time, strongly suggesting that the use of vacuum further assisted in the polycondensation of phenolic oligomers. Based on these outcomes, a cluster to cluster model is proposed, whereby vacuum application promoted crosslinking reactions of the phenolic resin, creating microporous regions within the clusters, and mesoporous regions between the clusters. © 2016 Elsevier B.V
ISSN: 0376-7388

hal-01683220
https://hal.univ-antilles.fr/hal-01683220
DOI : 10.1016/j.memsci.2016.11.002

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Carbonised template silica membranes were synthesised and investigated for water desalination for brackish (0.3wt%), sea water (3.5wt%) and brine (7.5wt%) NaCl solutions at temperatures range from 22 to 60°C. The membranes were prepared by a two-step base catalysed sol-gel method using tetraethyl orthosilicate TEOS as the silica precursor and triblock copolymer of Pluronic® P123 as the templating agent. The P123 silica membranes calcined under vacuum only produced high quality membranes by the interlayer-free method. The membranes were stable during testing of up to 250h under different thermal and salt concentration solutions, always delivering very high salt rejections >99.5%. It was found that by increasing the template concentration in the silica matrix from 5 to 50wt%, salt concentration polarisation was greatly reduced. As such, high water fluxes were measured up to 8.5kgm-2h-1 for brackish water and 6.6kgm-2h-1 for brine water. © 2014 Elsevier B.V.
ISSN: 0376-7388

hal-01683210
https://hal.univ-antilles.fr/hal-01683210
DOI : 10.1016/j.memsci.2014.10.026

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Mesoporous cobalt oxide silica matrices and membranes were successfully prepared using a dual acid-base catalysed sol-gel and interlayer-free approach for desalination applications. The effects of cobalt addition (0-35 mol%) on the structure-property relationship of the silica materials and membrane performance were systematically studied as a function of feed salt concentration (0.3-7.5 wt.% NaCl) and temperature (22-60 °C). As cobalt concentration increases beyond 5 mol%, the concentration of tricobalt tetroxide and proportion of silica mesopores were found to increase within the matrices. Silica membranes with high amount of tricobalt tetroxide (35 mol%) were found to be highly mesoporous with water fluxes of 20, 11.3 and 7.7 kg m-2 h-1 for the 0.3, 3.5 and 7.5 wt.% solutions at 60 °C, respectively, with >99.7% salt rejection at all times. This is attributed to the high pore volume (mesopores formation) and structural robustness of the silica network provided by the presence of tricobalt tetroxide. Even higher performance was achieved for low tricobalt tetroxide (mol%) silica membranes with water fluxes of 47.6 (0.3 wt.%) and 31.5 (3.5 wt.%) kg m-2 h-1 at 60 °C, respectively, though with reduced salt rejections of 90%. © 2015 Elsevier B.V.
ISSN: 0011-9164

hal-01683209
https://hal.univ-antilles.fr/hal-01683209
DOI : 10.1016/j.desal.2015.02.034

Éditeur(s) : HAL CCSD Oxford University Press
Résumé : International audience
The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations.
ISSN: 0305-1048

hal-01146849
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01146849
DOI : 10.1093/nar/gkv350
PUBMED : 25897122

Éditeur(s) : HAL CCSD MDPI
Résumé : International audience
AbstractThis review provides a global overview of microporous silica based membranes for desalination via pervaporation with a focus on membrane synthesis and processing, transport mechanisms and current state of the art membrane performance. Most importantly, the recent development and novel concepts for improving the hydro-stability and separating performance of silica membranes for desalination are critically examined. Research into silica based membranes for desalination has focussed on three primary methods for improving the hydro-stability. These include incorporating carbon templates into the microporous silica both as surfactants and hybrid organic-inorganic structures and incorporation of metal oxide nanoparticles into the silica matrix. The literature examined identified that only metal oxide silica membranes have demonstrated high salt rejections under a variety of feed concentrations, reasonable fluxes and unaltered performance over long-term operation. As this is an embryonic field of research several target areas for researchers were discussed including further improvement of the membrane materials, but also regarding the necessity of integrating waste or solar heat sources into the final process design to ensure cost competitiveness with conventional reverse osmosis processes. © 2012 by the authors.
ISSN: 2073-4441

hal-01683200
https://hal.univ-antilles.fr/hal-01683200
DOI : 10.3390/w4030629