Éditeur(s) : Inter-Research
Résumé : The widespread use of Agent Orange (a mixture of phenoxyl herbicides) over Southern Vietnam by US Forces led to the decimation of mangrove forests in the Mekong Delta. Mangrove trees Avicennia alba were sampled across the Mekong Delta; their age was assessed using models based on internode growth and samples were genotyped for 6 microsatellite loci. The evolution of genetic diversity over time elapsed since local extinction was reconstructed and compared with the genetic diversity of an unaffected population from Thailand, The results show that genetic diversity of the A. alba population is still increasing in the Mekong Delta 3 decades after the end of the Vietnam War, but is reaching an asymptotic level that is comparable to the adjacent non-affected population of Thailand. This might be a sign of genetic recovery, but may also reveal a limitation, either of genetic enrichment due to current predominance of auto-recruitment or of demographic increase due to intraspecific competition in this pioneer species. In any case, these results, although encouraging, demonstrate that genetic recovery after complete or almost complete population depletion continues over a longer time-scale than apparent demographic recovery.
Marine Ecology Progress Series (0171-8630) (Inter-Research), 2009-09 , Vol. 390 , P. 129-135

Droits : Inter-Research 2009
http://archimer.ifremer.fr/doc/2009/publication-6898.pdf
DOI:10.3354/meps08183
http://archimer.ifremer.fr/doc/00000/6898/

Éditeur(s) : HAL CCSD Elsevier Masson
Résumé : International audience
The maintenance in the long run of a positive carbon balance under very low irradiance is a prerequisite for survival of tree seedlings below the canopy or in small gaps in a tropical rainforest. To provide a quantitative basis for this assumption, experiments were carried out to determine whether construction cost (CC) and payback time for leaves and support structures, as well as leaf life span (i) differ among species and (ii) display an irradiance-elicited plasticity. Experiments were also conducted to determine whether leaf life span correlates to CC and payback time and is close to the optimal longevity derived from an optimization model. Saplings from 13 tropical tree species were grown under three levels of irradiance. Specific-CC was computed, as well as CC scaled to leaf area at the metamer level. Photosynthesis was recorded over the leaf life span. Payback time was derived from CC and a simple photosynthesis model. Specific-CC displayed only little interspecific variability and irradiance-elicited plasticity, in contrast to CC scaled to leaf area. Leaf life span ranged from 4 months to >26 months among species, and was longest in seedlings grown under lowest irradiance. It was always much longer than payback time, even under the lowest irradiance. Leaves were shed when their photosynthesis had reached very low values, in contrast to what was predicted by an optimality model. The species ranking for the different traits was stable across irradiance treatments. The two pioneer species always displayed the smallest CC, leaf life span, and payback time. All species displayed a similar large irradiance-elicited plasticity.
ISSN: 1631-0691

hal-01095975
https://hal-agroparistech.archives-ouvertes.fr/hal-01095975
DOI : 10.1016/j.crvi.2011.01.007

Éditeur(s) : Elsevier
Résumé : A study was conducted using a bioenergetics approach to generate information on energy requirement and feed utilization of Litopenaeus stylirostris. Animals (initial mean weight 21 +/- 1 g were fed ad libitum six experimental diets, ranging from 25 to 58% crude protein (CP), for 50 days. Weight gain increased from 21 to 30 g with increasing dietary protein level. Survival rates averaged 80%. Basal metabolism (HeE) and heat increment of feeding (HiE) were monitored using respirometry. HeE was on average I U shrimp(-1) day(-1) or 47 U kg live weight(-1) day (22 kJ/kg(0.8). d(-1)), slightly more than what is observed in fish. HiE averaged 0.2 W/sbrimp(-1) day(-1) or 10 W kg live weight(-1) day(-1) (4 kJ/kg(0.8) d(-1)). It represented 3 1 % and 12% digestible energy intake (DET) for shrimp fed on 58% CP and 25% CP diet respectively. Non-fecal (UE + ZE) energy calculated on the basis of N-ammonia excretion averaged 0.2 jig N-ammonia/g dry wt./ mn or 25 J live shrimp(-1) day(-1) in fasting stage and increased to 40 J in post-prandial stage. Ammonia production increased with increasing dietary crude protein (CP). The O:N ratio indicated that protein was increasingly used as an energy substrate as CP increased. The information was used to construct an energy budget for shrimp fed a protypical 40% CP diet. Gross energy intake (IE) was estimated at 6.5 W live shrimp(-1) day(-1); digestible energy intake (DEI) at 5, urinary and branchial excretion (UE +ZE) at 1.2, total heat production (HE) at 3.2; recovered energy (RE) at 0.6 (or 11% DEI). L. stylirostris adults issued from domesticated strain appeared to be more efficiently utilizing (i.e. converting into carcass energy) protein than carbohydrates. This preliminary energy budget can be used to construct theoretical feed requirement and waste outputs model for L. stylirostris. (C) 2007 Published by Elsevier B.V.
Aquaculture (0044-8486) (Elsevier), 2007-10 , Vol. 271 , N. 1-4 , P. 439-448

Droits : 2007 Published by Elsevier B.V.
http://archimer.ifremer.fr/doc/2007/publication-6263.pdf
DOI:10.1016/j.aquaculture.2006.05.062
http://archimer.ifremer.fr/doc/00000/6263/

Éditeur(s) : Gauthier-Villars
Résumé : Several models for the evolution of complex life histories have assumed a carrying capacity for both larval and postlarval stages. In addition, the densities of larvae in laboratory experiments are often so high that there is competition for food. Published values for maximal clearance rates and estimated abundances of larvae suggest that these assumptions and experimental conditions are unrealistic for most marine larvae. For most ciliated larvae, maximum clearance rates are at most a few mi of water daily, and their estimated larval concentrations are at most one to several larvae per liter. Therefore these larvae appear to be too scarce for their grazing to affect their food supply. Larvae of most species are also scarce relative to co-occurring planktonic animals that feed on particles in the same size range. Larvae of many species are scarce relative to co-occurring larvae with a similar feeding apparatus. These observations suggest that larvae of most species have a negligible effect on their food supply. Exceptions could occur when a single species of larva dominates the zooplankton; such circumstances appear to be rare, although extreme aggregations of larvae dominated by a single species could be missed by pump or net samples. Analogous but more conjectural arguments can be made for density-dependent attraction of predators to larval prey. These inferences apply to single species, not to meroplanktonic larvae as a whole: in some coastal waters, larvae of benthic invertebrates comprise a large portion of the multicellular planktonic animals. Also, a species' larval growth may be food-limited in many waters, even when the abundance of food is independent of the abundance of its larvae.
Oceanologica Acta (0399-1784) (Gauthier-Villars), 1996 , Vol. 19 , N. 3-4 , P. 399-407

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/00094/20495/18164.pdf
http://archimer.ifremer.fr/doc/00094/20495/

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
Background: The Hippo pathway regulates growth rate and organ size in fly and mouse, notably through control of cell proliferation. Molecular interactions at the heart of this pathway are known to have originated in the unicellular ancestry of metazoans. They notably involve a cascade of phosphorylations triggered by the kinase Hippo, with sub‑ sequent nuclear to cytoplasmic shift of Yorkie localisation, preventing its binding to the transcription factor Scalloped, thereby silencing proliferation genes. There are few comparative expression data of Hippo pathway genes in non‑ model animal species and notably none in non‑bilaterian phyla.Results: All core Hippo pathway genes could be retrieved from the ctenophore Pleurobrachia pileus and the hydro‑ zoan cnidarian Clytia hemisphaerica, with the important exception of Yorkie in ctenophore. Expression study of the Hippo, Salvador and Scalloped genes in tentacle " cellular conveyor belts " of these two organisms revealed striking differences. In P. pileus, their transcripts were detected in areas where undifferentiated progenitors intensely prolifer‑ ate and where expression of cyclins B and D was also seen. In C. hemisphaerica, these three genes and Yorkie are expressed not only in the proliferating but also in the differentiation zone of the tentacle bulb and in mature tentacle cells. However, using an antibody designed against the C. hemiphaerica Yorkie protein, we show in two distinct cell lineages of the medusa that Yorkie localisation is predominantly nuclear in areas of active cell proliferation and mainly cytoplasmic elsewhere.Conclusions: This is the first evidence of nucleocytoplasmic Yorkie shift in association with the arrest of cell prolifera‑ tion in a cnidarian, strongly evoking the cell division‑promoting role of this protein and its inhibition by the activated Hippo pathway in bilaterian models. Our results furthermore highlight important differences in terms of deployment and regulation of Hippo pathway genes between cnidarians and ctenophores.
ISSN: 2041-9139

Droits : http://creativecommons.org/licenses/by/
hal-01286578
http://hal.upmc.fr/hal-01286578
http://hal.upmc.fr/hal-01286578/document
http://hal.upmc.fr/hal-01286578/file/comparative.pdf
DOI : 10.1186/s13227-016-0041-y

Éditeur(s) : HAL CCSD
Résumé : International audience
Energy is a critical enabler. In tropical countries, access to modern electricity is vital to reducing poverty and improving health, increasing productivity and promoting economic growth. However, the International Energy Agency reported in 2015 more than 1.2 billion people still did not have access to electricity in 2013, around 80% of them live in developing and tropical countries. Then, the same agency report also in 2016 around 6.5 million premature deaths each year can be attributed to air pollution. Therefore, it is time to support appropriate renewable energy developments, particularly the river hydrokinetic developments seems to be a better solution in tropics because of large and powerful rivers in these areas.In French Guiana, 35% of the inland populations are still not connected to the electrical grid (Région Guyane, 2012). This could be ascribed to the fact that extending grid wires hundreds of kilometers through difficult terrain and thick jungles just to serve a small remote village is economically unviable initiative (Ajan et al., 2003; Anyi et al., 2010). As an alternative, French Guiana and most of the tropical countries resort to diesel-powered generators which requires significant imports of expensive fuel, difficult to bring into remote areas (Région Guyane, 2012).This works proposes guidelines to estimate river hydrokinetic fluxes in the vicinity of remote communities in tropics. The method is applied to identify and characterise potential sites along an important reach of the Maroni river in French Guiana. First, a novel method to carry out river terrain elevation model is presented and some results about the Maroni river are reported. It begins from how to conduct ADCP survey, which corrections on them should be made and ends up by interpolating bathymetry over curvilinear profiles which handle the flow lines. That approach involves how mutli-source data (sparse ADCP-cross profiles, incomplete LiDAR tiles and hydroligic data) are merged and combined to estimate local cross section shape, maximum water depth and carry out cross profile in ungauged sites.This is followed by a deep characterisation about time-evolution of hydrokinetic fluxes field in the areas of interest by implementation of a full 2D hydrodynamic model (TELEMAC2D) over an important reach of the Maroni river. To optimise computational cost, river sections outside the areas of interest are modelled as a porous media where only the flows variables up and down stream must fulfil the field data.
CAS
Deshaies, Guadeloupe

hal-01514240
https://hal.archives-ouvertes.fr/hal-01514240

Éditeur(s) : HAL CCSD Botanical Society of America
Résumé :  
Tree buckling risk (actual height/critical buckling height) is an important biomechanical trait of plant growth strategies, and one that contributes to species coexistence. To estimate the diversity of this trait among wide samples, a method that minimizes damage to the plants is necessary. On the basis of the rarely used, complete version of Greenhill's model (1881, Proceedings of the Cambridge Philosophical Society 4(2): 65-73), we precisely measured all the necessary parameters on a sample of 236 saplings of 16 species. Then, using sensitivity (variance) analysis, regressions between successive models for risk factors and species ranks and the use of these models on samples of self- and nonself-supporting saplings, we tested different degrees of simplification up to the most simple and widely used formula that assumes that the tree is a cylindrical homogeneous pole. The size factor had the greatest effect on buckling risk, followed by the form factor and the modulus of elasticity of the wood. Therefore, estimates of buckling risk must consider not only the wood properties but especially the form factor. Finally, we proposed a simple but accurate method of assessing tree buckling risk that is applicable to a wide range of samples and that requires mostly nondestructive measurements.
ISSN: 0002-9122

hal-01032059
https://hal.archives-ouvertes.fr/hal-01032059

Éditeur(s) : HAL CCSD Ecological Society of America
Résumé : CABI:20153174020
Understanding how plants are constructed - i.e., how key size dimensions and the amount of mass invested in different tissues varies among individuals - is essential for modeling plant growth, carbon stocks, and energy fluxes in the terrestrial biosphere. Allocation patterns can differ through ontogeny, but also among coexisting species and among species adapted to different environments. While a variety of models dealing with biomass allocation exist, we lack a synthetic understanding of the underlying processes. This is partly due to the lack of suitable data sets for validating and parameterizing models. To that end, we present the Biomass And Allometry Database (BAAD) for woody plants. The BAAD contains 259634 measurements collected in 176 different studies, from 21084 individuals across 678 species. Most of these data come from existing publications. However, raw data were rarely made public at the time of publication. Thus, the BAAD contains data from different studies, transformed into standard units and variable names. The transformations were achieved using a common workflow for all raw data files. Other features that distinguish the BAAD are: (i) measurements were for individual plants rather than stand averages; (ii) individuals spanning a range of sizes were measured; (iii) plants from 0.01-100 m in height were included; and (iv) biomass was estimated directly, i.e., not indirectly via allometric equations (except in very large trees where biomass was estimated from detailed sub-sampling). We included both wild and artificially grown plants. The data set contains the following size metrics: total leaf area; area of stem cross-section including sapwood, heartwood, and bark; height of plant and crown base, crown area, and surface area; and the dry mass of leaf, stem, branches, sapwood, heartwood, bark, coarse roots, and fine root tissues. We also report other properties of individuals (age, leaf size, leaf mass per area, wood density, nitrogen content of leaves and wood), as well as information about the growing environment (location, light, experimental treatment, vegetation type) where available. It is our hope that making these data available will improve our ability to understand plant growth, ecosystem dynamics, and carbon cycling in the world's vegetation.
ISSN: 0012-9658

hal-01535227
https://hal.archives-ouvertes.fr/hal-01535227
DOI : 10.1890/14-1889.1
PRODINRA : 306122

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
TIF1γ (Transcriptional Intermediary Factor 1 γ) has been implicated in Smad-dependent signaling by Transforming Growth Factor beta (TGF-β). Paradoxically, TIF1γ functions both as a transcriptional repressor or as an alternative transcription factor that promotes TGF-β signaling. Using ordinary differential-equation models, we have investigated the effect of TIF1γ on the dynamics of TGF-β signaling. An integrative model that includes the formation of transient TIF1γ-Smad2-Smad4 ternary complexes is the only one that can account for TGF-β signaling compatible with the different observations reported for TIF1γ. In addition, our model predicts that varying TIF1γ/Smad4 ratios play a critical role in the modulation of the transcriptional signal induced by TGF-β, especially for short stimulation times that mediate higher threshold responses. Chromatin immunoprecipitation analyses and quantification of the expression of TGF-β target genes as a function TIF1γ/Smad4 ratios fully validate this hypothesis. Our integrative model, which successfully unifies the seemingly opposite roles of TIF1γ, also reveals how changing TIF1γ/Smad4 ratios affect the cellular response to stimulation by TGF-β, accounting for a highly graded determination of cell fate.
ISSN: 1932-6203

hal-00851483
https://hal.archives-ouvertes.fr/hal-00851483
https://hal.archives-ouvertes.fr/hal-00851483/document
https://hal.archives-ouvertes.fr/hal-00851483/file/pone.0033761.pdf
DOI : 10.1371/journal.pone.0033761

Éditeur(s) : Cambridge Univ Press
Résumé : This paper offers a theoritical and empirical model of ecosystem-based fishery management. A multi-species and multi-fleet integrating Lotka-Volterra trophic dynamics as well as production and profit assessments is developed and applied to the coastal fishery of French Guiana. This small-scale fishery constitutes a challenging example with high fish biodiversity, several non-selective fleets and a potentially increasing local food demand due to demographic growth. The dynamic model is calibrated with 13 species and four fleets using monthly catch and effort data from 2006 to 2009. Several contrasted fishing scenarios including status quo, total closure, economic and viable strategies are then simulated. They are compared from the viewpoints of both biodiversity preservation and socioeconomic performance, assuming fixed landing prices and fixed costs. We show that fishing outputs, including food supply and fleet profitability, can be sustained on average but a loss of species cannot be avoided.
Environment And Development Economics (1355-770X) (Cambridge Univ Press), 2013-06 , Vol. 18 , P. 245-269

Droits : Cambridge University Press 2013
http://archimer.ifremer.fr/doc/00124/23483/21311.pdf
http://archimer.ifremer.fr/doc/00124/23483/21375.pdf
DOI:10.1017/S1355770X13000065
http://archimer.ifremer.fr/doc/00124/23483/

Éditeur(s) : Institut national agronomique Paris Grignon
Résumé : The flat oyster Ostrea edulis L. is the indigenous oyster of the Atlantic as well as the Mediterranean coasts of Europe. Its commercial exploitation dates back to Antiquity but its breeding is now threatened by two parasitic protozoa, among which Bonamia ostreae. Various aspects of the genetics of this species' natural and farmed populations have been studied with the aid of microsatellite markers. At first, the implementation and the screening of two partial genomic libraries made it possible to identify 28 new microsatellite loci. Analysis of the segregation of 12 of these loci and of two enzymatic loci shows that most microsatellite loci are transmitted in a Mendelian way, but some loci have significant segregation distortions. Moreover, seven linkage groups, of which four contain at least two markers, were identified in Ostrea edulis. The genetic variability of three populations selected for one or two generations for resistance to Bonamia ostreae was analysed with the aid of 5 microsatellite loci. In spite of the absence of genealogical data, we have shown that these selected populations were descended from a very low number of founding genitors (from 3 to 15 depending on the population) and for two populations, we were able to reconstruct the genealogy and the relationships between the individuals were identified. These selected populations have, in addition to a very low genetic variability, real and at times high levels of consanguinity. These results have a significant implication for the continuation of the selection programme (consanguinity management, augmentation of genetic variability by introducing wild genitors). The geographical structuring of the genetic variability of natural populations of Ostrea edulis has been analysed with the aid of 5 microsatellite loci on a sampling covering almost the entire distribution area of the species (from Norway to the Adriatic Sea). The results are consistent with those published in the literature and using enzymatic markers. The populations show a low level of differentiation that could correspond to a model of isolation by distance. The Atlantic populations, which have a reduced polymorphism, could be descended from post-glacial recolonisation from Mediterranean populations that had survived the glaciations of the Quaternary Period. The current distribution of flat oyster populations is surely also subject to anthropogenic activities. Finally, the genetic bases of the heterozygosis-growth correlation were studied in a natural population with the aid of enzymatic and microsatellite markers. Although leads favouring the direct contribution of enzymatic loci have been found, biases in the sampling design make it impossible to come to a formal conclusion. However, this study has made it possible to show that the capture of individuals over a short period (around ten days) leads to a sampling of a population descended from a very low number of founding genitors, in contradiction with the generally accepted idea that marine bivalve populations are large panmictic populations with significant, efficient numbers. These results confirm in a natural population the observations of a significant reduction of efficient sizes in hatchery populations.
L'huître plate Ostrea edulis L. est l'huître indigène des côtes européennes aussi bien atlantiques que méditerranéennes. Son exploitation commerciale remonte à l'Antiquité mais son élevage est aujourd'hui menacé par deux protozoaires parasites dont Bonamia ostreae. Différents aspects de la génétique des populations naturelles et cultivées de cette espèce ont été étudiés à l'aide de marqueurs microsatellites. Dans un premier temps, la réalisation et le criblage de deux banques génomiques partielles ont permis l'identification de 28 nouveaux locus microsatellites. L'analyse de la ségrégation de 12 de ces locus et de deux locus enzymatiques montre que la plupart des locus microsatellites sont transmis de façon mendélienne, mais certains locus présentent des distorsions de ségrégation importantes. Par ailleurs, sept groupes de liaison dont quatre contiennent au moins deux marqueurs ont été identifiés chez Ostrea edulis. La variabilité génétique de trois populations sélectionnées depuis une ou deux générations pour une résistance à Bonamia ostreae a été analysée à l'aide de 5 locus microsatellites. Malgré l'absence de données généalogiques, nous avons montré que ces populations sélectionnées étaient issues d'un très faible nombre de géniteurs fondateurs (de 3 à 15 selon les populations) et pour deux populations, la généalogie a pu être reconstituée et les liens de parenté entre les individus ont été identifiés. Ces populations sélectionnées présentent, outre une très faible variabilité génétique, des niveaux de consanguinité réels et parfois élevés. Ces résultats ont une implication importante pour la continuation du programme de sélection (gestion de la consanguinité, augmentation de la variabilité génétique par introduction de géniteurs sauvages). La structuration géographique de la variabilité génétique des populations naturelles d'Ostrea edulis a été analysée à l'aide de 5 locus microsatellites sur un échantillonnage couvrant presque toute l'aire de répartition de l'espèce (de la Norvège à la Mer Adriatique). Les résultats sont cohérents avec ceux publiés dans la littérature et utilisant des marqueurs enzymatiques. Les populations montrent un niveau de différenciation faible qui pourrait correspondre à un modèle d'isolement par la distance. Les populations atlantiques, qui présentent un polymorphisme réduit, pourraient être issues de recolonisation post-glaciaire à partir de populations méditerranéennes ayant survécu aux glaciations du Quaternaire. La répartition actuelle des populations d'huître plate est certainement aussi soumise aux actions anthropiques. Enfin, les bases génétiques de la corrélation hétérozygotie-croissance ont été étudiées dans une population naturelle à l'aide de marqueurs enzymatiques et microsatellites. Bien que des pistes en faveur de la contribution directe des locus enzymatiques aient été trouvées, des biais dans le dispositif expérimental ne permettent pas de conclure de façon formelle. Cependant, cette étude a permis de montrer que le captage d'individus sur une faible période (une dizaine de jours) conduit à l'échantillonnage d'une population issue d'un nombre très réduit de géniteurs fondateurs, en contradiction avec l'idée reçue que les populations de bivalves marins sont de larges populations panmictiques à effectif efficace important. Ces résultats confirment dans une population naturelle les observations de réduction importante des tailles efficaces dans des populations d'écloserie.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/1998/these-1919.pdf
http://archimer.ifremer.fr/doc/00000/1919/

Éditeur(s) : Elsevier Sci Ltd
Résumé : A multi-scale global hindcast of ocean waves is presented that covers the years 1994-2012, based on recently published parameterizations for wind sea and swell dissipation [Ardhuin, F., Rogers, E., Babanin, A., Filipot, J.-F., Magne, R., Roland, A., van der Westhuysen, A., Queffeulou, P., Lefevre, J.-M., Aouf, L., Collard, F., 2010. Semi-empirical dissipation source functions for wind-wave models: Part I. Definition, calibration and validation. J. Phys. Oceanogr. 40 (9), 1917-1941]. Results from this hindcast include traditional wave parameters, like the significant wave height and mean periods, and we particularly consider the accuracy of the results for phenomenal sea states, with significant heights above 14 m. Using unbiased winds, there is no evidence of a bias in wave heights even for this very high range. Various spectral moments were also validated, including the surface Stokes drift and mean square slopes that are relevant for wave-current interactions modelling and remote sensing, and also spectra of seismic noise sources. The estimation of these parameters is made more accurate by the new wave growth and dissipation parameterizations. Associated air-sea fluxes of momentum and energy are significantly different from what is obtained with the WAM-Cycle 4 parameterization, with a roughness that is practically a function of wind speed only. That particular output of the model does not appear very realistic and will require future adjustments of the generation and dissipation parameterizations.
Ocean Modelling (1463-5003) (Elsevier Sci Ltd), 2013-10 , Vol. 70 , P. 174-188

Droits : 2012 Elsevier Ltd. All rights reserved.
http://archimer.ifremer.fr/doc/00155/26582/25477.pdf
DOI:10.1016/j.ocemod.2012.12.001
http://archimer.ifremer.fr/doc/00155/26582/

Éditeur(s) : HAL CCSD American Chemical Society
Résumé : International audience
Constitutive activation of the PI3K/mTOR signaling pathway contributes to carcinogenesis and metastasis in most, if not all, breast cancers. From a chromene backbone reported to inhibit class I PI3K catalytic subunits, several rounds of chemical syntheses led to the generation of a new collection of chromologues that showed enhanced ability to kill PI3K-addicted cancer cells and to inhibit Akt phosphorylation at serine 473, a hallmark of PI3K/mTOR activation. This initial screen uncovered a chromene designated DHM25 that exerted potent antitumor activity against breast tumor cell lines. Strikingly, DHM25 was shown to be a selective and covalent inhibitor of mTOR using biochemical and cellular analyses, modeling, and a large panel of kinase activity assays spanning the human kinome (243 kinases). Finally, in vivo, this novel drug was an efficient inhibitor of growth and metastasis of triple-negative breast cancer cells, paving the way for its clinical application in oncology
ISSN: 0022-2623

hal-01187307
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01187307
DOI : 10.1021/acs.jmedchem.5b00991
PUBMED : 26237138

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Saccharomyces cerevisiae is an established model organism for the molecular analysis of fundamental biological processes. The genomes of numerous strains have been sequenced, and the transcriptome and proteome ofmajor phases during the haploid and diploid yeast life cycle have been determined. However, much less is known about dynamic changes of the proteome when cells switch from mitotic growth to meiotic development. We report a quantitative protein profiling analysis of yeast cell division and differentiation based on mass spectrometry. Information about protein levels was integrated with strand-specific tiling array expression data. We identified a total of 2366 proteins in at least one condition, including 175 proteins showing a statistically significant > 5-fold change across the sample set, and 136 proteins detectable in sporulating but not respiring cells. We correlate protein expression patterns with biological processes and molecular function by Gene Ontology term enrichment, chemoprofiling, transcription interference and the formation of double stranded RNAs by overlapping sense/antisense transcripts. Our work provides initial quantitative insight into protein expression in diploid respiring and differentiating yeast cells. Critically, it associates developmentally regulated induction of antisense long noncoding RNAs and double stranded RNAs with fluctuating protein concentrations during growth and development.
ISSN: 1874-3919

hal-01485858
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01485858
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01485858/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01485858/file/Becker%20et%20al.%20-%20The%20protein%20expression%20landscape%20of%20mitosis%20and%20me.pdf
DOI : 10.1016/j.jprot.2016.12.016

Éditeur(s) : HAL CCSD
Résumé : International audience
The main biological function of reaction wood is to act as “muscle” for trees, enabling them to control their posture and right stems when they are permanently disturbed from their set-point inclination by gravity or winds. The key property to achieve this function is the development of high mechanical stress during the formation of reaction wood cells, called “maturation strains”. Moreover, this function is basically performed through the asymmetric formation of wood (in quantity or quality) around the tree circumference. This asymmetry enables stems to bend upward or to compensate for the downward bending induced by gravity, as an asymmetric force associated to maturation strains creates a bending moment (i.e. one side of the stem “pulls” the other one). We will discuss the traits (cross sectional size and shape, wood features as G fibers or microfibril angle, eccentric growth even in usual or extreme cases as buttresses, total biomass growth and height of center of mass, stem lean and set-point angle) involved to understand how the posture control works. We will give simple formulas to estimate a “muscle efficiency” from biomechanical modeling. We will give practical methods to estimate all the involved traits, especially maturation strains from direct and indirect measurements, in peripheral functional wood or by retrospective dendrochronological analysis. Then, we will illustrate how tree stem tropisms and especially gravitropism, widely studied by physiologists, are key processes in natural ecosystems, through practical examples from tropical rainforest tree communities and regeneration of European mixed beech forests. Using the previous definition of postural control efficiency, we will show that the cross section size is rapidly a limiting factor, opposing the extreme strategies of flexible small stems, which bend easily but also right themselves quickly, to stiff big stems. Lastly, as wood in living trees ensures general storage, defence, vascular and skeletal functions, we will ask general questions about synergies and trade-offs between posture control and other functions.
Botany 2014 : new frontiers in botany
Boise, United States

hal-01627031
https://hal.archives-ouvertes.fr/hal-01627031

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Metalloproteases involved in extracellular matrix remodeling play a pivotal role in cell response by regulating the bioavailability of cytokines and growth factors. Recently, the disintegrin and metalloprotease, ADAMTS1 has been demonstrated to be able to activate the transforming growth factor TGF-β, a major factor in fibrosis and cancer. The KTFR sequence from ADAMTS1 is responsible for the interaction with the LSKL peptide from the latent form of TGF-β, leading to its activation. While the atomic details of the interaction site can be the basis of the rational design of efficient inhibitory molecules, the binding mode of interaction is totally unknown. In this study, we show that recombinant fragments of human ADAMTS1 containing KTFR sequence keep the ability to bind the latent form of TGF-β. The recombinant fragment with the best affinity is modeled to investigate the binding mode of LSKL peptide with ADAMTS1 at the atomic level. Using a combined approach with molecular docking and multiple independent molecular dynamics (MD) simulations, we provide the binding mode of LSKL peptide with ADAMTS1. The MD simulations starting with the two lowest energy model predicted by molecular docking shows stable interactions characterized by 3 salt bridges (K3-NH3+ with E626-COO−; L4-COO− with K619-NH3+; L1-NH3+ with E624-COO−) and 2 hydrogen bonds (S2-OH with E623-COO−; L4-NH with E623-COO−). The knowledge of this interaction mechanism paves the way to the design of more potent and more specific inhibitors against the inappropriate activation of TGF-β by ADAMTS1 in liver diseases
ISSN: 1476-9271

hal-01269916
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01269916
DOI : 10.1016/j.compbiolchem.2016.01.012
PUBMED : 26878129

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The cyanobacteria-derived neurotoxin β-methylamino-l-alanine (BMAA) represents a plausible environmental trigger for amyotrophic lateral sclerosis (ALS), a debilitating and fatal neuromuscular disease. With the eutrophication of water bodies, cyanobacterial blooms and their toxins are becoming increasingly prevalent in France, especially in the Brittany region. Cyanobacteria are monitored at only a few recreational sites, preventing an estimation of exposure of the human population. By contrast, phosphorus, a limiting nutrient for cyanobacterial growth and thus considered a good proxy for cyanobacteria exposure, is monitored in many but not all surface water bodies. Our goal was to develop a geographic exposure indicator that could be used in epidemiological research. We considered the total phosphorus (TP) concentration (mg/L) of samples collected between October 2007 and September 2012 at 179 monitoring stations distributed throughout the Brittany region. Using readily available spatial data, we computed environmental descriptors at the watershed level with a Geographic Information System. Then, these descriptors were introduced into a backward stepwise linear regression model to predict the median TP concentration in unmonitored surface water bodies. TP concentrations in surface water follow an increasing gradient from West to East and inland to coast. The empirical concentration model included five predictor variables with a fair coefficient of determination (R2 = 0.51). The specific total runoff and the watershed slope correlated negatively with the TP concentrations (p = 0.01 and p < 10− 9, respectively), whereas positive associations were found for the proportion of built-up area, the upstream presence of sewage treatment plants, and the algae volume as indicated by the Landsat red/green reflectance ratio (p < 0.01, p < 10− 6 and p < 0.01, respectively). Complementing the monitoring networks, this geographical modeling can help estimate TP concentrations at the watershed level, delivering a proxy for cyanobacteria exposure that can be used along with other risk factors in further ALS epidemiologic case–control studies
ISSN: 0160-4120

hal-01175538
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01175538
DOI : 10.1016/j.envint.2015.04.007
PUBMED : 25913322

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
New petrographic and microstructural observations, mineral equilibria modelling and U/Pb (monazite) geochronological studies were carried out to investigate the relationships between deformation and metamorphism across the Rehamna massif (Moroccan Variscan belt). In this area, typical Barrovian (muscovite to staurolite) zones developed in Cambrian to Carboniferous metasedimentary rocks that are distributed around a dome-like structure. First assemblages are characterized by the presence of locally preserved andalusite, followed by prograde evolution culminating at 6 kbar and 620 °C in the structurally deepest staurolite zone rocks. This Barrovian sequence was subsequently uplifted to supracrustal levels, heterogeneously reworked at greenschist facies conditions, which was followed locally by static growth of andalusite, indicating heating to 2.5–4 kbar and 530–570 °C. The 206Pb/238U monazite age of 298.3 ± 4.1 Ma is interpreted as minimum age of peak metamorphic conditions, whereas the ages of 275.8 ± 1.7 Ma and 277.0 ± 1.1 Ma date decompression and heating at low pressure, in agreement with previous dating of Permian granitoids intruding the Rehamna massif. The prograde metamorphism occurred during thickening and associated horizontal flow in the deeper crust (S1 horizontal schistosity). The horizontally disposed metamorphic zones were subsequently uplifted by a regional scale antiform during ongoing N–S compression. The re-heating of the massif follows late massive E–W shortening, refolding and retrograde shearing of all previous fabrics coevally with regionally important intrusions of Permian granitoids. We argue that metamorphic evolution of the Rehamna massif occurred several hundred kilometres from the convergent plate boundaries in the interior of continental Gondwanan plate. The tectonometamorphic history of the Rehamna massif is put into Palaeozoic plate tectonic perspective and Late Carboniferous reactivation of (Devonian)–Early Carboniferous basins formed during stretching of the north Gondwana margin and formation of the Palaeotethys Ocean. The inherited heat budget of these magma-rich basins plays a role in the preferential location of this intracontinental orogen. It is shown that rapid transition from lithospheric stretching to compression is characterized by specific HT type of Barrovian metamorphism, which markedly differs from similar Barrovian sequences along Palaeozoic plate boundaries reported from Variscan Europe.
ISSN: 0263-4929

hal-01468009
https://hal.archives-ouvertes.fr/hal-01468009
DOI : 10.1111/jmg.12214

Résumé : La tuberculose, maladie très ancienne, est plus que jamais présentée sur la scène sanitaire mondiale avec 9 millions de nouveaux cas par an. Cette maladie, qui demeure une cause majeure de mortalité, est un des problèmes les plus difficiles à résoudre en santé publique et à échelle internationale. Les diverses programmes de lutte, lancés par l’Organisation Mondiale de la Santé (OMS), pour prévenir et garantir la guérison des patients tuberculeux, se heurtent à des difficultés qui hypothèquent leur efficacité. En effet, l'expansion du virus de rinimunodéficience humaine (VIII) et son influence néfaste sur la susceptibilité à la tuberculose, l'accroissement rapide de la tuberculose multirésistante, la pauvreté ainsi que la croissance démographique, sont un ensemble de facteurs préjudiciables à l'application des mesures préventives et curatives. Les contextes économiques difficiles conduisant indubitablement au cumul de ces facteurs, ont fait une césure entre les pays riches et les pays pauvres quant à l'incidence et la révolution de la tuberculose à échelle mondiale. Pour atténuer la disparité des résultats des luttes antituberculeuses, les méthodologies employées en épidémiologie de la tuberculose doivent s'inscrire dans une démarche d'efficacité. Les marqueurs moléculaires, indispensables à l'identification et à la classification des souches appartenant au complexe Mycobacterium tuberculosis (MTC) ont chacun des potentialités qui leur sont propres dont il convient de cerner pour une utilisation adéquate dans les études épidémiologiques et phylogénétiques. Le but de cette thèse consiste à extraire des connaissances nouvelles des résultats de génotypage stockées dans les bases de données, connaissances relatives au polymorphisme du support génomique pour estimer la contribution de chaque marqueur dans la classification de MTC. Le recours à différentes méthodes de reconstruction phylogénétique et de modélisation des données fut indispensable. A la lumière des résultats obtenus, cette thèse propose une nouvelle méthodologie de classification, pour rétablissement d'une phylogéographie robuste de MTC en relation avec l'histoire des migrations humaines qui aurait débutée en Afrique subsaharienne. Chaque méthode de génotypage ayant une efficience et un cout propres, qu'il convient de mesurer par rapport aux moyens disponibles et aux résultats escomptes, il est donc intéressant de renforcer la connaissance des marqueurs et de proposer différentes alternatives menant à la classification des mycobactéries. Ainsi, les résultats obtenus dans cette thèse apportent plus de cohérence aux solutions proposées pour la caractérisation des clones de MTC circulant dans le monde.
Tuberculosis, very old disease, is more than ever presented on the global health scene with 9 million new cases per year. This disease, which remains a major cause of mortality is one of the most intractable public health and international issues. The various control programs, launched by the World Health Organization (WHO) to prevent and guarantee the cure of tuberculosis patients face difficulties that undermine their effectiveness. Indeed, the expansion of human virus rinimunodéficience (VIII) and its negative influence on susceptibility to tuberculosis, the rapid growth of multidrug-resistant tuberculosis, poverty and population growth, are a set of factors detrimental to application of preventive and curative measures. The difficult economic circumstances undoubtedly leading to accumulation of these factors have a break between rich and poor countries about the impact and the revolution of tuberculosis worldwide. To address the disparity of the results of tuberculosis struggles, the methodologies used in epidemiology of tuberculosis must be part of a process efficiency. Molecular indispensable to the identification and classification of strains belonging to the Mycobacterium tuberculosis complex (MTC) markers each have their own potentials that need to be identified for proper use in epidemiological and phylogenetic studies. The purpose of this thesis is to extract new knowledge of the results of genotyping data stored in databases, knowledge of the polymorphism of genomic carrier to estimate the contribution of each marker in the classification of TCM. The use of different methods of phylogenetic reconstruction and modeling data was essential. In light of the results obtained, the thesis proposes a new classification methodology for a robust recovery phylogeography of TCM in connection with the history of human migration have started in sub-Saharan Africa. Each genotyping method with cost efficiency and equity, should be measured in relation to the resources available and discounts results, it is interesting to strengthen the knowledge of markers and propose alternatives leading to the classification of mycobacteria. Thus, the results obtained in this thesis bring more coherence to the proposed characterization of clones MTC circulating worldwide solutions.

http://www.theses.fr/2012AGUY0518/document

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Wasilewski et al. (1979) concluded that no magnetic remanence existed in the uppermost mantle and that even if present, such sources would be at temperatures too high to contribute to long wavelength magnetic anomalies (LWMA). However, new collections of unaltered mantle xenoliths indicate that the uppermost mantle could contain ferromagnetic minerals. 1. The analysis of some LWMA over cratons and forearcs suggest magnetic sources in the uppermost mantle. 2. The most common ferromagnetic phase in the uppermost mantle is stoichiometric magnetite. Assuming a 30 km-thick crust, and crustal and mantle geotherms of 15 °C/km and 5 °C/km, respectively, the 600 °C Curie temperature implies a 30 km-thick layer of mantle. 3. The uppermost mantle is cooler than 600 °C in Archean and Proterozoic shields (> 350 °C), subduction zones (> 300 °C) and old oceanic basins (> 250 °C). 4. Recently investigated sets of unaltered mantle xenoliths contain pure magnetite inclusions in olivine and pyroxene formed in equilibrium with the host silicate. 5. The ascent of mantle xenoliths occurs in less than a day. Diffusion rates in olivine suggest that the growth of magnetite possible within this time frame cannot account for the size and distribution of magnetite particles in our samples. 6. Demagnetization of natural remanent magnetization (NRM) of unaltered mantle xenoliths unambiguously indicates only a single component acquired upon cooling at the Earth's surface. This is most easily explained as a thermoremanent magnetization acquired by pre-existing ferromagnetic minerals as xenoliths cool rapidly at the Earth's surface from magmatic temperatures, acquired during ascent. 7. Modern experimental data suggest that the wüstite-magnetite oxygen buffer and the fayalite-magnetite-quartz oxygen buffer extend several tens of km within the uppermost mantle. 8. The magnetic properties of mantle xenoliths vary consistently across tectonic settings. In conclusion, the model of a uniformly non-magnetic mantle should be revisited. Keywords
ISSN: 0040-1951

hal-01053923
https://hal.archives-ouvertes.fr/hal-01053923
DOI : 10.1016/j.tecto.2014.01.004