Éditeur(s) : George A. Smathers Libraries, University of Florida George A. Smathers Libraries, University of Florida ( Gainesville, FL )

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 : International audience
ISSN: 1752-0894

hal-01667978
https://hal.archives-ouvertes.fr/hal-01667978
DOI : 10.1038/s41561-017-0028-x

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
We describe an experimental system including monitoring of temperature, pressure, pH, oxidation reduction potential and optical density at 600 nm, designed for studying the role of microorganisms on the geological sequestration Of CO2 and its transformation into solid carbonate phases. Measurements were performed in an artificial ground water (AGW) supplemented with urea (2 g.l(-1)) and equilibrated at controlled temperatures with a gaseous phase before bacterial inoculation. We used the ureolytic strain Bacillus pasteurii as a model carbonate precipitating bacteria and showed that it can successfully promote strong pH increases by ureolysis in the AGW equilibrated with CO2 pressures of up to I bar. Increasing salinities (5.8,13.5 and 35.0 g.l(-1)) have a positive effect on the rate of pH increase, whereas the effect of increasing temperatures (30,35 and 38 degrees C) is less important. Calcium is also shown to have a specific positive influence on the rate of ureolysis. The number of viable cells present in solution decreases greatly during the carbonate precipitation event but the population partially recovers once precipitation is over.
ISSN: 0009-2541

hal-00445282
https://hal.archives-ouvertes.fr/hal-00445282
DOI : 10.1016/j.chemgeo.2008.12.012

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 National Academy of Sciences
Résumé : International audience
All evolutionary biologists are familiar with evolutionary units that evolve by vertical descent in a tree-like fashion in single lineages. However, many other kinds of processes contribute to evolutionary diversity. In vertical descent, the genetic material of a particular evolutionary unit is propagated by replication inside its own lineage. In what we call introgressive descent, the genetic material of a particular evolutionary unit propagates into different host structures and is replicated within these host structures. Thus, introgressive descent generates a variety of evolutionary units and leaves recognizable patterns in resemblance networks. We characterize six kinds of evolutionary units, of which five involve mosaic lineages generated by introgressive descent. To facilitate detection of these units in resemblance networks, we introduce terminology based on two notions, P3s (subgraphs of three nodes: A, B, and C) and mosaic P3s, and suggest an apparatus for systematic detection of introgressive descent. Mosaic P3s correspond to a distinct type of evolutionary bond that is orthogonal to the bonds of kinship and genealogy usually examined by evolutionary biologists. We argue that recognition of these evolutionary bonds stimulates radical rethinking of key questions in evolutionary biology (e.g., the relations among evolutionary players in very early phases of evolutionary history, the origin and emergence of novelties, and the production of new lineages). This line of research will expand the study of biological complexity beyond the usual genealogical bonds, revealing additional sources of biodiversity. It provides an important step to a more realistic pluralist treatment of evolutionary complexity.
ISSN: 0027-8424

hal-01544803
https://hal.archives-ouvertes.fr/hal-01544803
DOI : 10.1073/pnas.1206541109

Éditeur(s) : HAL CCSD Elsevier Masson
Résumé : Contaminant migration in aquifers is one of the most debated issues in hydrogeology, as most experimental results display large deviations from the standard (asymptotic) Fickian dispersion theories. Multi-scale investigation and high-resolution sensors are required to determine the origin of non-asymptotic dispersion and validate models. For this, a set of multi-scale Single-Well Injection-Withdrawal (SWIW) tracer tests using a new dual-packer probe CoFIS, including a high resolution optical sensor TELog, are presented. When compared to standard techniques such as salinity measurements, it is shown that high-resolution optical measurements allow an improved characterization of the long-lasting non-asymptotic dispersion mechanisms.
ISSN: 1631-0713

hal-00445250
https://hal.archives-ouvertes.fr/hal-00445250
DOI : 10.1016/j.crte.2009.07.012

Éditeur(s) : HAL CCSD Météo et Climat
Résumé : International audience
Les risques hydrométéorologiques sont au coeur du programme de recherche HyMeX sur le cycle de l'eau en Méditerranée. HyMeX a pour ambition d'améliorer leur prévision, de mieux connaître leur variabilité à l'échelle pluriannuelle et de renseigner sur leur évolution, dans le contexte du changement climatique. À cette fin, deux campagnes de mesures dédiées à ces événements extrêmes (SOP1 : pluies intenses et crues rapides ; SOP2 : vents forts et formation d'eaux denses) sont organisées en Méditerranée nord-occidentale, entre septembre 2012 et mars 2013.
ISSN: 0026-1181

hal-00829760
https://hal.archives-ouvertes.fr/hal-00829760
DOI : 10.4267/2042/48793

Éditeur(s) : HAL CCSD Météo et Climat
Résumé : International audience
D'initiative française, le projet international HyMeX a pour objectif d'améliorer la compréhension du cycle de l'eau en Méditerranée, de sa variabilité, de l'échelle de l'événement météorologique aux échelles saisonnières et interannuelles, et de ses caractéristiques sur une décennie, dans un contexte de changement global. Le projet est motivé par le rôle déterminant des processus de mésoéchelle, couplés entre l'atmosphère, la mer et la terre, sur la variabilité du système climatique et sur le déclenchement d'événements hydrométéorologiques extrêmes (précipitations et inondations, vents forts et convection océanique, canicules et sécheresses). Le projet vise enfin à évaluer les conséquences de ces événements extrêmes sur la vulnérabilité sociale et économique de cette région et sa capacité d'adaptation.
ISSN: 0026-1181

hal-00828758
https://hal.archives-ouvertes.fr/hal-00828758
https://hal.archives-ouvertes.fr/hal-00828758/document
https://hal.archives-ouvertes.fr/hal-00828758/file/meteo_2013_80_23%20%281%29.pdf
DOI : 10.4267/2042/48792

Éditeur(s) : HAL CCSD BRGM
Résumé : National audience
Proceedings 1ère Journée 'Alea Gravitaire'
Orléans, France

hal-00533951
https://hal.archives-ouvertes.fr/hal-00533951

Éditeur(s) : HAL CCSD Météo et Climat
Résumé : International audience
Le premier volet du projet Cyprim vise à mieux identifier les précurseurs des cyclogenèses et des précipitations intenses en région méditerranéenne. Cet article en présente les principaux résultats. Il est question des ingrédients météorologiques à l'origine de ces systèmes, de la grande à la mésoéchelle, des causes des fortes intensités, localisations et parfois stationnarité des récipitations associées. Le coeur de l'article présente des méthodes d'identification des anomalies de tourbillon potentiel liées à l'occurrence d'événements précipitants intenses et dresse une climatologie de ces anomalies. Les perspectives d'exploitation de cette information pour améliorer la qualité des prévisions sont évoquées. ENGLISH VERSION: The first part of the CYPRIM project (Cyclogenesis and intense precipitations in the Mediterranean region) aims at a better identification of the precursor structures of cyclogenesis and heavy precipitation in the Mediterranean region. This article presents the main results. It mentions the meteorological ingredients from which these systems originate from the large to themesoscale, the reasons for large intensities, the localization and sometimes stationarity of the associated precipitations. The heart of the article shows methods for identifiying potential vorticity anomalies involved in the occurrence of heavy precipitation events and sets up a climatology of these anomalies.The perspectives of the usefulness of this information for improving forecast quality are discussed.
ISSN: 0026-1181

insu-00448250
https://hal-insu.archives-ouvertes.fr/insu-00448250
DOI : 10.4267/2042/28828

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Three soil DNA extraction procedures (homemade protocols and commercial kit) varying in their practicability were applied to contrasting soils to evaluate their efficiency in recovering: (i) soil DNA and (ii) bacterial diversity estimated by 16S rDNA pyrosequencing. Significant differences in DNA yield were systematically observed between tested procedures. For certain soils, 10 times more DNA was recovered with one protocol than with the others. About 15 000 sequences of 16S rDNA were obtained for each sample which were clustered to draw rarefaction curves. These curves, as well as the PCA ordination of community composition based on OTU clustering, did not reveal any significant difference between procedures. Nevertheless, significant differences between procedures were highlighted by the taxonomic identification of sequences obtained at the phylum to genus levels. Depending on the soil, differences in the number of genera detected ranged from 1% to 26% between the most and least efficient procedures, mainly due to a poorer capacity to recover populations belonging to Actinobacteria, Firmicutes or Crenarchaeota. This study enabled us to rank the relative efficiencies of protocols for their recovery of soil molecular microbial biomass and bacterial diversity and to help choosing an appropriate soil DNA extraction procedure adapted to novel sequencing technologies.
ISSN: 1751-7915

hal-01546177
https://hal.archives-ouvertes.fr/hal-01546177
DOI : 10.1111/j.1751-7915.2011.00307.x

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
ISSN: 1752-0894

hal-01668923
https://hal.archives-ouvertes.fr/hal-01668923
DOI : 10.1038/s41561-017-0028-x

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
Background: The Ras/Raf/MEK/ERK signaling pathway is involved in essential cell processes and it is abnormally activated in similar to 30 % of cancers and cognitive disorders. Two ERK isoforms have been described, ERK1 and ERK2; ERK2 being regarded by many as essential due to the embryonic lethality of ERK2 knock-out mice, whereas mice lacking ERK1 are viable and fertile. The controversial question of why we have two ERKs and whether they have differential functions or display functional redundancy has not yet been resolved. Results: To investigate this question we used a novel approach based on comparing the evolution of ERK isoforms' sequences and protein expression across vertebrates. We gathered and cloned erk1 and erk2 coding sequences and we examined protein expression of isoforms in brain extracts in all major clades of vertebrate evolution. For the first time, we measured each isoforms' relative protein level in phylogenetically distant animals using anti-phospho antibodies targeting active ERKs. We demonstrate that squamates (lizards, snakes and geckos), despite having both genes, do not express ERK2 protein whereas other tetrapods either do not express ERK1 protein or have lost the erk1 gene. To demonstrate the unexpected squamates' lack of ERK2 expression, we targeted each ERK isoform in lizard primary fibroblasts by specific siRNA-mediated knockdown. We also found that undetectable expression of ERK2 in lizard is compensated by a greater strength of lizard's erk1 promoter. Finally, phylogenetic analysis revealed that ERK1 amino acids sequences evolve faster than ERK2' s likely due to genomic factors, including a large difference in gene size, rather than from functional differences since amino acids essential for function are kept invariant. Conclusions: ERK isoforms appeared by a single gene duplication at the onset of vertebrate evolution at least 400 Mya. Our results demonstrate that tetrapods can live by expressing either one or both ERK isoforms, supporting the notion that ERK1/2 act interchangeably. Substrate recognition sites and catalytic cleft are nearly invariant in all vertebrate ERKs further suggesting functional redundancy. We suggest that future ERK research should shift towards understanding the role and regulation of total ERK quantity, especially in light of newly described erk2 gene amplification identified in tumors.
ISSN: 1471-2148

hal-01546165
https://hal.archives-ouvertes.fr/hal-01546165
DOI : 10.1186/s12862-015-0450-x

Éditeur(s) : HAL CCSD Elsevier
Résumé : We investigate experimentally the alteration of fractured class-G cement flowed by CO2-rich brine. The experiment mimics a mechanically damaged rough-walled fractured cement annulus at temperature 60 °C and pressure 10 MPa. The experiment consists of flowing a reservoir-equilibrated brine mixed with CO2 (partial pressure of 2.3 MPa) through the fracture of average aperture 14 μm at constant flow rate (100 μL min−1). This flow rate corresponds to pressure gradient representative of an average in situ hydrodynamic condition. Results indicate an intense alteration of the cement with a large removal of mass at the scale of the sample. However, the fracture alteration patterns are triggered by the initial heterogeneity of the fracture aperture; the aperture of the low aperture zones tends to decrease due to calcite precipitation whereas preferential paths develop in the zones of higher aperture associated. Nevertheless, the expected large permeability increase triggered by the mass removal is mitigated by the precipitation of a low density Si-rich amorphous material. The alteration rate will decrease with time because of the increasing distance of diffusion between the fracture where the reactants are actively renewed by advection and the portlandite and C-S-H dissolution fronts. The different zones of reaction can be adequately modeled by a simple 1D diffusion-reaction model using published kinetics coefficients and extrapolation to larger times than the experiment time can be drawn. Altogether, and in addition to the previous studies of the alteration of fractured well cement annulus, this study shows that the leakage potential is strongly controlled by the initial distribution of the aperture along the fracture: low aperture zones will tend to self-heal while localized flow in connected high aperture paths will be perennial.
ISSN: 1750-5836

hal-01346006
https://hal.archives-ouvertes.fr/hal-01346006
DOI : 10.1016/j.ijggc.2016.01.032

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The parasitic life cycle of Leishmania includes an extracellular promastigote stage that occurs in the gut of the insect vector. During that period, the sucrose metabolism and more specifically the first glycosidase of this pathway are essential for growth and survival of the parasite. We investigated the expression of the invertase BfrA in the promastigote and amastigote stages of three parasite species representative of the three various clinical forms and of various geographical areas, namely Leishmania major, L. donovani and L. braziliensis. Thereafter, we cloned, overexpressed and biochemically characterized this invertase BfrA from L. major, heterologously expressed in both Escherichia coli and L. tarentolae. For all species, expression levels of BfrA mRNA were correlated to the time of the culture and the parasitic stage (promastigotes > amastigotes). BfrA exhibited no activity when expressed as a glycoprotein in L. tarentolae but proved to be an invertase when not glycosylated, yet owing low sequence homology with other invertases from the same family. Our data suggest that BfrA is an original invertase that is located inside the parasite. It is expressed in both parasitic stages, though to a higher extent in promastigotes. This work provides new insight into the parasite sucrose metabolism
ISSN: 0008-6215

hal-01187142
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01187142
DOI : 10.1016/j.carres.2015.07.001
PUBMED : 26279524