Éditeur(s) : HAL CCSD
Résumé : International audience
Understand the dynamics of the fresh-salt water interface in aquifers is a key issue to comprehend mixing processand to quantity the discharge of nutrients in to coastal areas. In order to go beyond the current knowledge inthis issue an experimental site has been set up at the alluvial aquifer Riera Argentona (Barcelona – Spain). Thesite comprises 16 shallow piezometers installed between 30 and 90 m from the seashore, with depths rangingbetween 15 and 25 meters. The seawater interface is being monitored using several techniques, the combinationof which will help us to understand the spatial and temporal behaviour of the mixing zone and the geochemicalprocesses occurring there. Specially the deepest piezometers are equipped with electrodes in order to performcross-hole electrical resistivity tomography (CHERT). In addition, all piezometers are also equipped with FiberOptic cable to perform distributed temperature measurements. Two single steel armoured fibre optic cable lines ofaround 600m length were installed in all boreholes. The objective is to use the cable both as passive and activetemperature sensor. The first is being done for the continuous monitoring of temperature whereas; the secondprovides a higher temperature resolution used to monitor field experiments.Periodic CHERT measurements are carried out between the piezometer equipped with electrodes, resultingin parallel and perpendicular vertical cross sections of the site resistivity. The position of the fresh-salt waterinterface can be identified due to the resistivity contrast between the saline and fresh water. Preliminary resultsof periodic distributed temperature measurements will be also be used to monitor the position of the mixing zonethanks to the contrast and seasonal temperature changes. Periodic down-hole EC profiles will be used to validatethe method.AcknowledgementsThis work was funded by the projects CGL2013-48869-C2-1 y CGL2013-48869-C2-2-R of the Spanish Government.We would like to thank SIMMAR (Serveis Integrals de Manteniment del Maresme) and the ConsellComarcal del Maresme in the construction of the research site
European Geosciences Union General Assembly 2016
Vienne, Austria

insu-01308757
https://hal-insu.archives-ouvertes.fr/insu-01308757

Éditeur(s) : HAL CCSD Wiley/Blackwell
Résumé : 4 pages
International audience
This article documents the addition of 268 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Alburnoides bipunctatus, Chamaerops humilis, Chlidonias hybrida, Cyperus papyrus, Fusarium graminearum, Loxigilla barbadensis, Macrobrachium rosenbergii, Odontesthes bonariensis, Pelteobagrus vachelli, Posidonia oceanica, Potamotrygon motoro, Rhamdia quelen, Sarotherodon melanotheron heudelotii, Sibiraea angustata, Takifugu rubripes, Tarentola mauritanica, Trimmatostroma sp. and Wallago attu. These loci were cross-tested on the following species: Alburnoides fasciatus, Alburnoides kubanicus, Alburnoides maculatus, Alburnoides ohridanus, Alburnoides prespensis, Alburnoides rossicus, Alburnoides strymonicus, Alburnoides thessalicus, Alburnoides tzanevi, Carassius carassius, Fusarium asiaticum, Leucaspius delineatus, Loxigilla noctis dominica, Pelecus cultratus, Phoenix canariensis, Potamotrygon falkneri, Trachycarpus fortune and Vimba vimba.
ISSN: 1755-098X

hal-00823716
https://hal.archives-ouvertes.fr/hal-00823716
DOI : 10.1111/1755-0998.12095
PUBMED : 23521844

Éditeur(s) : Gauthier-Villars
Résumé : The benthic macroinvertebrate assemblages of the Argentine continental shelf were studied from samples of molluscs, echinoderms and bryozoans collected by the RN Shinkai Maru. Two major faunal groups were distinguished: one inhabiting the warmer inner shelf off Buenos Aires and northern Patagonia, and the other occupying the colder middle and outer shelf off Buenos Aires and most of the Patagonian shelf. These results confirm the traditional biogeographic division of the Argentine continental shelf into two provinces: Argentine and Magellanic. Furthermore, the results suggest the possibility of subdividing the Atlantic sector of the Magellanic province into two districts: Patagonian and Malvinean, under the influence of the Patagonian and the Malvinas current, respectively.
Oceanologica Acta (0399-1784) (Gauthier-Villars), 1992 , Vol. 15 , N. 6 , P. 687-698

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/00101/21234/18851.pdf
http://archimer.ifremer.fr/doc/00101/21234/

Éditeur(s) : HAL CCSD American Geophysical Union
Résumé : International audience
This paper presents a multicontinuum approach to model fractal temporal scaling of catchment response in hydrological systems. The temporal scaling of discharge is quantified in frequency domain by the transfer function HðxÞ, which is defined as the ratio between the spectra of catchment response and recharge time series. The transfer function may scale with frequency x as HðxÞ x2b. While the classical linear and Dupuit models predict exponents of b52 and b51, observations indicate scalings with noninteger exponents b. Such behaviors have been described by multifractal models, which, however, often lack a relation to the medium characteristics. We revisit and extend the classical linear Dupuit aquifer models and discuss their physical meanings in the light of the resulting aquifer dynamics. On the basis of these classical models, we derive a multicontinuum approach that provides physical recharge models which are able to explain fractal behaviors with exponents 1=2 < b < 2. Furthermore, this approach allows to link the fractal dynamics of the discharge process to the physical aquifer characteristics as reflected in the distribution of storage time scales. We systematically analyze the catchment responses in the proposed multicontinuum models, and identify and quantify the time scales which characterize the dynamics of the catchment response to recharge.
ISSN: 0043-1397

insu-00952537
https://hal-insu.archives-ouvertes.fr/insu-00952537
https://hal-insu.archives-ouvertes.fr/insu-00952537/document
https://hal-insu.archives-ouvertes.fr/insu-00952537/file/russian.pdf
DOI : 10.1002/2013WR014255

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
OBJECTIVES: To compare virological effectiveness in patients who continued on a virologically successful first-line boosted protease inhibitor (PI)-containing combination antiretroviral therapy (cART) regimen or who switched to a PI-free cART including efavirenz, nevirapine or abacavir. METHODS: From the French Hospital Database on HIV, we selected 439 patients with undetectable viral load (VL) on a first-line boosted PI-containing cART regimen who switched to a PI-free combination including efavirenz, nevirapine or abacavir. Each of these patients was matched with three patients who continued to take their first-line cART regimen, on the basis of gender, age, CD4 cell count, VL, date of cART initiation and the duration of VL undetectability. Time to virological failure (VF) was analysed with Kaplan-Meier curves and Cox models. RESULTS: The 12 month probabilities of VF were 3.7% and 5.7% in non-switch and switch patients, respectively, and 3.9%, 7.2% and 9.0% in patients switching to efavirenz-, nevirapine- and abacavir-containing cART, respectively. After adjustment, only patients switching to abacavir-containing cART had a higher risk of VF than non-switch patients (adjusted hazard ratio, 1.99; 95% confidence interval, 1.05-3.79). CONCLUSIONS: Switching from a virologically successful first-line boosted PI-containing cART regimen to a non-nucleoside reverse transcriptase inhibitor-containing cART regimen containing either efavirenz or nevirapine is virologically safe, while switching to abacavir-containing cART should be avoided.
ISSN: 0305-7453

hal-00875284
https://hal.archives-ouvertes.fr/hal-00875284
DOI : 10.1093/jac/dkr208
PUBMED : 21636583

Éditeur(s) : HAL CCSD
Résumé : International audience
We assessed whether maternal employment during pregnancy - overall and in selected occupational sectors - is associated with birth weight, small for gestational age (SGA), term low birth weight (LBW), length of gestation, and preterm delivery in a population-based birth cohort design. We used data from >200 000 mother-child pairs enrolled in 13 European birth cohorts and compared employed versus non-employed women. Among employees, we defined groups of occupations representing the main sectors of employment for women where potential reproductive hazards are considered to be present. The comparison group comprised all other employed women not included in the occupational sector being assessed. We performed meta-analyses of cohort-specific estimates and explored heterogeneity. Employees had a lower risk of preterm delivery than non-employees [adjusted odds ratio (OR adj) 0.86, 95% confidence interval (95% CI) 0.81-0.91]. Working in most of the occupational sectors studied was not associated with adverse birth outcomes. Being employed as a nurse was associated with lower risk SGA infants (OR adj0.91, 95% CI 0.84-0.99) whereas food industry workers had an increased risk of preterm delivery (OR adj1.50, 95% CI 1.12-2.02). There was little evidence for heterogeneity between cohorts. This study suggests that, overall, employment during pregnancy is associated with a reduction in the risk of preterm birth and that work in certain occupations may affect pregnancy outcomes. This exploratory study provides an important platform on which to base further prospective studies focused on the potential consequences of maternal occupational exposures during pregnancy on child development.
Scandinavian journal of work, environment & health

Droits : info:eu-repo/semantics/OpenAccess
hal-01151621
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01151621
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01151621/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01151621/file/Maternal%20occupation%20during%20pregnancy_supplementary%20material.pdf
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01151621/file/Maternal%20occupation%20during%20pregnancy_accepted.pdf

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Understanding long-term variability in the frequency of intense storm activity is important for assessing whether changes are controlled by climate evolution. Understanding this variability is also important for predicting present and future community vulnerability and economic loss. Our ability to make these assessments has been limited by the short (less than 50 years) instrument record of storm activity. Storm-induced deposits preserved in the sediments of coastal lagoons offer the opportunity to study the links between climatic conditions and storm activity on longer timescales. In this study, we present a record of these extreme climatic events that have occurred in the French Mediterrannean coast over the past 1500 years. The identification of these extreme events is based on the analysis of sediment cores from Gulf of Aigues-Mortes lagoons that contain a specific sedimentary and geochemical signature associated with intense storms.;Overwash deposits do not show any evidence of intense storm landfalls in the region for several hundred years prior to the late 17th century A.D. The apparent increase in intense storms around 250 years ago occurs during the latter half of the Little Ice Age, a time of lower continental surface temperatures. Comparison of the sediment record with palaeoclimate records indicates that this variability was probably modulated by atmospheric dynamics. The apparent increase of the superstorm activity during the latter half of the Little Ice Age was probably due to the thermal gradient increase leading to enhanced lower tropospheric baroclinicity over a large Central Atlantic/European domain and leading to a modification of the occurrence of extreme wind events along the French Mediterranean coast. A complete understanding of the relationship between climate fluctuations, storm activity, and the coastal response will be crucial to predicting the impacts of future climate change.
ISSN: 0031-0182

hal-00617525
https://hal.archives-ouvertes.fr/hal-00617525
DOI : 10.1016/j.palaeo.2010.11.009

Éditeur(s) : HAL CCSD Wiley-VCH Verlag
Résumé : International audience
ISSN: 1439-4235

hal-01234189
https://hal.archives-ouvertes.fr/hal-01234189
DOI : 10.1002/cphc.201500610

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Low-level exposure to polychlorinated biphenyl-153 (PCB-153) and dichlorodiphenyldichloroethylene (p-p'-DDE) can impair fetal growth; however, the exposure-response relationship and effect modifiers of such association are not well established. This study is an extension of an earlier European meta-analysis. Our aim was to explore exposure-response relationship between PCB-153 and p-p'-DDE and birth outcomes; to evaluate whether any no exposure-effect level and susceptible subgroups exist; and to assess the role of maternal gestational weight gain (GWG). We used a pooled dataset of 9377 mother-child pairs enrolled in 14 study populations from 11 European birth cohorts. General additive models were used to evaluate the shape of the relationships between organochlorine compounds and birth outcomes. We observed an inverse linear exposure-response relationship between prenatal exposure to PCB-153 and birth weight [decline of 194g (95% CI -314, -74) per 1μg/L increase in PCB-153]. We showed effects on birth weight over the entire exposure range, including at low levels. This reduction seems to be stronger among children of mothers who were non-Caucasian or had smoked during pregnancy. The most susceptible subgroup was girls whose mothers smoked during pregnancy. After adjusting for absolute GWG or estimated fat mass, a reduction in birth weight was still observed. This study suggests that the association between low-level exposure to PCB-153 and birth weight exists and follows an inverse linear exposure-response relationship with effects even at low levels, and that maternal smoking and ethnicity modify this association.
ISSN: 0160-4120

hal-01118572
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01118572
PUBMED : 25314142
DOI : 10.1016/j.envint.2014.09.013

Éditeur(s) : HAL CCSD European Geosciences Union
Résumé : International audience
Measurements of branch xylem density, D_x, were made for 1466 trees representing 503 species, sampled from 80 sites across the Amazon basin. Measured values ranged from 240 kg m^?3 for a Brosimum parinarioides from Tapajos in West Pará, Brazil to 1130 kg m^?3 for an Aiouea sp. from Caxiuana, Central Pará, Brazil. Analysis of variance showed significant differences in average D_x across the sample plots as well as significant differences between families, genera and species. A partitioning of the total variance in the dataset showed that geographic location and plot accounted for 33% of the variation with species identity accounting for an additional 27%; the remaining "residual" 40% of the variance accounted for by tree to tree (within species) variation. Variations in plot means, were, however, hardly accountable at all by differences in species composition. Rather, it would seem that variations of xylem density at plot level must be explained by the effects of soils and/or climate. This conclusion is supported by the observation that the xylem density of the more widely distributed species varied systematically from plot to plot. Thus, as well as having a genetic component branch xylem density is a plastic trait that, for any given species, varies according to where the tree is growing and in a predictable manner. Exceptions to this general rule may be some pioneers belonging to Pourouma and Miconia and some species within the genera Brosimum, Rinorea and Trichillia which seem to be more constrained in terms of this plasticity than most species sampled as part of this study.
ISSN: 1810-6277

hal-00298004
https://hal.archives-ouvertes.fr/hal-00298004
https://hal.archives-ouvertes.fr/hal-00298004/document
https://hal.archives-ouvertes.fr/hal-00298004/file/bgd-5-2003-2008.pdf

Éditeur(s) : HAL CCSD Geological Society of London
Résumé : International audience
The sediments of the Mauges Unit located in the internal zone provide an opportunity of studying the evolution of relief during Palaeozoic time. U-Pb dating on zircon and 39Ar/40Ar on white mica are used to constrain the age and nature of the sources. The first relief identified is marked by an Early Devonian unconformity interpreted as the opening of a northern back-arc basin. Detrital minerals are first reworked from underlying layers indicating a local supply. Magmatic zircons at c. 400 Ma then record the emergence of a magmatic arc. During the Middle Devonian, the gap in the sedimentary record is attributed to an emersion followed by the disappearance of the relief during the Late Devonian. At the Devonian-Carboniferous boundary, the main collision is followed by the onset of a relief. The continental sedimentation in the Ancenis Basin (late Tournaisian-Viséan) is a coarsening-upwards megasequence indicating an increasing and/or approaching relief. The detrital minerals record the progressive exhumation of Variscan metamorphic (mica at c. 350 Ma) and magmatic rocks (zircons at c. 390-340 Ma). The Serpukhovian-Bashkirian sedimentation records the erosion of a proximal metamorphic source (Champtoceaux with micas at c. 350-340 Ma) showing a much shorter drainage system
The Variscan Orogeny: Extent, Timescale and the Formation of the European Crust

ISBN : 978-1-86239-658-6
insu-01016985
https://hal-insu.archives-ouvertes.fr/insu-01016985
DOI : 10.1144/SP405.6

Éditeur(s) : HAL CCSD
Résumé : International audience
Characterizing the hydraulic properties of heterogeneous and complex aquifers often requires field scale investigations at multiple space and time scales to better constrain hydraulic property estimates. Here, we present and discuss results from the site of Ploemeur (Brittany, France) where complementary hydrological and geophysical approaches have been combined to characterize the hydrogeological functioning of this highly fractured crystalline rock aquifer. In particular, we show how cross-borehole flowmeter tests, pumping tests and frequency domain analysis of groundwater levels allow quantifying the hydraulic properties of the aquifer at different scales. In complement, we used groundwater temperature as an excellent tracer for characterizing groundwater flow. At the site scale, measurements of ground surface deformation through long-base tiltmeters provide robust estimates of aquifer storage and allow identifying the active structures where groundwater pressure changes occur, including those acting during recharge process. Finally, a numerical model of the site that combines hydraulic data and groundwater ages confirms the geometry of this complex aquifer and the consistency of the different datasets. The Ploemeur site, which has been used for water supply at a rate of about 106 m3 per year since 1991, belongs to the French network of hydrogeological sites H+ and is currently used for monitoring groundwater changes and testing innovative field methods.
AGU Fall Meeting 2014
San Francisco, United States

insu-01088596
https://hal-insu.archives-ouvertes.fr/insu-01088596

Éditeur(s) : HAL CCSD
Résumé : International audience
OBJECTIVE: To assess sperm production and aneuploidy in Hodgkin lymphoma (HL) and non-Hodgkin lymphoma (NHL) before and after treatments. DESIGN: Multicenter, prospective, longitudinal study of lymphoma patients analyzed before treatment and after 3, 6, 12, and 24 months. SETTING: University hospitals. PATIENT(S): Forty-five HL and 13 NHL patients were investigated before and after treatment. Treatment regimens were classified in two groups: ABVD (doxorubicin, bleomycin, vinblastine, dacarbazine) with or without (+/-) radiotherapy, and CHOP (doxorubicin, cyclophosphamide, vincristine, prednisone)/MOPP-ABV (mechlorethamine, oncovin, procarbazine, prednisone-doxorubicin, bleomycin, vinblastine). A control group of 29 healthy men was also studied. INTERVENTION(S): Semen analyses and aneuploidy study by FISH were performed at each time point. MAIN OUTCOME MEASURE(S): Comparison of mean sperm characteristics and percentage of sperm aneuploidy rates before and after treatment. RESULT(S): Before treatment, HL and NHL men had altered semen characteristics and higher sperm aneuploidy rates (median 0.76 [interquartile range 0.56-0.64]) than the control group (0.54 [0.46-0.74]). After treatment, sperm production was significantly lowered 3 and 6 months after ABVD +/- radiotherapy or CHOP/MOPP-ABV. After ABVD +/- radiotherapy, the aneuploidy rate increased significantly only at 3 months, and values obtained 1 or 2 years later were lower than pretreatment values. In contrast, in the CHOP/MOPP-ABV treatment group, semen characteristics and aneuploidy rate did not return to normal levels until 2 years after treatment. CONCLUSION(S): Lymphoma itself has consequences on sperm aneuploidy frequency before treatment. Moreover, lymphoma treatments have deleterious effects on sperm chromosomes related to treatment type and time since treatment. Patient counseling is essential concerning the transient but significant sperm aneuploidy induced by lymphoma and its treatments.
Fertility and sterility

hal-01477204
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01477204
DOI : 10.1016/j.fertnstert.2016.10.001
PUBMED : 27810161

Éditeur(s) : HAL CCSD American Society of Nephrology
Résumé : International audience
Since the recent publication of data showing favorable outcomes for patients with HIV-1 and ESRD, kidney transplantation has become a therapeutic option in this population. However, reports have documented unexplained reduced allograft survival in these patients. We hypothesized that the unrecognized infection of the transplanted kidney by HIV-1 can compromise long-term allograft function. Using electron microscopy and molecular biology, we examined protocol renal transplant biopsies from 19 recipients with HIV-1 who did not have detectable levels of plasma HIV-1 RNA at transplantation. We found that HIV-1 infected the kidney allograft in 68% of these patients. Notably, HIV-1 infection was detected in either podocytes predominately (38% of recipients) or tubular cells only (62% of recipients). Podocyte infection associated with podocyte apoptosis and loss of differentiation markers as well as a faster decline in allograft function compared with tubular cell infection. In allografts with tubular cell infection, epithelial cells of the proximal convoluted tubules frequently contained abnormal mitochondria, and both patients who developed features of subclinical acute cellular rejection had allografts with tubular cell infection. Finally, we provide a novel noninvasive test for determining HIV-1 infection of the kidney allograft by measuring HIV-1 DNA and RNA levels in patients' urine. In conclusion, HIV-1 can infect kidney allografts after transplantation despite undetectable viremia, and this infection might influence graft outcome.
ISSN: 1046-6673

hal-01121764
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01121764
DOI : 10.1681/ASN.2013050564
PUBMED : 24309185
PUBMEDCENTRAL : PMC3904571

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : The analysis of fine-scale spatial genetic structure (FSGS) within populations can provide insights into eco-evolutionary processes. Restricted dispersal and locally occurring genetic drift are the primary causes for FSGS at equilibrium, as described in the isolation by distance (IBD) model. Beyond IBD expectations, spatial, environmental or historical factors can affect FSGS. We examined FSGS in seven African and Neotropical populations of the late-successional rain forest tree Symphonia globulifera L. f. (Clusiaceae) to discriminate the influence of drift-dispersal vs. landscape/ecological features and historical processes on FSGS. We used spatial principal component analysis and Bayesian clustering to assess spatial genetic heterogeneity at SSRs and examined its association with plastid DNA and habitat features. African populations (from Cameroon and São Tomé) displayed a stronger FSGS than Neotropical populations at both marker types (mean Sp = 0.025 vs. Sp = 0.008 at SSRs) and had a stronger spatial genetic heterogeneity. All three African populations occurred in pronounced altitudinal gradients, possibly restricting animal-mediated seed dispersal. Cyto-nuclear disequilibria in Cameroonian populations also suggested a legacy of biogeographic history to explain these genetic patterns. Conversely, Neotropical populations exhibited a weaker FSGS, which may reflect more efficient wide-ranging seed dispersal by Neotropical bats and other dispersers. The population from French Guiana displayed an association of plastid haplotypes with two morphotypes characterized by differential habitat preferences. Our results highlight the importance of the microenvironment for eco-evolutionary processes within persistent tropical tree populations.
ISSN: 1932-6203

hal-01608324
https://hal.archives-ouvertes.fr/hal-01608324
DOI : 10.1371/journal.pone.0182515
PRODINRA : 403154
PUBMED : 28771629

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
ISSN: 2047-217X

hal-01429002
https://hal.archives-ouvertes.fr/hal-01429002
DOI : 10.1186/s13742-016-0118-5

Éditeur(s) : HAL CCSD Wiley
Résumé : Genetic variation is generally considered a prerequisite for adaptation to new environmental conditions. Thus the discovery of genetically depauperate but geographically widespread species is unexpected. We used 12 paternally inherited chloroplast microsatellites to estimate population genetic variation across the full range of an emblematic circum-Mediterranean conifer, stone pine (Pinus pinea L.). The same chloroplast DNA haplotype is fixed in nearly all of the 34 investigated populations. Such a low level of variation is consistent with a previous report of very low levels of diversity at nuclear loci in this species. Stone pine appears to have passed through a severe and prolonged demographic bottleneck, followed by subsequent natural- and human-mediated dispersal across the Mediterranean Basin. No other abundant and widespread plant species has as little genetic diversity as P. pinea at both chloroplast and nuclear markers. However, the species harbors a nonnegligible amount of variation at adaptive traits. Thus a causal relationship between genetic diversity, as measured by marker loci, and the evolutionary precariousness of a species, cannot be taken for granted
ISSN: 0014-3820

hal-01032062
https://hal.archives-ouvertes.fr/hal-01032062
DOI : 10.1111/j.1558-5646.2007.00294.x

Éditeur(s) : HAL CCSD American Geophysical Union (AGU)
Résumé : International audience
without
ISSN: 0278-7407

hal-00464176
https://hal.archives-ouvertes.fr/hal-00464176
DOI : 10.1029/2009TC002527

Éditeur(s) : HAL CCSD
Résumé : absent
SMBE Satellite meeting SMBEBA 2015 "Investigating biological adaptation with NGS: data and models"
Hameau de l'étoile, France

hal-01204227
https://hal.archives-ouvertes.fr/hal-01204227
PRODINRA : 307498

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